bluuebunny/crossref_metadata_2025_split huggingface dataset:
ETMR-09.In vitro modelling of embryonal tumors with multilayered rosettes (ETMR) and other novel brain tumor types.
Authors: Bunt Jens , Roosen Mieke , Stathi Phylicia , Polychronopoulos Panagiotis , Odé Zelda , Maas Joris , Kool Marcel 
Published: June 2022

Abstract
Over the last decade, molecular characterization has resulted in many tumors previously classified as central nervous system primitive neuroectodermal tumors (CNS-PNETs) now being classified into their own distinct tumor types. These novel types are often characterized by very specific genomic aberrations. For instance, embryonal tumors with multilayered rosettes (ETMR) harbor amplifications of miRNA cluster C19MC or complex DICER1 mutations, while in CNS neuroblastoma with FOXR2 activation structural aberrations result in aberrant FOXR2 expression. Despite the presence of distinct oncodrivers, our understanding of these tumors is still limited. To elucidate tumor biology and to discover tumor specific treatments, we need to uncover how these oncodrivers contribute to tumorigenesis. However, a bottleneck in basic and translational research of these novel tumor types, is the lack of representative preclinical models, especially in vitro. To overcome this hurdle, we aim to mimic tumor development in genetically modified brain organoids. Human brain organoids derived from pluripotent stem cells are generated to represent either the developing forebrain or cerebellum. To mimic oncodriving events, DNA plasmids are introduced via electroporation into the proposed cell-of-origin populations to knockout tumor suppressor genes or overexpress oncogenes. By detecting fluorescent proteins encoded by the plasmids, electroporated cells are followed over time. Based on our preliminary data, for instance, overexpression of C19MC results in ectopic expansion of the electroporated cells. Ongoing histological and molecular characterizations, including (single cell) transcriptomic and epigenomic analyses, will reveal to which extend these organoid models resemble the specific human tumor types. Although further validation is required, these organoid models provide a novel avenue to study especially brain tumor types with distinct oncodriving events for which patient-derived models have not yet been established. They also allow for in-depth analyses of the potential cells of origin and the contribution of different mutations to tumor biology.
ETMR-12. Novel cell models of CNS tumors with BCOR fusion or internal tandem duplication suggest FGFR and PDGFR as promising therapy targets
Authors: Kirchhofer Dominik , Lötsch-Gojo Daniela , Gabler Lisa , Jaunecker Carola N , Piontek Martin , Mayr Lisa , Englinger Bernhard , Pirker Christine , Mohr Thomas , Lämmerer Anna , Schmitt-Hoffner Felix , Boidol Bernd , Kubiceck Stefan , Peyrl Andreas , Azizi Amadeo A , Dorfer Christian , Haberler Christine , Kool Marcel , Berger Walter , Gojo Johannes 
Published: June 2022

Abstract
Central nervous system (CNS) tumors with BCOR internal tandem duplications (CNS-BCOR ITD) are aggressive malignancies recently included in the 2021 WHO Classification of CNS tumors. This entity is characterized by ITDs within the PUFD domain of BCOR, potentially interfering with protein-protein interactions and preventing non-canonical polycomb repressive complex 1.1 (ncPRC1.1) complex formation. Additionally, other BCOR alterations like frame shift mutations and gene fusions have been described. However, the underlying molecular mechanisms promoting tumor aggressiveness remain unknown. We established cell models from one patient harboring a BCOR frameshift mutation and another one with a concomitant BCORL1-fusion. Two additional models were derived from a patient with a CNS-BCOR ITD tumor. Multidrug screening uncovered high sensitivity against defined receptor tyrosine kinase (RTK) inhibitors (TKIs). In detail, ponatinib, nintedanib, and dovitinib reduced cell viability at half maximal inhibitory concentrations (IC50) in the low micro-molar range (&lt;2.5 µM). Expression analyses of the respective TKI targets suggested fibroblast growth factor receptor 3 (FGFR3) and platelet derived growth factor receptor A (PDGFRA) as central players in this response. RTK inhibition resulted in strongly impaired downstream MAPK and Pi3K/AKT signaling. Vice versa, exposure to the RTK ligands bFGF and PDGFAA increased S6, Erk and Akt phosphorylation. Next, we treated two patients – one with a BCOR frame shift mutation/BCORL1-gene fusion and one with an ITD with nintedanib – within a multimodal treatment approach and achieving complete remission and disease stabilization, respectively. Ultimately, we analyzed respective RTK ligands in patient cerebral spinal fluid (CSF) and found FGF18 and PDGFA to correlate with tumor treatment response and progression. Summarizing, we uncover a central role of defined RTK signaling modules in the malignant phenotype of CNS-BCOR-ITD and tumors harboring BCOR alterations and elucidate their potential as therapeutic targets. Currently, we aim to dissect the interconnection between BCOR/BCORL1 alterations and RTK hyperactivation.
ETMR-14. The single-cell landscape of pineoblastoma identifies developmental origins and exposes novel therapeutic vulnerabilities.
Authors: Gudenas Brian , Englinger Bernhard , Liu Anthony P Y , Ahmad Sheikh Tanveer , Meredith David , Pfaff Elke , Paul Leena , Hadley Jennifer , Batts Melissa , Klimo Paul , Boop Frederick A , Gajjar Amar , Robinson Giles , Orr Brent , Lin Hong , Alexandrescu Sanda , Jones David T W , Filbin Mariella G , Northcott Paul A 
Published: June 2022

