bluuebunny/crossref_metadata_2025_split huggingface dataset:
CNSC-31. CRISPR FUNCTIONAL SCREEN IDENTIFIES A NOVEL LONG NONCODING RNA MODULATING GLIOBLASTOMA INVASION
Authors: Tsung Kathleen , Han Jane , Liu Kristie , Loh Eddie , Attenello Frank 
Published: November 2022

Abstract

INTRODUCTION
Glioblastoma(GBM) invasion studies traditionally target coding genes. Long noncoding RNAs (lncRNAs), are transcripts without coding potential, with limited data regarding function. We leveraged CRISPR-interference, repressing lncRNA transcription via Cas9-KRAB, to evaluate invasive function of GBM-associated lncRNAs in a CRISPRi functional screen.

METHODS
2,307 candidate lncRNAs were assembled from GBM differential gene expression. Guide RNAs targeting candidates were lentivirally incorporated into GBM screening populations. Screen populations were evaluated via Matrigel invasion, comparing sgRNA populations before/after a 24-hour invasion period. ASO treatment evaluated pharmacologic targeting of candidate lncRNAs. Top screening candidates were evaluated in a patient derived glioma stem cell (GSC) line, USC02, as well as U87 and U251 commercial lines. Differential gene expression was assessed in multiple cell lines following lncRNA knockdown via RNA-seq followed by GSEA and pathway analysis was evaluated to assess downstream mechanistic candidates affected by lncRNA KD.

RESULTS
Forty-eight lncRNAs were significantly associated with GBM invasion, with lncRNA repression associated with decreased invasion of 31-85%(p&lt; 0.01). Individual validation of a candidate lncRNA KD, LH02236, confirmed 85% decrease in tumor cell invasion versus control. Evaluation of gene expression across normal cortex and tumor samples from GSEA/TCGA datasets revealed LH02236 is significantly more expressed in GBM versus low grade glioma, and in low grade glioma versus normal cortex. Expression of LH02236 was significantly associated with patient survival (p&lt; 0.0001). Gene expression analysis of LH02236 knockdown revealed Sox10 to be highly correlated with lncRNA expression across multiple cell lines.

CONCLUSION
Large scale CRISPRi screening identified LH02236, a previously unannotated lncRNA, as essential to invasion in patient lines. Gene expression is significantly associated with tumor grade and patient survival. Analysis of knockdown across multiple cell lines suggests Sox 10, commonly associated with GSC function, is modulated by this novel lncRNA.
TMIC-85. MICROGLIA REPLACEMENT CHANGES THE TRANSCRIPTIONAL PROFILE OF TUMOR ASSOCIATED MYELOID CELLS IN MURINE MODELS OF BRAIN MALIGNANCIES
Authors: Mader Marius , Rodrigues Adrian , Chernikova Sophia , Wong Zheng Hao Samuel , Wang Yuelong , Petritsch Claudia , Wernig Marius , Gephart Melanie Hayden 
Published: November 2022

