bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPCO-57. INTEGRATED ANALYSIS OF BULK AND SINGLE-CELL RNA SEQUENCING DATA OF PRIMARY AND METASTATIC PEDIATRIC MEDULLOBLASTOMA
Authors: Orozco Ana Isabel Castillo , Danieau Geoffroy , Khazaei Niusha , Aghababazadeh Masoumeh , Khatami Marjan , Garzia Livia 
Published: November 2024

Abstract
Medulloblastoma (MB) is a highly aggressive and the most common brain tumor in childhood. MB presents a high intertumoral heterogeneity, with at least four molecular subgroups identified (SHH, WNT, Group 3, and Group 4). Metastatic MB, or Leptomeningeal Disease (LMD), is predominantly found in the MB Group 3 type. Although LMD represents a main clinical challenge, its molecular mechanisms remain poorly characterized. Recent research has shown that primary and MB metastasis diverge dramatically. Our work has focused on establishing therapy naïve Group 3 Patient-Derived Xenografts models of primary and metastatic Medulloblastoma to conduct transcriptomic profiling at the bulk and single-nuclei RNAseq levels to identify genetic drivers/pathways that sustain leptomeningeal disease compartment. Our results show various signaling pathways enriched across LMD models, such as MYC targets, unfolded protein response, and fatty acid metabolism. Using single-sample GSEA analysis (ssGSEA) and deconvolution approaches, we have also identified that our PDXes models retain neoplastic subpopulations previously identified in MB single-cell sequencing studies. Similarly, we have identified slight differences in cell subpopulation proportions between primary and leptomeningeal compartments. Our single-nuclei studies have confirmed these results and differentially expressed genes previously found in bulk RNAseq analyses. These results suggest the presence of cell populations enriched in the metastatic compartment with an aberrant transcription phenotype and adaptations in fatty acid metabolism to survive the leptomeningeal space. In conclusion, our work supports the notion that primary and LMD retain subpopulation clusters present in MB Group 3 tumors with different proportions in the metastatic compartment shown by bulkRNAseq deconvolution and single nuclei RNA analysis. We also show that primary and LMD are transcriptionally different, with various enriched pathways in the metastatic compartment and shared among LMD Group 3 PDX models. Through these approaches, we aim to elucidate the genetic dependencies of metastatic Medulloblastoma that will help for targeted therapies.
ANGI-07. A CASE OF HYPERBARIC OXYGEN USED AS A TREATMENT MODALITY FOR ANAPLASTIC ASTROCYTOMA
Authors: Boldig Catherine , Jaffer Muhammad , Pina Yolanda , Mokhtari Sepideh 
Published: November 2024

Abstract
Although its precise mechanism is unclear, hyperbaric oxygen is thought to impede the growth of tumor cells by inhibiting tumor hypoxia, a known driver for angiogenesis. We present a case of a 32-year-old pilot who developed sudden onset aphasia and disorientation which led to hospitalization and imaging. He was diagnosed with anaplastic astrocytoma and underwent resection, radiation, and chemotherapy with temozolomide. Approximately one year later, MRI showed enlarging non-enhancing T2/FLAIR hyperintense mass in the right temporal lobe. He received 4 cycles of lomustine. Four months later, MRI showed slight increase in the size of ring enhancement around the treatment area. These findings were thought to be related to treatment-related changes. After 4 doses of bevacizumab every 2 weeks, there was improvement in surrounding vasogenic edema. However, after 7 doses, his MRI brain demonstrated increase in treatment-related changes with more vasogenic edema. He also had worsening left-sided weakness, unable to lift his left arm against gravity, dysarthria, and cognitive slowing. MRI perfusion supported treatment-related changes rather than tumor growth. He then started hyperbaric oxygen treatments and after 20 sessions of treatment, his vasogenic edema and his left-sided weakness improved. After 60 sessions of hyperbaric oxygen, he noticed further improvement in his strength and short-term memory. Four months after completion of his hyperbaric oxygen, he was found to have increasing size of ring-enhancing lesion and was restarted on hyperbaric oxygen treatments in addition to bevacizumab and low-dose temozolomide. He completed a total of 100 rounds of hyperbaric treatments. MRI showed improvement and stability. His left-sided weakness continued to improve. Hyperbaric oxygen alone or combined with other treatment modalities may be a promising therapy to improve quality of life. Further research will assist with mechanisms through which hyperbaric oxygen works and patient outcomes.
ANGI-08. SPATIAL TRANSCRIPTOMIC COMPARISONS OF GLIOBLASTOMA TISSUE REVEAL UPREGULATION OF NEURODEVELOPMENTAL PATHWAYS AND SYNAPTIC GENES IN INFILTRATING TUMOR CELLS
Authors: Harwood Dylan , Pedersen Vilde , Bager Nicolai , Schmidt Ane , Stannius Tobias , Areškevičiūtė Aušrinė , Josefsen Knud , Nørøxe Dorte , Scheie David , Rostalski Hannah , Lü Maya , Locallo Alessio , Lassen Ulrik , Bagger Frederik , Weischenfeldt Joachim , Heiland Dieter , Vitting-Seerup Kristoffer , Michaelsen Signe , Kristensen Bjarne 
Published: November 2024

