bluuebunny/crossref_metadata_2025_split huggingface dataset:
LGG-45. Genetic dependencies inMYB/MYBL1-driven pediatric low-grade glioma models
Authors: Condurat Alexandra-Larisa , Jones Jill , Gonzalez Elizabeth , Doshi Jeyna , Zhou Kevin , Tsai Jessica W , Khadka Prasidda , Buchan Graham B J , Rouleau Cecile , Pelton Kristine , Abid Tanaz , Goodale Amy , Persky Nicole , Beroukhim Rameen , Ligon Keith , Root David , Piccioni Federica , Bandopadhayay Pratiti 
Published: June 2022

Abstract
AIM: Pediatric low-grade gliomas (pLGGs) are a heterogenous group of tumors, diverse in their localization, histology, mutational landscape, clinical behavior, and treatment response. Genomic alterations impacting the MYB family of transcription factors were identified in two distinct pLGG subtypes: Angiocentric Gliomas (AG) and Diffuse Astrocytomas (DA). The molecular profiles and therapeutic vulnerabilities associated with these genomic alterations remain unexplored. In this study we highlight the use of genome-wide CRISPR/Cas9 knock-out screens for an unbiased identification of translatable therapeutic targets. METHODOLOGY: Given the lack of patient-derived pLGG cell lines, we engineered in vitro pLGG mouse and human neural stem cell (NSC) models to harbor pLGG-relevant genomic alterations. We performed single cell RNA sequencing to investigate the transcriptional profiles driven by these mutations and to dissect the central regulatory networks enabling tumorigenesis. Specific genetic dependencies associated with MYB/MYBL1 mutations were screened using the Brie genome-wide mouse CRISPR lentiviral knock-out pooled library, consisting of 78,637 single guide RNAs (sgRNAs) targeting 19,674 mouse genes. RESULTS: We have successfully generated in vitro NSC-based pLGG models crucial to deepening our knowledge on pLGG biology and the identification of translatable therapeutic targets. Genome-scale CRISPR/Cas9 knock-out screens in isogenic NSCs models, expressing distinct MYB/MYBL1 alterations or a control transgene, revealed several differential genetic dependencies. Among the top identified dependencies are regulators of cell-stress response, cell-cycle progression, and modulators of the ubiquitin-proteasome degradation pathway. CONCLUSION: Genome-wide CRISPR knock-out screens are a powerful tool for the unbiased identification of mutation-specific genetic dependencies that can be explored as candidates for precision medicine approaches.
LGG-49. Subependymal giant cell astrocytoma associated with a cortical tuber: A case report
Authors: Quinot Valerie Anne , Rössler Karl , Feucht Martha , Kasprian Gregor , Gelpi Ellen , Haberler Christine 
Published: June 2022

Abstract
Subependymal giant cell astrocytomas (SEGAs) are circumscribed gliomas strongly associated with tuberous sclerosis (TS). TS, a rare genetic disorder caused by inactivating mutations in either of the TSC genes (TSC1/2), leads to upregulation of the mTOR pathway and consecutive cell growth. CNS manifestations other than SEGAs include cortical tubers, white matter glioneuronal hamartomas and subependymal nodules (SENs), which, although regarded as distinct morphological phenotypes, share certain histological characteristics including ballooned astrocytes and giant ganglion-like cells. SEGAs, thought to develop from the median ganglionic eminence (MGE), are most commonly located periventricularly. However, rare cases of extraventricular SEGAs have been reported. We report a case of a cortico-subcortically located SEGA in a TS patient. A two-month-old female TS patient with multiple cortical tubers presented with treatment-resistant epilepsy. A 4cm sized tuber located in the right temporal lobe, showing a transmantle sign on MRI but no typical imaging appearance of SEGA, was surgically resected. Histological evaluation revealed typical morphological characteristics of a tuber with dysmorphic neurons, balloon cells and calcifications in the cortex and adjacent white matter. Focally, a cortico-subcortically located, well delineated area with increased cellularity and morphological features of a SEGA was found. Single mitotic figures were detectable. Immunhistochemically, these cells were strongly positive for GFAP, vimentin, and nestin. Scattered S100-, NeuN-, MAP2- and SMI32-positive cells were present. No expression of class-III-b-tubulin and TTF1a was found. pS6 was expressed in a small fraction of cells. CD34 showed a dense capillary network within the lesion. This case is consistent with prior case reports of SEGA-tissue in tubers of TS patients. However, the SEGA tissue of this case did not display TTF1a-expression, characteristic for SEGAs and considered as a marker for cells originating from the MGE, thus implying a different cellular lineage.
LGG-59. Identifying hidden drivers of low-grade glioma tumor growth
Authors: Misek Sean , Fultineer Aaron , Condurat Alexandra , Zhou Kevin , Root David , Persky Nicole , Boehm Jesse , Bandopadhayay Pratiti , Beroukhim Rameen 
Published: June 2022