Abstract
Tumor associated microglia and macrophages (TAMs) represent a main cell type of brain malignancies and demonstrate complex interactions with cancerous cells and the tumor microenvironment. These interactions have important implications for the progression and treatment of malignant central nervous system (CNS) tumors. In a non-oncological context, it has been shown that endogenous microglia can be replaced by peripheral hematopoietic cells by genetic or pharmacological intervention. A highly efficient replacement protocol (Shibuya et al, Sci Transl Med 2022, PMID:35294256) utilizing myeloablative bone marrow transplantation (BMT) followed by microglial depletion via pharmacological inhibition of the Colony-stimulating factor-1 receptor (CSF-1R) leads to almost complete repopulation of the CNS myeloid niche by circulation-derived myeloid cells (CDMCs). We investigated if this approach could be utilized to integrate CDMCs into brain tumors and study associated changes in the TAM signature. Microglia replacement in immune-competent mice was followed by intracranial transplantation of syngeneic cell lines of either high-grade glioma (GL261) or breast cancer metastasis (E0771). Lineage tracing proved high intra- and peri-tumoral chimerism of BMT-graft derived cells among CNS myeloid cells in both models two weeks after tumor cell injection. Tumor associated CDMCs (TA-CDMCs) showed a similarly activated morphology as naïve TAMs. We used single cell RNA sequencing of CD45-positive cells to further profile the transcriptomic identity of glioma TA-CDMCs. Pathway enrichment analysis revealed an upregulation of immune response pathways in TA-CDMCs compared to regular TAMs, including the overexpression of genes relevant for the regulation of T cell activation, suggesting possible modification of the glioma immune-environment. Strategies to manipulate the myeloid niche have the potential to provide further understanding of the pathobiology of TAMs and to build the basis for novel cell therapeutic approaches in the neuro-oncological domain.
MODL-02. GLIOMA ORGANOID MODEL PHENOTYPICALLY RECAPITULATES KEY ASPECTS OF MALIGNANT TRANSFORMATION IN GLIOBLASTOMA
Authors: Zhao Yi , Kant Shiva , Kesarwani Pravin , Hubert Christopher , Nakano Ichiro , Fullmer Joseph , Chinnaiyan Prakash 
Published: November 2022

Abstract
Glioblastoma (GBM) displays extensive intra-tumoral heterogeneity, serving as a major obstacle for effective treatment. The identification of molecular subtypes offered promise for personalized treatment regimens in GBM, however, it has seen been determined these subtypes are reflective of intra- rather than inter-tumoral heterogeneity, with proneural (PN) and mesenchymal (MES) subtypes corresponding to the infiltrative edge and peri-necrotic core of a tumor, respectively. Further, plasticity between subtypes has been identified, with PN-to-MES transition being described as a mode of resistance. Our laboratory utilizes patient-derived, subtype-specific GBM neurospheres as a model to understand GBM heterogeneity and have previously demonstrated that these models faithfully recapitulate human disease, with PN-neurospheres expressing Olig2, having a metabolic phenotype consistent with low-grade glioma, and an indolent growth pattern in vivo when compared to aggressive, CD44 expressing MES-neurospheres. In parallel, our group demonstrated 3D-organoid models of GBM recapitulate the tumor ecology of this malignancy ex vivo. Therefore, we sought to determine if this model could be utilized to provide a window into the plasticity of GBM molecular subtypes. Consistent with their phenotype when grown as neurospheres, MES-organoids had a homogeneous distribution of proliferating cells and retained CD44 expression. In contrast, cellular heterogeneity emerged in PN organoids that could be morphologically divided into an outer, cell-dense rim and an inner core with a lower cell density. The outer rim, recapitulating a perivascular niche, contained proliferating cells, and the inner core contained necrotic cells, mimicking the hypoxic microenvironment of GBM. Intriguingly, PN organoids retained Olig2 expression in the edge, however, actively transitioned into a MES-like state in the core, expressing CD44 and metabolic reprogramming consistent with malignant transformation. Collectively, these finding support that microenvironment contributes towards PN-MES transition and PN organoid models may serve as a tool to provide a window into specific molecular and metabolic factors contributing towards transformation.
MODL-13. Sensitivity of Tumor Treating Fields (TTFields) treatment planning to healthy tissue segmentation inaccuracies
Authors: Ze’evi Oshrit , Marciano Tal , Naveh Ariel 
Published: November 2022