Abstract
Glioblastoma remains one of the deadliest brain malignancies. First-line therapy consists of maximal surgical tumor resection, chemotherapy, and radiotherapy. Malignant cells escape surgical resection by migrating into the surrounding healthy brain tissue, where they give rise to the recurrent tumor. Gene expression profiling allows glioblastoma tumor cores to be classified into mesenchymal, proneural, and classical subtypes, each with distinct genetic alterations and cellular compositions. In contrast, the adjacent brain parenchyma where infiltrating malignant cells escape surgical resection is less characterized in patients. Using single-cell and multicellular resolution spatial transcriptomics on tissues from both the tumor core and infiltrated brain tissue (n = 11), we compared the transcriptional profiles of malignant cells in these regions. Malignant cells near regions with microvascular proliferation showed increased expression of genes related to vascular homeostasis. Within tumor cores, proneural and mesenchymal subtypes exhibited distinct spatial gene expression patterns, although these differences were reduced in the infiltrated brain tissue, apart from gene expression due to chromosomal alterations specific to the proneural subtype. We identified two transcriptional patterns of brain infiltration, with the dominant pattern showing a transition from mesenchymal to proneural states. This transition was accompanied by increased expression of genes linked to neurodevelopmental pathways and glial cell differentiation. Additionally, one gene module upregulated in infiltrating malignant cells was predictive of poor patient survival and enriched for genes associated with differentiated neuronal cells. Together, our findings provide an updated view of the spatial landscape of glioblastomas and infiltrated brain tissue, furthering our understanding of the malignant cells that invade healthy brain. This insight offers new avenues for targeted therapy after surgical resection of the primary tumor.
ANGI-10. NETWORK ANALYSIS ESTABLISHES CSF2RA’S REGIONAL INFLUENCE ON HYPOXIA RESPONSE IN THE INVASIVE RIM OF HIGH GRADE GLIOMA
Authors: Flick Matthew , Stevens Victoria , Sereduk Christopher , Plaisier Christopher , Barajas Ramon , Hu Leland , Kannan Kasthuri , Tran Nhan 
Published: November 2024

Abstract

BACKGROUND
High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer. Standard of care surgery employs Magnetic Resonance Imaging to identify the contrast enhancing (CE) core for resection, leaving a non-enhancing (NE) invasive rim of tumor which contributes to recurrence. The hypoxic tumor microenvironment is thought to drive invasion into healthy brain, and understanding cellular responses to hypoxia may provide insight into combatting recurrence. Here, we apply a graph network to integrate regionally heterogeneous data from a unique dataset of spatially-localized CE and NE biopsies from a large cohort of patients with HGG to identify gene networks regulating hypoxia response and invasion.

METHODS
RNA-sequencing of 1159 differentially expressed genes across 159 IDH-wt biopsies (74 patients) from NE/CE regions were represented as nodes in a Neo4j graph network. Candidate genes for network random walks occurred exclusively within NE communities detected by modularity optimization and were localized by cell-type using single-cell RNA-sequencing (scRNAseq). CSF2RA was selected as source (walk length = 5; 10,000 walks/source node). Frequently occurring genes (one-tailed test) in walks were ranked by correlation with CSF2RA expression in NE samples and analyzed by gene set enrichment analysis for biological processes (clusterProfiler). CSF2RA and hypoxia gene expression were visualized with DoHeatmap in composite NE/CE scRNAseq profiles.

RESULTS
CSF2RA, an immune receptor, was upregulated (logFC = 0.789) in NE samples, scRNAseq myeloid populations, and Glycolytic/Plurimetabolic glioma subtype. CSF2RA random walk genes (n=46) enriched metabolic/proliferative signatures. CSF2RA expression correlated negatively with hypoxia genes globally and regionally (NE/CE), while NE/CE scRNAseq revealed distinct cellular expression patterns of CSF2RA and hypoxia response genes.