Abstract
Pineoblastoma (PB) is a rare and aggressive childhood brain tumor with highly variable age and treatment-associated outcomes. Our recent bulk tumor analyses of DNA methylation and mutational landscapes uncovered four discrete PB molecular subgroups (PB-miRNA1, PB-miRNA2, PB-MYC/FOXR2, and PB-RB), providing a major advance in our understanding of biological and clinical heterogeneity. However, developmental origins of PB subgroup heterogeneity and mechanisms governing how specific genetic alterations promote malignancy remain unknown. To resolve the cellular origins of PB, we assembled a large single-nucleus RNA-sequencing cohort (n=32) of primary PB tumors, including representatives from each subgroup. Transcriptomic analysis identified subgroup-specific gene expression programs driving intra-tumoral heterogeneity. In addition, we discovered substantial differences in the expression of miRNA biogenesis genes between the PB-miRNA1 and PB-miRNA2 subgroups, providing mechanistic support for their distinct subgroup identities despite overlapping driver events. The MYC/FOXR2 subgroup was characterized by over-expression of the FOXR2 proto-oncogene in bulk RNA-seq, which we validated in single-nuclei and identified co-expressed downstream target genes. To map PB subgroups to their putative developmental beginnings, we created a single-cell transcriptional atlas of the murine pineal gland across 11 developmental stages (E11-P21). Trajectory inference within the developing pineal gland revealed a differentiation continuum of early, mid, and mature alpha-/beta pinealocytes. Cross-species correlation and deconvolution identified significant associations between multiple PB subgroups and specific differentiation states of the pinealocyte lineage, suggestive of developmental origins. Characterization of pinealocyte development informed generation of biologically faithful disease models, including a novel genetically engineered mouse model of the PB-RB subgroup. PB-Rb1 mouse tumors were histologically and molecularly validated for their fidelity to human tumor counterparts, exhibiting up-regulation of key pinealocyte lineage markers that are diagnostic in patients. Finally, high-throughput drug screening identified several promising pharmacological candidates that may attenuate consequences of Rb1 deficiency in affected children.
ETMR-16. Embryonal tumors with multi-layered rosettes: A case series in treatment for newly diagnosed children
Authors: Tran Hung , Margol Ashley , Cotter Jennifer , Szymanski Linda , O’Halloran Katrina , Tamrazi Benita , Michaiel George , Christian Eisha , Esfahani Darian , Davidson Tom Belle 
Published: June 2022