Abstract
TTFields are FDA approved for treating patients with GBM. TTFields utilize low intensity electric fields with intermediate frequency (100-500 kHz) that disrupt cellular processes critical for cancer cell viability and tumor progression. TTFields have been shown to disrupt multiple phases of the cell cycle including metaphase, anaphase, and telophase, resulting in cellular apoptosis. TTFields are administered through two pairs of capacitive arrays placed on the patient’s scalp. As TTFields are a dose dependent therapy, optimization of array layout for maximizing field intensity may improve survival rates of patients. Thus, Novocure is developing a treatment planning system, in which MR images are used to create a patient-specific model, which in turn is used for simulating electric fields distribution. However, the segmentation process of the MRIs is prone to errors that may influence the choice of array layout, and consequently provide lower TTFields dose than possible. To test the sensitivity of layout chosen to such inaccuracies, we placed different array layouts on the highly detailed MIDA head model and simulated the resulting LMiPD from each configuration. We then simplified the model in several phases and compared the resulting array layout ranking between the full model and each simplified model. Our results show that though the calculated LMiPD is very sensitive to the quality of the model, the ranking pattern between the detailed and simplified models is similar. Some alterations do occur, but this mostly happens when the LMiPD values between switched layouts are very close, rendering these alterations clinically insignificant. Based on these results, we conclude that the ranking order of array layouts by LMiPD dose does not significantly change between detailed and simplified head models even though the LMiPD dose itself is sensitive to the quality of the head model.
MODL-24. ESTABLISHING A CLINICALLY RELEVANT CT AND ASSOCIATED RADIOMICS PIPELINE FOR INTRACRANIAL RODENT TUMOUR MODELS
Authors: Connor Kate , Conroy Emer , White Kieron , Shiels Liam , Keek Simon , Ibrahim Abdalla , Gallagher William , Clerkin James , Sweeney Kieron , O'Brien David , Cryan Jane , Heffernan Josephine , Brett Francesca , Lambin Philippe , Woodruff Henry , Byrne Annette 
Published: November 2022

Abstract
While magnetic resonance imaging (MRI) is the predominant imaging modality for glioblastoma (GBM), pre-clinical MRI scanner availability is limited. As pre-clinical CT is more widely available and cost-effective, this study aimed to 1) establish preclinical-GBM CT and CT-radiomic workflows, 2) identify whether CE-CT could detect murine orthotopic GBM tumours on two CT instruments [TRIUMPHX-O-CT; IVISSPECTRUM-CT], 3) assess whether CT-radiomic features could distinguish tumour from normal tissue, and support earlier detection of tumours, 4) verify translation of pre-clinical CT-radiomic pipelines to, and assess pre-clinical CT-features in, clinical CE-CT scans.U87R-Luc2(n=25) and NFpp10a-Luc2(n=10) orthotopic GBM models were established and tumours monitored via bioluminescence imaging (BLI). Concurrently, mice underwent CE-CT (IV-iodine/300mg/mL/50kV-scan). Extracted radiomic features (PyRadiomics) underwent dimensionality reduction (Spearman correlation; &gt;0.85). Remaining features were analysed (Recursive feature elimination (RFE)/RepeatedCV/randomforest) in normal and tumour tissue and across timepoints (TRIUMPHX-O-CT-Wk3vsWk6,Wk6vsWk9/12; IVISSPECTRUM-CT-Wk6vsWk9/12).CE-CT and radiomic pipelines were successfully established for orthotopic GBM models, using both CT-systems. On visual assessment of images, BLI was significantly more sensitive, with tumours detectable at Wk1 (BLI) vs Wk9 (CE-CT). However, RFE analysis identified CT-radiomic features (first_order&glcm) which differentiated tumour from normal tissue (TRIUMPHX-O-CT). A subsequent feature set (first_order,glcm,gldm&glzm) were identified (TRIUMPHX-O-CT/IVISSPECTRUM-CT), detecting tumours earlier (Wk3&Wk6) than possible by visual assessment of CTs. Preclinical radiomic methods were successfully applied to exploratory clinical CE-CT scans(n=10). Here, several preclinical CT-features (e.g. Zone_Entropy) showed increased intensity in tumour regions. Overall experimental BLI is the most sensitive method for pre-clinical intracranial tumour detection. However, analysis of clinically relevant CT-radiomic features may facilitate tumour identification and earlier tumour detection (Wk3/Wk6-TRIUMPHX-O-CT/Wk6-IVISSPECTRUM-CT) than possible by visual assessment of CT (Wk9). Clinically relevant CT-derived radiomic features may therefore support intracranial rodent tumour assessment. Importantly, preclinical radiomic methods successfully translate to clinical CT-radiomic analysis. Parallel trends in tumour-specific feature intensities across pre-clinical and clinical scans suggest species conservation of features.
MODL-28. DEVELOPING A STRATEGY FOR MODELING HIGH-GRADE GLIOMA IN GӦTTINGEN MINIPIGS
Authors: Tora Muhibullah S , Lei Kecheng , Nagarajan Purva P , Bray David P , Rindler Rima S , Neill Stewart G , Zhang Michelle , Texakalidis Pavlos , Krasnopeyev Andrey , Gergye Crystal , James Raphael , Oshinski John N , Federici Thais , Bruce Jeffrey N , Canoll Peter , Boulis Nicholas M 
Published: November 2022