Abstract
Genomic drivers of pediatric low-grade gliomas (pLGGs) converge on alterations that activate the MAPK pathway. However, expression of individual driver oncogenes fails to induce tumor formation with high penetrance and, paradoxically, expression of these oncogenes suppresses growth in vitro. This, combined with the non-monotonic tumor growth rate in patients, suggests that there are “hidden drivers” beyond a single driver oncogene that are necessary to support tumor growth. The goal of this project is to leverage high-throughput functional genomics strategies to identify these hidden drivers of pLGG. Our preliminary data indicates that genes which modulate differentiation are required for the survival of LGG cells, suggesting that these genes may be hidden drivers of LGG tumor growth. Additionally, we hypothesize that secreted factors in the tumor microenvironment regulate pLGG tumor growth, potentially by modulating differentiation. In total, genes which cooperate with pLGG driver oncogenes to promote tumor growth may represent a new class of therapeutic targets and may explain the complex patterns of tumor growth that are observed in patients.
MEDB-02. The identification and functional characterization of circular RNA Circ_63706 in sonic hedgehog medulloblastomas
Authors: Pokhrel Rudramani , Katsushima Keisuke , Stapleton Stacie , Jallo George , Raabe Eric , Eberhart Charles G , Perera Ranjan J 
Published: June 2022

Abstract
Circular RNAs (circRNAs) are increasingly recognized as stable and specific biomarkers and therapeutic targets in many cancers, but little is known about their function, subtype specificity, and biomarker potential in medulloblastomas. Medulloblastoma is a central nervous system tumor that predominantly affects children and always requires aggressive therapy. Understanding and identifying novel disease-related molecular mechanisms and pathways are essential for developing optimal and novel therapies. To identify medulloblastoma subgroup-specific circRNAs, we subjected RNA-seq data from 175 clinical medulloblastoma samples representing the four subgroups to a statistical and machine learning (random forest classification) pipeline. Circular RNA circ_63706 expression was specific to the sonic hedgehog (SSH) group, which was confirmed through in situ hybridization analysis of clinical tissue samples. Functional characterization of circ_63706 by siRNAs and shRNAs demonstrated that cell proliferation, invasion, and apoptosis are perturbed in circ_63706 cells and inhibited in vivo tumor growth. These novel medulloblastoma-specific circular RNAs are emerging as important oncogenes that not only provide valuable mechanistic insights into how medulloblastomas develop but also how they can be used as biomarkers and therapeutic targets. These results pave the way for the specific identification and personalized treatment of different medulloblastoma subgroups.
MEDB-08. Inhibition of different mitotic targets demonstrated distinct DNA damage and cell death response in p53-mutant medulloblastoma
Authors: Huang Shiying , Pan Jie-Ling , Karthik Sekar , Du YuChen , Lin Qi , Lau Ching C , Adekunle Adesina , Su Jack M F , Major Angela , Elghetany M Tarek , Hui Kam-Man , Li Xiaonan , Teo Wan-Yee 
Published: June 2022