Abstract
BACKGROUND: Embryonal tumors with multi-layered rosettes (ETMRs) are rare pediatric brain tumors with poorly defined prognostic features, standard of care treatments or outcome data. Recent data suggest that high-dose chemotherapy and radiotherapy is correlated with improved survival compared to chemotherapy alone. CASE DESCRIPTIONS: Four patients with newly diagnosed ETMRs were treated with 2 cycles of induction chemotherapy per PBTC-026 using isotretinoin, vorinostat, vincristine, cisplatin, etoposide, cyclophosphamide with added intrathecal topotecan. Second look surgery was performed if not in complete remission (CR). Consolidation was with three cycles of marrow-ablative chemotherapy (carboplatin and thiotepa) with autologous hematopoietic cell rescue followed by focal irradiation and 12 cycles of maintenance chemotherapy with intrathecal topotecan, vorinostat and isotretinoin. Patient 1 was a 3-year-old female with right parietal tumor, localized, and achieved gross total resection (GTR). Patient 2 was an 11-month-old male with posterior fossa tumor, localized, and achieved subtotal resection. Patient 3 was a 9-month-old female with posterior fossa tumor with near GTR, and metastasis to T12/L1 and L3/L4. [DTB1] [HNT2] Patient 4 was a 34-month-old male with a right frontal lobe tumor, localized and achieved GTR. Patient 1 is now 18 months from diagnosis and in CR. Patient 2 had second look surgery both after induction and consolidation but suffered neurologic injury to the brainstem which led family to decline further therapy. He is currently 14 months from diagnosis with stable residual disease. Patient 3 had local disease recurrence following radiation therapy at 10 months post diagnosis[DTB3] [HNT4] , prior to maintenance. Patient 4 remains in CR at 13 months from diagnosis, currently in maintenance with vorinostat and isotretinoin but declined intrathecal topotecan. CONCLUSION: This case series adds to current knowledge of intensive multi-modal therapy for newly diagnosed ETMR. Further study to define standard optimal treatments in this high-risk group of patients is warranted.
GCT-06. Management of a congenital intracranial teratoma: a case report and review of literature
Authors: Shatara Margaret , Cantor Evan , Ramos Kristie N , Yu Jonathan , Hassan Ahmad , Shimony Joshua S , Han Peng Cheng , Meyer Ashley , Ogle Andrea , McHugh Michele , Green Tammy , Beck Mary , Cluster Andrew , Brossier Nicole , Rubin Joshua , Dahiya Sonika , Abdelbaki Mohamed S , Strahle Jennifer 
Published: June 2022

Abstract
INTRODUCTION: Congenital intracranial teratomas (CITs) are rare tumors occurring in the first 60 days of life, often associated with dismal prognosis, posing challenges in both oncologic and surgical management. METHODS: We report a patient with a congenital mature teratoma diagnosed prenatally, who underwent successful surgical resection following neoadjuvant chemotherapy. We also performed an updated literature review on CIT outcomes. RESULTS: A newborn female, diagnosed prenatally with a complex midline intracranial echogenic mass, underwent postnatal brain MRI which demonstrated a supratentorial large complex enhancing mass with solid and cystic components, with associated obstructed hydrocephalus. Serum alpha-fetoprotein (AFP) and beta-human chorionic gonadotropin were normal for age. Tumor biopsy revealed mature teratoma. AFP obtained from cyst fluid during fenestration was significantly elevated at 8 weeks of life. Due to concerns for possible malignant transformation and in an attempt to alter tumor vascularity facilitating surgical resection, the patient received two cycles of neoadjuvant carboplatin and etoposide, followed by tumor resection without significant intraoperative bleeding. There was no evidence of immature components on final pathology. The patient remains without tumor recurrence, now 9 months, since surgical resection. Review of literature yielded 76 cases of CITs: eight patients with mature teratoma, of which six remained alive following tumor resection. Five patients with immature teratoma received chemotherapy prior to resection; three remained alive post-resection (follow-up range 3-20 years). DISCUSSION: CITs are typically associated with poor prognosis, with reported one-year survival of 7.2-12%. Surgical excision is the mainstay of treatment, often limited by intraoperative hemorrhage. Neoadjuvant chemotherapy has been employed as a successful strategy to reduce tumor volume and vascularity in a variety of pediatric brain tumors; more specifically, carboplatin and etoposide are utilized as neoadjuvant chemotherapy for non-germinomatous germ cell tumors to facilitate excision in older children. Their role in CITs requires further evaluation.
GCT-09. Transcriptome and methylome profiles of CNS germ cell tumors and their comparison with testicular counterpart
Authors: Takami Hirokazu , Elzawahry Asmaa , Mamatjan Yasin , Kato Mamoru , Hama Natsuko , Shibata Tatsuhiro , Nakazato Yoichi , Nishikawa Ryo , Matsutani Masao , Ichimura Koichi 
Published: June 2022

Abstract
BACKGROUND: The pathophysiology of CNS germ cell tumors (GCTs) has yet to be fully unraveled, resulting in the paucity of treatment options. The biological comparison with its testicular counterpart has not been interrogated. METHODS: In total, 84 cases of CNS GCT were investigated for methylation and transcriptome analyses, and an integrative analysis of the normal cells undergoing embryogenesis and testicular GCTs was conducted. RESULTS: Transcriptome analysis revealed germinoma and non-germinomatous GCTs (NGGCTs) were clearly separated. On transcriptome, germinoma was characterized by primitive cell state, closely related to primordial germ cell (PGC) with meiosis/mitosis potentials. NGGCT had a feature of more differentiated cell state directed toward organogenesis. Germinoma was subdivided into two clusters on integrated transcriptome and methylation analysis, and they are different in the age distribution and tumor cell content. CNS and testicular GCTs were divided based on histology, either germinoma/seminoma or NGGCT/non-seminomatous GCTs on methylation. Expression analysis mainly clustered them depending on the site of origin and histology. CONCLUSIONS: Expression profiles of CNS GCTs distinctly reflect the histological variabilities. Germinoma may be clustered into two groups, with possible differentiation in treatment intensity in the future. GCTs at CNS and gonads seem to have a mutual cell-of-origin and similar genomic backgrounds, which potentiates site-agnostic treatment development.
GCT-14. The Impact of Residual Disease on the Outcomes of Central Nervous System Germinomas – A Single Institution Experience
Authors: Cantor Evan , Cochrane Anne , Ogle Andrea , Meyer Ashley , Brossier Nicole M , Shatara Margaret , Cluster Andrew , Abdelbaki Mohamed S 
Published: June 2022