Abstract

BACKGROUND
The current literature does not describe a reproducible large animal model of intracranial high-grade glioma (HGG). Prior work has demonstrated the feasibility of inducing HGG de-novo in rodents by targeting specific oncogenic pathways. Here we report our approach to the production of supratentorial HGG in a series of minipigs through lentiviral gene transfer and subsequent initial characterization of a porcine glioma cell line.

METHODS
Four minipigs received injections into the subcortical white matter using a combination of lentiviral vectors expressing platelet-derived growth factor beta (PDGF-B), HRAS, and shRNA-p53. Animals underwent behavioral monitoring through porcine neurobehavioral scoring (PNS) and veterinary monitoring. Magnetic resonance imaging (MRI) was conducted at endpoint prior to necropsy. Post-mortem tissue biopsies underwent tissue culture and neuropathologic evaluation with hematoxylin and eosin (H&E) staining, immunohistochemistry, and immunofluorescent staining. Data are presented using appropriate statistical tests where relevant and descriptive statistics.

RESULTS
Two pigs received 50ul injections and reached endpoint by the end of post-operative week 1 and 2. Two pigs received 25 ul injections and were asymptomatic until a pre-determined endpoint of 4 weeks. MRI scans at endpoint demonstrated contrast enhancing, mass forming lesions at the site of injection with evidence of hemorrhage and perilesional edema, consistent with high-grade glioma. On H&E staining high-grade glioma growth was identified in 100% of animals. We observed immunopositivity for tumor markers GFAP, OLIG2, NG2, SOX2, and PDGFRA, as well as redox markers, and microenvironmental features consistent with high-grade glioma. Porcine glioma cell cultures were found to have significantly greater proliferative rate compared to control, and demonstrated GFAP, OLIG2, PDGFRA, and CD68 immunopositivity.

CONCLUSIONS
Lentiviral gene transfer represents a feasible strategy for glioma modeling in the Gӧttingen minipig. With our described methodology, we present a realistic strategy for reproducible modeling of intracranial glioma as a platform for preclinical neurosurgical development programs.
MODL-29. IN SILICO MODELING TO PREDICT ONCOGENICITY AND POTENTIAL TARGETABILITY OF NOVEL FGFR VARIANTS IN PEDIATRIC LOW GRADE GLIOMA
Authors: Laxer Ben , Nobre Liana , Tabori Uri , Vadivel Arun Anguraj , Levine Adrian , Johnson Monique , Ryall Scott , Ku Michelle , Milos Scott , Hawkins Cynthia 
Published: November 2022