Abstract
BACKGROUND: In normal cells, cell cycle is tightly regulated by mitotic proteins to ensure smooth transition through each phase of cell division. Here, we examine two proteins – KIF11, a mitotic kinesin, responsible for assembly and maintenance of mitotic spindle during mitosis; and MELK, a serine/threonine kinase, essential for mitotic progression. Cancer cells can upregulate MELK and KIF11 to promote uncontrolled cell division and protect the cells from apoptotic cell death, leading to tumorigenesis. AIMS: We investigated the response of p53-mutant medulloblastoma (MB) by inhibiting KIF11 and MELK separately to study the effects on cell cycle progression and cell death mechanisms. RESULTS: Cell proliferation was suppressed by inhibition of either KIF11 or MELK in MB, independent of p53-mutant status. Regardless of p53-mutant status, inhibiting KIF11 induced cell cycle arrest at G2/M. In contrast, inhibiting MELK (IC50 dose) induced more prominent G2/M arrest in p53-mutant cells compared to p53-wildtype cells. In p53-mutant MB, arrested cells during MELK inhibition subsequently underwent apoptotic cell death at 24h and 48h. With KIF11 inhibition, p53-mutant cells at 24h were already in necrotic stage. p53-mutant cells reached necrotic stage in a shorter time with KIF11 inhibition than MELK inhibition. On immunoblotting, independent of p53-mutant status, KIF11 inhibition produces more significant increase in DNA damage marker and c-PARP indicative of apoptosis, compared to MELK inhibition. Treatment with KIF11 or MELK inhibitor increased p53 protein expression in p53-wildtype (normal stress response). However, in p53-mutant cells, p53 protein expression decreased post-KIF11-inhibition, but remained unchanged post-MELK inhibition. In-vivo, inhibiting KIF11 was less tolerable in a patient-derived orthotopic xenograft model with p53-mutation. CONCLUSION: Inhibition of either mitotic target KIF11 or MELK, can induce anti-proliferative effects in MB. In p53-mutant MB, DNA damage and cell death response with KIF11-inhibition are more marked.
MEDB-09. Unraveling the role of unfolded protein response in medulloblastoma cancer stem cells
Authors: Spinello Zaira , Abballe Luana , Splendiani Elena , Giannatale Angela Di , Giangaspero Felice , Mastronuzzi Angela , Ferretti Elisabetta , Miele Evelina , Catanzaro Giuseppina 
Published: June 2022

Abstract
Medulloblastoma (MB) is the most common malignant childhood brain tumor. The current clinical approach consists of multimodal strategies with debilitating long-term effects and risk of tumor recurrence. Medulloblastoma stem cells (MBSCs) are a fraction of tumor cells with high proliferation potential and the capability to adapt to adverse/restrictive conditions in tumor milieu thus driving the refractoriness to conventional therapies. Recently, high basal levels of Unfolded Protein Response (UPR) molecules have been found in tumors of different tissue-origin and are correlated with poor prognosis and low patient survival. However, little is known about the role of UPR in MB. We investigated the expression and activation of UPR players in MBSCs. Human group 3 MB (G3MB) cell lines, specifically CHLA-01, D283- and D341-Med, were grown in Vitamin A and/or FBS or in stem selective medium (B27™) for 72 h before collection. Cells were fixed, stained with proper primary antibodies and images were acquired by confocal microscopy. The analysis of the transcription factors ATF-4 and CHOP revealed their elevated nuclear expression and co-localization, which resulted to be more marked in G3MB stem-like cells than in the differentiated ones. Also the ATF-6 branch was investigated, in differentiating conditions D283 and D341-Med showed a greater activation of ATF-6, represented by its nuclear localization, in respect to stem cells, while CHLA-01 did not show differences. Conversely XBP1, the transcription factor downstream IRE1 signaling, was not expressed in the three cell lines. Lastly, a Kaplan-Meier analysis on MB patients showed a worse prognosis with a shorter survival rate of patients expressing high ATF4 transcript levels. Our results reveal, even in resting conditions, preferential activation of the PERK branch in G3MB cells grown in stem-like condition suggesting that ATF-4 might be a promising therapeutic and prognostic factor to specifically target the stem compartment in aggressive MB.
MEDB-11. MYC overexpression and SMARCA4 loss in cerebellar granule cell precursors cooperate to drive medulloblastoma formation in mice
Authors: Göbel Carolin , Holdhof Dörthe , Schoof Melanie , Kresbach Catena , Schüller Ulrich 
Published: June 2022