CONCLUSION
CSF2RA expression may prime NE glioma cells for invasion by altering hypoxia response. The genetic network bridging CSF2RA and hypoxia response may be a targetable mechanism of tumor recurrence.
ANGI-12. THE IMPACT OF STANDARD-OF-CARE TREATMENT ON THE RELATIONSHIP BETWEEN CELL DENSITY AND SOX2 POSITIVITY IN GLIOBLASTOMA PATIENTS AT AUTOPSY
Authors: Bobholz Samuel , Lowman Allison , Aaronsen Daniel , Winiarz Aleksandra , Dueweg Savannah , Flatley Michael , Nath Biprojit , Kyereme Fitzgerald , Connelly Jennifer , Mrachek Kelly , Krucoff Max , Banerjee Anjishnu , LaViolette Peter 
Published: November 2024

Abstract

INTRODUCTION
Sex-determining region Y-box 2 (SOX2) staining highlights pluripotent cells and provides an early sign of tumor cell invasion in glioblastoma patients. This infiltration can often occur at the single cell level and can occur in the absence of lower resolution histological tumor features such as hypercellularity. This study assessed the impact of standard treatment regimens on the relationship between cellularity and SOX2+% at death using autopsy samples as ground truth.

METHODS
A total of 36 IDH-wildtype glioblastoma patients were included for this study (23M/13F, mean age=61.9). Tissue samples from both suspected tumor invasion and suspected normal tissue were collected for each patient, which were then stained for SOX2, digitized at 40X resolution, and segmented into positive staining nuclei percentage using a color deconvolution algorithm. These samples were then aligned to the MRI using in-house MATLAB-based software, where manually defined control points placed on areas of architectural similarity are used to compute a transform that corrects for nonlinear shrinkage of the tissue sample due to post-mortem processing. The association between SOX2+% and cell density was then computed per subject, and compared between patients who received SOC (radiation and temozolomide) treatment following surgery (as well as additional treatment per case, n=31) and patients who opted for no additional treatment following surgery (n=5).

RESULTS
Patients who received no additional treatment showed substantially higher correlation between cell density and SOX2+% than patients who had received SOC (t=2.90, p=0.006). No association with overall survival was observed (r=0.17, p=0.329).

CONCLUSIONS
These results indicate a decoupling between hypercellularity and SOX2+% associated with standard GBM treatments, indicating that radiation and other treatments induce a more heterogenous tumor microenvironment that could lead to single-cell tumor invasion beyond gross histological markers of tumor presence.
ANGI-14. DRUGGABLE GENOME CRISPR SCREEN IN 3D HYDROGEL DEVICES REVEALS TARGETABLE KINASES AND PHOSPHATASES IMPLICATED IN CYTOSKELETAL REORGANIZATION IN INVADING GBM CELLS
Authors: Hu Mufeng , Weldy Anna , Akins Erin , Jain Saket , Chang Alexander , Kumar Sanjay , Aghi Manish 
Published: November 2024

Abstract
The invasive nature of glioblastoma cells into adjacent brain tissues is a key factor in its unfavorable prognosis. To decipher the mechanisms driving glioblastoma invasion, we developed microdissectable biomimetic 3D hydrogel invasion devices containing hyaluronic acid hydrogels decorated with integrin-binding peptides (RGD) and crosslinked with protease-cleavable crosslinkers. The ability to disassemble these devices and interrogate cells in the core vs. invasive fraction allows for high throughput screens. We thus performed a screen in GBM43 cells expressing CRISPR/Cas9 and a 13,250 gRNA library targeting the 2550 genes in the druggable human genome. Of seven initial hits from this screen, only two could be validated by single gene CRISPR and use of a drug to target the hit - ACP1 (also known as LMW-PTP) and Aurora Kinase B (AURKB). Integration of ChIP-seq and RNA-seq revealed no plausible transcriptional targets of ACP1 and AURKB that could drive invasion. Proximity labeling with the TurboID system identified CTTN (cortactin), an actin binding protein whose phosphorylation is integral to the formation of lamellipodia and invadopodia, as phosphorylated by AURKB and Ephrin A2 (EPHA2), whose dephosphorylation controls cell morphology, adhesion, migration and invasion by modifying the organization of the actin cytoskeleton and influencing the activities of integrins and intercellular adhesion molecules, as dephosphorylated by ACP1. These findings underscore the delicate balance between kinase and phosphatase activities in regulating the actin cytoskeleton broadly and at the cell’s front or “leading edge,” offering new therapeutic targets to disrupt the invasion that is a hallmark of glioblastoma.
BIOM-03. DABRAFENIB AND STEROIDS FOR THE TREATMENT OF ERDHEIM-CHESTER DISEASE WITH EXTENSIVE CENTRAL NERVOUS SYSTEM INVOLVEMENT
Authors: Yuen Carlen , Bao Silin , Aung Mya Sandi , Shishodia Rhea , Kong Xiao-Tang 
Published: November 2024