Abstract
BACKGROUND: CNS Germinomas are highly radio-sensitive tumors with an excellent survival rate of more than 90%. The current standard of care combines chemotherapy with reduced-dose radiotherapy to minimize the adverse effects and long-term effects associated with radiotherapy. In the latest Children’s Oncology Group clinical trial (ACNS1123 stratum 2), patients with residual or progressive disease following chemotherapy can be considered for a “second-look” surgery to assess tumor viability. Patients with residual disease who do not undergo second-look surgery receive 24 Gy of whole ventricular radiation with a 12 Gy boost compared to 18 Gy plus boost given to patients in complete remission or without viable tumor on second-look. Conversely, the International Society of Paediatric Oncology (SIOP) protocol does not stratify based on response to chemotherapy, and the Korean SMC GCT trial uses 18 Gy CSI plus boost for all patients regardless of chemotherapy response. METHODS: Single center retrospective chart review of germinoma patients treated at St Louis Children’s Hospital between 2011 and 2021. RESULTS: We analyzed data for all 15 germinoma patients treated between 2011 and 2021. Five patients had residual disease following chemotherapy. Of these five, one had complete remission at the end of radiotherapy, one had partial response, and three had stable disease. All patients remain relapse-free with time of follow-up ranging between 6.3-109.3 months from the end of therapy (median 24 months). CONCLUSION: None of the five patients with residual disease following chemotherapy demonstrated disease progression following chemotherapy and radiotherapy. Future prospective clinical trials are needed in order to test the possibility of treating germinomas patients who have residual disease after chemotherapy with a low dose of radiotherapy similar to that used in patients with complete remission.
GCT-17. Recurrence of CNS germ cell tumors (GCTs) along biopsy and ventriculostomy tracts
Authors: McGlynn Mary Claire , Drogosiewicz Monika , Reiners Stephanie , Abdelbaki Mohamed 
Published: June 2022

Abstract
BACKGROUND: Central nervous system (CNS) germinoma relapses are rare. However, the latest Children’s Oncology Group (COG), ACNS1123 stratum 2, described three relapses along the biopsy tract out of eight total relapses; two along the biopsy and endoscopic third ventriculostomy (ETV) tract and one along the biopsy tract and external ventricular drain. Given these findings, we sought to describe other cases of GCT recurrence along surgical tracts. METHODS: We performed a literature review from 1980-2021 to identify cases of GCT recurrence along biopsy and ventriculostomy tracts. RESULTS: Three patients with pineal lesions were identified (13, 14, and 34-years old). All underwent ETV, cerebrospinal fluid (CSF) sampling, and tumor biopsy. Two patients had uncomplicated postoperative courses. One developed persistent hydrocephalus and underwent repeat ventriculostomy. Two were diagnosed with pure germinoma and treated with focal radiotherapy of 45 Gy alone or chemotherapy and radiation (50.4 Gy to the tumor volume and 36 Gy to adjacent high-risk area). The third was treated with methotrexate and corticosteroids. All three had recurrence on surveillance MRI (1-3 years after diagnosis). One had recurrence at the ventriculostomy bur hole site, and two had recurrence along the ventriculostomy tract. On biopsy, all three lesions were germinomas. One received pre-radiation chemotherapy and palliative radiation (36 Gy to surgical bed and 30.6 Gy to surrounding high-risk area). Another received chemotherapy and craniospinal radiation of 15 Gy. The third had a complicated post-biopsy course. He ultimately underwent chemotherapy and radiation (24 Gy). All were still alive at time of report. Two were disease free at 12 and 18 months, while one was still receiving chemotherapy. CONCLUSION: Recurrence along the biopsy or ventriculostomy tract is rarely reported in the literature. Future evaluation to determine the incidence could inform if biopsy and ventriculostomy tracts should be included in the radiation therapy field.
GCT-21. Long-term outcome and follow up of intracranial germ cell tumors: Reduced-dose radiotherapy and intensified chemotherapy improves clinical outcome and quality of life for long-term survivors
Authors: Kagawa Naoki , Miyamura Takako , Yamasaki Kai , Hirayama Ryuichi , Kijima Noriyuki , Okita Yoshiko , Nakagawa Tomoyoshi , Hara Junichi , Kishima Haruhiko 
Published: June 2022