Abstract
Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30 % of cases carry genetic alterations in MYC, SMARCA4 or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined an overexpression of MYC with a loss of SMARCA4 in cerebellar granule cell precursors. Cells were isolated from 7-day-old Math1-creERT2::Smarca4fl/fl pups after tamoxifen-induced loss of SMARCA4. Subsequently, MYC overexpression was achieved by lentiviral transduction, and transduced cells were transplanted into immunodeficient CD1nu/nu recipient mice. Preliminary results show tumor formation in 5/19 transplanted mice (26 %) after 6 months. SMARCA4 loss in all tumor cells was confirmed both immunohistochemically and on a genetic level and suggests a dependency of tumor growth on SMARCA4 loss. In a next step, additional cohorts will clarify if tumor development is accelerated by or even dependent on the loss of SMARCA4 in our model. Additionally, the neoplastic potential of tumor cells will be verified with the aid of secondary recipient mice. To evaluate to what extent the generated tumors are comparable to human Group 3 medulloblastomas, tumors will be extensively analyzed on a morphological, transcriptional, and epigenetic level. Altogether, we hope to establish a suitable mouse model for SMARCA4 mutated Group 3 medulloblastoma that will help to elucidate the role of SMARCA4 in tumor development and to identify new therapeutic targets.
MEDB-13. Neurocognitive and radiological follow-up of children under 5 years of age treated for medulloblastoma according to the HIT-SKK protocol
Authors: Merlin Marie-Sophie , Schmitt Emmanuelle , Mezloy-Destracque Malika , Dufour Christelle , Riffaud Laurent , Puiseux Chloé , De Carli Emilie , Bodet Damien , Icher Céline , Doz François , Faure-Conter Cécile , Pagnier Anne , Pluchart Claire , Thouvenin-Doulet Sandrine , Lejeune Julien , Thi-Lambert Phi-Linh Nguyen , Chastagner Pascal 
Published: June 2022

Abstract
BACKGROUND: HIT-SKK protocol is used for the treatment of low risk medulloblastomas in young children with the aim of eliminating cranial irradiation and its long-term side effects, in particular neuropsychological (NP) sequelae. This therapy includes IV and intraventricular (ITV) methotrexate (MTX) potentially responsible for leukoencephalopathy (LE) and neurocognitive disorders.The objectives are to describe the risk factors and the course of LE, and to investigate its impact on long-term neurocognitive and behavioural outcome. METHODS: A French retrospective, multicenter study including 35 children under 5 years of age, treated between 2009 and 2017, with a median follow up of 72 months. All follow-up MRIs including assessment of the severity of the LE (Fazekas and CTCAE grading) and all NP evaluations were centrally rewieved. RESULTS: 25/34 evaluable patients presented a LE during follow up, in a median delay of 2 months (1 - 17 months) after the start of chemotherapy. Grade 2 and 3 abnormalities were correlated with higher cumulative dose of ITV -MTX (p=0,01). Full Scale IQ (FSIQ) and Wechsler indexes were in the average or low average of the reference population. FSIQ was deficient in 7/20 evaluable patients. Processing speed (PSI) was the most frequently impaired neurocognitive domain: 9/20 patients with borderline or very low score, all having received a significantly higher cumulative dose of ITV-MTX (p=0,04). A decrease in overall NP scores was observed in patients for whom grade 2 or 3 LE persisted at the end of follow-up with an average FSIQ estimated at 82.1 (SD 16.9) versus 94.2 (SD 20.6). This decrease was significant for PSI (p=0,049). LE and neurocognitive impairments were not correlated with a younger age at diagnosis. CONCLUSION: This study confirmed the responsibility of MTX, and in particular ITV-MTX therapy in the onset and, most often, persistence of LE and its association with neurocognitive disorders.
MEDB-16. Persistent radiological lesions at the end of primary therapy in childhood medulloblastoma: residual lesion or active residual tumor?
Authors: Schömig Lena , Obrecht Denise , Mynarek Martin , Bison Brigitte , Schwarz Rudolf , Pietsch Torsten , Rutkowski Stefan , Benesch Martin 
Published: June 2022