Abstract
Erdheim-Chester disease (ECD) is an exceedingly rare non–Langerhans cell CD68+ CD1a- S100- histiocytic multi-organ disease. Diagnosis of ECD is often delayed due to non-specific radiographic findings and heterogeneous lesional tissue. Increasingly, the role of genomic alterations is being recognized for both diagnosis and treatment of ECD. More than half of ECD patients harbor the BRAFV600E mutation. Evaluation for this mutation be can falsely negative on immunohistochemical staining and confirmation with molecular analyses is recommended. We present a case of the 44 year-old male with BRAFV600E-positive ECD treated successfully with steroids followed by single-agent dabrafenib.
BIOM-04. SINGLE-CELL RNA SEQUENCING PROTOCOL OF THE HUMAN METASTATIC PROSTATE SPINE TUMOR MICROENVIRONMENT
Authors: Nguyen Annee , Haines Corinne , Price Meghan , Baeta Cesar , Hockenberry Harrison , Johnson Eli , Goodwin C Rory 
Published: November 2024

Abstract

INTRODUCTION
90% of spine tumor patients can develop metastases with debilitating complications, such as sensorimotor dysfunction, paralysis, and spinal instability. As spine tumor patients have limited eligibility to participate in clinical trials and have heterogenous tumor pathology, there is a distinct lack of therapeutic targets and prognostication markers of disease. Thus, there is a distinct need for molecular profiling of spine tumors.

OBJECTIVE
We describe an OR-to-bench-top processing of spine tumors for single-cell omic studies, with samples from a metastatic prostate cancer patient to demonstrate the ability to compare molecular markers and microenvironments of difficult-to-process spine tumors and adjacent normal tissue.

METHODS
Under IRB protocol #Pro00101198, patients undergoing spine surgery with the Department of Neurosurgery at Duke University were consented for tissue collection. Vertebral osseous metastases and adjacent normal tissue were confirmed histologically (H&E, immunohistochemistry) and radiologically (MRI, PET, CT, and x-ray). Tissues were manually and enzymatically homogenized in serum-free media with collagenase A and DNAse I to obtain a single cell suspension. Cells were then filter sterilized, erythrolyzed, counted to determine live-death ratio, resuspended to 10-20 million cells per mL, then cryopreserved for downstream standard library preparation for single-cell sequencing using the 10X genomics platform. Downstream analysis was performed using Seurat pipeline, InferCNV analysis, and SingleR.

RESULTS
P404S and PSA expression confirmed tumor was prostate in origin. Radiological imaging and H&E staining confirmed the presence of T7 osseous metastasis. Uniform manifold approximation and project (UMAP) plots identified 12 unique clusters of immune cell subpopulations between normal and tumorous vertebrae, with their own subsets of differentially expressed genes.

CONCLUSION
We have developed a protocol to generate granular single cell molecular profiling for spine tumors and metastases. Applications of this protocol can aid in identifying therapeutic targets, molecular predictors of disease, and potentiate increased eligibility of patients for clinical trials.
BIOM-05. FUSION TRANSCRIPTOME LANDSCAPE IN GLIOBLASTOMA
Authors: Aulakh Sonikpreet , Xiu Joanne , Kothari Shawn , Sengupta Soma , Glantz Michael , Ahluwalia Manmeet , Nicolaides Theodore , Gilbert Mark 
Published: November 2024

Abstract

BACKGROUND
For most patients with glioblastoma (GBM), no truly effective salvage therapies exist. However, there are compelling examples in oncology where gene fusions lead to functioning oncoproteins that are highly effective targets (ie BCR-ABL1 in CML). Using a large genomic database, we sought to determine the prevalence of fusion transcripts in GBMs.

METHODS
A total of 4392 GBMs were tested at Caris Life Sciences (Phoenix, AZ). Mutations were detected by NextGen sequencing of DNA (592-gene panel or whole exome sequencing); gene fusions were detected by Whole Transcriptome Sequencing. All tumors were wild type for IDH1/2. Significance was tested by Fisher-Exact and ChiSquare and adjusted by Benjamini-Hochberg (q &lt;0.05).