Abstract
Pediatric Low grade gliomas (pLGGs) are largely driven by alterations in the RAS-MAPK pathway. The third most commonly mutated gene in pLGGs is the FGFR1 gene, having alterations including fusions, duplications or missense mutations. Accurate identification of these alterations has become increasingly important as FGFR inhibitors enter the therapeutic space. Here we describe a case of a pLGG patient with an FGFR1 W289_insW290 found through NGS in the tumor at diagnosis, and progression, without additional alterations. This extracellular, third-Ig domain mutation has not been reported. Transcriptional and proteomic profiling of the tumor showed low MAPK and high PIK-AKT pathway activation when compared to other gliomas. Literature review identified disorders of bone formation with similar mutations in the homologous FGFR2 gene. One such mutation, FGFR2 W290G favors inter-receptor disulfide bond formation over the normal intra-receptor disulfide bond. To determine if this insertion is a possible driver mutation in our pLGG case, Alphafold2 protein simulation software was used to make in silico models; quality metrics from both Alphafold2 and VADAR1.8 were used. Structure simulations of the FGFR1 insertion mutant (pLDDT = 81.8) and the mutant FGFR2 W290G (pLDDT = 83.4), were generated and compared to a protein data base, experimentally determined structure of wildtype FGFR1. When monomers of all three structures were aligned using PyMol, the root mean square deviations were &lt; 1.5 indicating the structures are correct or the same. Based on these results we concluded that, like the known FGFR2 mutation, this insertion is predicted to cause hyperactivity by inducing prolonged dimerization due to an aberrant inter-receptor disulfide bond but any structural or functional differences only occur when receptors are dimerized. We are currently generating isogenic cell line models to test this hypothesis and treat these cell lines with inhibitors to determine which treatments might work best for our patient.
MODL-33. AN ANIMAL MODEL OF GLI2-AMPLIFIED MEDULLOBLASTOMA
Authors: Murad Najiba , Liu Xiao , Tao Ran , Pei Yanxin 
Published: November 2022

Abstract
Medulloblastoma (MB) is the most common malignant brain tumor affecting children. Among the known subtypes of MB, GLI2-amplified SHH-MB associated with P53 mutations has the worst prognosis, and a 5-year survival rate of less than 30%. Moreover, GLI2-amplified MBs are non-responsive to SMO inhibitors, the only targeted treatment option available for SHH-MB. To address this treatment gap, there is an urgent need to identify novel potential therapeutic targets, an effort that requires better understanding of key cellular and molecular mechanisms underlying GLI2-amplified MB. To that end, we generated a mouse model of GLI2-amplified MB and identified GL12 as the critical driver of tumorigenesis, and granule cell progenitors (GCPs) as the cells of tumor origin. We further found that GLI2 specifically drives embryonic, but not neonatal, Math1+ GCPs to form SHH-MB tumors. An scRNA-seq analysis revealed MAPK pathway activation specifically in embryonic Math1+ GCPs. The MAPK pathway was activated in mouse and human GLI2-driven MB tumors, and a MEK/ERK inhibitor significantly inhibited GLI2-driven MB in vivo. Based on these findings, we hypothesize that GLI2-driven MB originates from a specific population of Math1+ GCPs during a discrete temporal interval in cerebellar development, and that targeting MAPK/MEK/ERK pathway components represents a novel approach to treatment of GLI2-amplified MB.
MODL-36. EXPRESSION OF YAP1-MAML2 AND CONSTITUTIVELY ACTIVE YAP1 DRIVE THE FORMATION OF MENINGIOMA-LIKE TUMORS IN MICE THAT RESEMBLE NF2-MUTANT MENINGIOMAS
Authors: Szulzewsky Frank , Arora Sonali , Arakaki Aleena , Sievers Philipp , Bonnin Damian Almiron , Paddison Patrick , Sahm Felix , Cimino Patrick , Gujral Taranjit , Holland Eric 
Published: November 2022