Abstract
BACKGROUND: Magnetic resonance imaging (MRI) of patients with medulloblastoma (MB) often shows persistent residual findings after primary treatment. Criteria for characterizing these lesions and consensus on further therapeutic approaches are not established. MATERIAL AND METHODS: Eighty-four patients ≥4 years with centrally reviewed residual lesions on MRI at the end of primary therapy with initial surgery between 2000 and 2018 were identified. Data were extracted from the German HIT-MED database. RESULTS: Median age at initial diagnosis was 9.3 (4.0-20.8) years. 91.7% were histologically classified as CMB, 7.1% as LC/AMB and 1.2% as DMB. The majority (65.5%) of the evaluated cohort was assigned to molecular subgroup 4, 24.1% to group 3, 6.8% to WNT, 3.4% to SHH. Median follow-up for survivors was 5.96 (1.41-16.67) years. Univariate analysis revealed that patients showing an overall partial response (PR) to primary therapy have a significantly lower risk of progression of residual lesions compared to patients with stable disease (SD) (5-year PFS [PR]: 62.5±7,0; 5-year PFS [SD]: 35.9±12.8; 5-year OS [PR]: 85.6±5.1; 5-year OS [SD]: 54.1±13.7; p=0.02 [PFS], p=0.04 [OS]). Additionally, patients with multiple residual lesions (M+ and R+) were at higher risk of progression (5-year PFS [R+ only]: 72.4±12.0, 5-year PFS [R+/M+]: 22.9±17.9; p=0.02 [PFS]). Further procedures after the end of primary therapy (additional resections, chemotherapy, radiotherapy) did not impact on PFS and OS. These results were confirmed by multivariate Cox regression. For molecular or histological type no significant effect was found, presumably due to small cohort. CONCLUSION: PFS in patients with residual lesions at the end of primary treatment depends on the overall response to primary therapy. Additional procedures do not seem to be superior compared to watch-and-wait strategies. Decisions regarding further therapies should be scrutinized on a case-by-case basis. Further identification of biomarkers is warranted.
MEDB-22. iPSC-derived cerebellar organoid model for hereditary genetic predisposition in SHH-medulloblastoma
Authors: Manz Frederik , Haag Daniel , Pfister Stefan M , Kutscher Lena 
Published: June 2022