Abstract
BACKGROUND: Intracranial germ cell tumors (iGCT) are heterogeneous tumors with several histopathology. Chemoradiotherapy is effective and required for treatment against them, but optimal treatment intensity should be selected from the viewpoint of both improvement of clinical outcome and avoidance of late complications. We introduced a protocol with reduced-dose radiotherapy and intensified chemotherapy for iGCT. OBJECTIVE: We retrospectively analysed the clinical outcome, especially for non-germinomatous germ cell tumors and long-term clinical outcome of late complications, enrollment and employment, as indicators of quality of life (QOL). MATERIALS AND METHODS: Thirty-eight children and young adults (28 men and 10 women) with iGCTs treated in our institution from 1997 to 2013 were enrolled in this study. They consisted of 26 germinomas including HCG-producing cases and 12 non-germinomatous GCTs (NGGCT). Local irradiation was selected for all patients, and the dose of irradiation was 23.4-54 Gy. The whole-brain irradiation was made in patients who had intracranial dissemination, but any prophylactic irradiation to the whole brain and spinal cord was not performed. For NGGCT, high-dose chemotherapy and peripheral blood stem cell transplantation (PBSCT) were introduced. Second-look surgeries were performed for cases with residual tumors after induction chemotherapies. RESULTS: In germinoma group and NGGCT group, 10-year progression-free survival was 86% and 84%, 10-year overall survival was 93% and 91%, respectively. About late complications, endocrinological replacement (39%), cerebrovascular disease such as cavernous hemangioma and arterial stenosis (18%), secondary neoplasm (2.6%) were observed. Regarding QOL, enrollment and return to school rate was 92% and employment and the return rate was 89%, which were influenced by hemipararesis associated with basal ganglia lesion, intractable epilepsy and whole-brain irradiation. CONCLUSION: Reduced-dose radiotherapy and intensified chemotherapy for iGCT, especially NGGCT, improved the clinical outcome and QOL of long-term survivors, suppressing late complications. Further comprehensive follow-up and analysis are needed.
HGG-02. Epigenetic transcription regulation and 3D genome structure in pediatric high-grade glioma
Authors: Huang Tina , Wang Juan , Hu Ye , Piunti Andrea , Bartom Elizabeth , Shilatifard Ali , Yue Feng , Saratsis Amanda 
Published: June 2022

Abstract
INTRODUCTION: Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid brain tumors. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding Histone H3. To investigate whether the H3K27M mutant protein is associated with distinct chromatin structure affecting transcription regulation, we generated the first high-resolution Hi-C and ATAC-Seq maps of pHGG cell lines, and integrated these with tissue and cell genomic data. METHODS: We generated sequencing data from patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1, normal brainstem n=1). Analyses included cell line RNA-Seq, ChIP-Seq (H3K27ac, H3K27me3, H3K27M) and genome-wide chromatin conformation capture (Hi-C), as well as tissue ATAC-Seq. Publicly available pediatric glioma tissue ChIP-Seq data was integrated with cell data. CRISPR knock-down of target enhancer regions was performed. RESULTS: We identified tumor-specific enhancers and regulatory networks for known oncogenes in DIPG and GBM. In DIPG, FOX, SOX, STAT and SMAD families were among top H3K27Ac enriched motifs. Significant differences in Topologically Associating Domains (TADs) and DNA looping were observed at OLIG2 and MYCN in H3K27M mutant DIPG, relative to wild-type GBM and normal cells. Pharmacologic treatment targeting H3K27Ac (BET and Bromodomain inhibition) altered these 3D structures. Functional analysis of differentially enriched enhancers in DIPG implicated SOX2, SUZ12, and TRIM24 as top activated upstream regulators. Distinct genomic structural variations leading to enhancer hijacking and gene co-amplification were identified at A2M, JAG2, and FLRT1. CONCLUSION: We show genome structural variations enhancer-promoter interactions that impact gene expression in pHGG in the presence and absence of the H3K27M mutation. Our results imply that tridimensional genome alterations may play a critical role in the pHGG epigenetic landscape and thereby contribute to pediatric gliomagenesis. Further studies examining the impact of the alterations are therefore underway.