Abstract
YAP1 is a transcriptional co-activator and oncogene under the control of the Hippo Signaling Pathway. Functional inactivation of Hippo Pathway tumor suppressors, including NF2, are frequent events in human cancers. Meningiomas are the most common primary brain tumors, and a large percentage exhibit heterozygous loss of chromosome 22 (harboring the NF2 gene) and functional inactivation of the remaining NF2 gene copy, implicating oncogenic YAP activity in the pathobiology of almost half of these tumors. An alternate type of activating YAP1 mutation are YAP1 gene fusions that have been identified in several cancer subtypes. Recently, fusions between YAP1 and MAML2 have been identified in a subset of pediatric NF2-wild type meningiomas. Here, we show that the expression profile of human YAP1-MAML2-positive pediatric meningiomas resembles that of the common NF2-mutant meningiomas based on global and YAP-related gene expression signatures. We then use the RCAS/tv-a system for postnatal gene transfer and show that the intracranial expression of YAP1-MAML2 in neonatal mice results in the formation of meningioma-like tumors that exert a similar gene expression pattern as seen in human YAP1 fusion-positive and NF2-mutant meningiomas and regulate classical YAP1 target genes. We demonstrate that YAP1-MAML2 exerts oncogenic YAP activity that is resistant to inhibitory Hippo pathway signaling and relies on the interaction with TEAD transcription factors. Pharmacological disruption of this interaction is sufficient to inhibit the viability of YAP1-MAML2-expressing mouse tumors ex vivo. Finally, we show that constitutively active YAP1 (S127/397A-YAP1) is also sufficient to cause the formation of similar meningioma-like tumors suggesting that the YAP component of the gene fusion is the critical driver of these tumors. In summary, our results implicate YAP1-MAML2 as a sufficient oncogenic driver in YAP1-MAML2 fusion-positive meningiomas, which mimic NF2-mutant meningiomas, and highlight TEAD-dependent YAP activity as a potential therapeutic target in these tumors.
CNSC-38. EGFR AMPLIFICATION IS A PUTATIVE RESISTANCE MECHANISM FOR NSCLC-LM PATIENTS WITH TKI THERAPY AND IS ASSOCIATED WITH POOR OUTCOME
Authors: Yang Hainan , Wen Lei , Zhou Caicun 
Published: November 2022

Abstract

BACKGROUND
Leptomeningeal metastases (LM) have become increasingly common in NSCLC patients who harbor epidermal growth factor receptor (EGFR) mutation treated with EGFR-TKI and are correlated with inferior prognosis. Evidence in prior research demonstrated that EGFR amplification was more likely presented in advanced clinical stages and was associated with worse survival. However, whether the EGFR amplification is a prognostic marker in NSCLC-LM is still inconclusive.

METHODS
This study enrolled patients diagnosed with NSCLC-LM from June 2019 to September 2021, who had received previous EGFR-TKI at Guangdong Sanjiu Brain Hospital. Cerebrospinal fluid (CSF) samples were collected and subjected to targeted next-generation sequencing (NGS) of 168 cancer-related genes. Clinical characteristics and overall survival (OS) were compared in patients with and without EGFR amplification.

RESULTS
This study enrolled 53 NSCLC-LM patients, all of whom had EGFR mutations. TP53 and EGFR amplification are the two most frequent mutations in the study cohort, presenting 72% (38 of 53) and 40% (21 of 53), respectively. The rate of EGFR amplification was much higher at the time of leptomeningeal progression than at initial diagnosis (p&lt; 0.01). Karnoskfy performance status was poorer (p=0.021), and CSF pressure was higher (p=0.0067) in patients with than without EGFR amplification. A multivariable Cox proportional hazard regression model showed that EGFR amplification was an independent prognostic factor for poorer OS (8.3 vs 15 months; p=0.017). Median OS was shorter in NSCLC-LM patients with mutated than wild-type TP53, but the differences was not statistically significant (10 vs 17.3 months, p=0.184).

CONCLUSIONS
EGFR gene amplification could be a potential resistance mechanism to EGFR-TKI failure in NSCLC-LM and is associated with inferior clinical outcomes.