Abstract
Medulloblastoma is one of the most common malignant embryonal brain tumors in children. Medulloblastomas of the Sonic Hedgehog (SHH) group arise from excessive proliferation of granule neuron progenitor (GNP) cells during cerebellar development. Genetic predisposition accounts for nearly 40% of all pediatric SHH-medulloblastomas. Recently, ELP1, a novel predisposition gene, was shown to be germline mutated in 15% of SHH-medulloblastoma patients. ELP1 encodes the scaffolding member of the Elongator complex and is required for efficient translation. Heterozygous mutations in ELP1 have been associated with the neural disorder Familial Dysautonomia, but not cancer. ELP1-associated medulloblastomas frequently harbor somatic PTCH1 co-mutations. It remains unclear how ELP1 affects the GNP lineage during normal cerebellar development and tumorigenesis in pediatric SHH-medulloblastoma patients. To characterize ELP1 mutations in the GNP lineage in vitro, we established a cerebellar organoid model from human induced pluripotent stem cells (iPSCs). We genetically inserted an EGFP reporter downstream of the endogenous GNP-specific ATOH1 locus in control iPSCs and generated cerebellar organoids according to published protocols. Marker gene and protein expression levels confirmed the cerebellar identity of the 3D model. Furthermore, activation of the EGFP reporter in single cells within the organoid highlighted the specification of putative GNPs. Next, we will determine the specific cell state of putative iGNPs and compare to human GNPs identified in our scRNAseq cerebellum atlas. To analyze tumorigenesis through ELP1 loss, we will introduce patient-specific ELP1mutations into ATOH1-EGFP iPSCs. Cerebellar organoids derived from ELP1-, PTCH1-deficient and control iPSCs will serve as models to study GNP proliferation, differentiation, apoptosis and tumor formation. Combining genome editing, in vitro 3D differentiation and functional studies, we will characterize the novel predisposition gene ELP1in GNPs during cerebellar development. In addition, we will determine the interplay of ELP1and PTCH1 co-mutations, predisposing SHH-medulloblastoma formation.
MEDB-26. Outcomes of children with standard-risk and high-risk medulloblastoma treated with pre-irradiation chemotherapy and risk-adapted craniospinal irradiation: a report on patients from the Polish Pediatric Neuro-oncology Group
Authors: Perek-Polnik Marta , Cochrane Anne , Chojnacka M , Drogosiewicz M , Filipek I , Swieszkowska E , Tarasinska M , Kowalczyk P , Abdelbaki Mohamed S , Dembowska-Bagińska Bożenna 
Published: June 2022

Abstract
BACKGROUND: The last two decades have witnessed several efforts to minimize the adverse sequelae of craniospinal irradiation (CSI), a standard of care treatment modality in medulloblastoma. This has been accomplished by adding chemotherapy to the treatment backbone. The use of pre-irradiation chemotherapy has also been previously reported. In one of the largest studies to date, we analyze treatment outcomes in children with standard and high-risk medulloblastoma treated with pre-irradiation chemotherapy followed by reduced-dose radiotherapy in SR and maintenance chemotherapy. METHODS: Data from the Polish Pediatric Neuro-oncology Group (PPNG) was analyzed in patients greater than 3 years of age with newly-diagnosed medulloblastoma. RESULTS : Among 138 patients, median age at diagnosis was 7.9 years and median follow-up was 5.5 years. Comprehensive molecular subgrouping was not available for all patients at the time of data collection. Of 60 standard-risk patients, there was pre-irradiation disease recurrence in one patient. One patient expired prior to radiation due to metastatic disease. Of 78 high-risk patients, one had pre-irradiation recurrence. Overall survival (OS) for high-risk patients at 3 and 5 years (± standard error) was 89.2 ± 4.0% and 81.3 ± 5.8%, respectively. OS for standard-risk patients at 3 and 5 years was 92.5 ± 3.8% and 88.2 ± 5.1%, respectively. Among high-risk patients, event-free survival (EFS) at 3 and 5 years was 82.5 ± 5.3% and 81.0 ± 5.6%. Among standard-risk patients, 3-year EFS was 89.2 ± 4.6% and 5-year EFS was 86.8 ± 5.3%. CONCLUSION : This study demonstrates promising survival outcomes in pediatric medulloblastoma patients treated with pre-irradiation chemotherapy followed by reduced-dose CSI and adjuvant chemotherapy. Such an approach may be helpful if delays in starting radiotherapy are expected, which is usually the case in many institutions around the globe.