RESULTS
Overall, pathogenic fusions were found in 428 (9.7%). The most prevalent were FGFR3 [N=159 (37%), highest FGFR3:TACC3, N=134], MET [N=92 (21%), highest PTPRZ1:Met, N=31; ST7:MET N=25; CAPZA2: MET, N=23), EGFR [N=87(20%), highest EGFR:SETP14, N=21 and SEC61G: EGFR, N=19], NTRK2 (N=27), PDGFRA (N=23), ROS1 (N=14) and BRAF (N=10). Other actionable fusions including ALK (N=3), NTRK3 (N=3), RAF1(N=3), RET (N=3), NTRK1(N=2) were seen. Tumors with fusions were more likely to have pathogenic gene amplifications including: MET (7.5% vs. 0.7%), FGFR3 (5% vs. 0.2%), CDK4 (17% vs. 11%) and MDM2 (12% and 7.5%) but less frequent EGFR mutation (6.1% vs. 18%), amplification (6.1% vs. 18%) and EGFRvIII mutation (11.9% vs. 22.5%), RB1 (2.9% vs. 11.5%) and TP53mutation (22% vs. 30%) (all q&lt;0.05). EGFR fusions are enriched with EGFR amplification (92%) and EGFRvIII mutation (51%); cMET fusion with MET amplification (40%).

CONCLUSIONS
Comprehensive molecular profiling reveals that approximately 10% of IDH WT GBMs carry oncogenic fusions that may be therapeutic targets. Broad spectrum of observed fusions underscores the need for novel clinical trial designs to allow efficient enrollment for prospective testing of potential targeted agents.
BIOM-06. NOGGIN CONTRIBUTES TO BRAIN METASTATIC COLONIZATION OF LUNG CANCER CELLS
Authors: Yang Seung Ho 
Published: November 2024

Abstract
Brain metastasis is a common complication among patients with lung cancer, yet the underlying mechanisms remain unclear. In this study, we aimed to investigate the pathogenesis of brain metastasis in lung cancer. We established highly colonizing metastatic lung cancer cells, A549-M2, through multiple implantations of A549 human lung cancer cells in the carotid artery of athymic nude mice. Compared to parental cells (M0), M2 cells demonstrated slower growth in culture plates and soft agar, as well as lower motility and higher adhesion, key characteristics of mesenchymal-epithelial transition (MET). Further analysis revealed that M2 cells exhibited decreased expression of epithelial-mesenchymal transition markers, including ZEB1 and Vimentin. M2 cells also demonstrated reduced invasiveness in co-culture systems. RNA sequencing and gene set enrichment analysis confirmed that M2 cells underwent MET. Intriguingly, depletion of Noggin, a BMP antagonist, was observed in M2 cells, and replenishment of Noggin restored suppressed migration and invasion of M2 cells. In addition, Noggin knockdown in control M0 cells promoted cell attachment and suppressed cell migration, suggesting that Noggin reduction during brain colonization causes inhibition of migration and invasion of metastatic lung cancer cells. Our results suggest that lung cancer cells undergo MET and lose their motility and invasiveness during brain metastatic colonization, which is dependent on Noggin.
BIOM-13. COMBINED MGMT PROMOTER METHYLATION AND LOW GENE BODY METHYLATION IS A SUPERIOR PREDICTOR OF ALKYLATING AGENT RESPONSE THAN PROMOTER METHYLATION ALONE IN GLIOBLASTOMA
Authors: Nuechterlein Nicholas , Cimino P J 
Published: November 2024

Abstract

BACKGROUND
The DNA methylation status of the promoter region of O-6-methylguanine-DNA methyltransferase (MGMT) is a critical predictor of temozolomide response in newly diagnosed glioblastoma. However, MGMT-STP27, the dominant method for MGMT promoter methylation determination from methylation array data, considers only methylation probes located in the promoter region. In this study, we propose a robust MGMT classifier that considers MGMT methylation probes in both the promoter and gene body regions.

METHODS
We leveraged glioblastoma DNA methylation and/or gene expression data published by the TCGA (N=312), GLASS (N=276), and Capper et al. (N=535). We correlated MGMT gene expression and MGMT probe methylation in datasets with paired expression and methylation data. We formulated an MGMT methylation score that measured the difference between MGMT promoter probe methylation and gene body probe methylation. We then compared the prognostic utility of this score with the MGMT-STP27 model on patients treated with upfront alkylating agents in multiple datasets in both univariate and multivariate analyses.

RESULTS
We found that MGMT expression was prognostic in TCGA (OS HR=1.5, p=0.027, PFS HR=1.9, p=0.001) and GLASS (OS HR=1.4, p=0.088, PFS HR=1.6, p=0.03) glioblastomas among patients treated with alkylating agents. MGMT expression was negatively correlated with MGMT promoter methylation and positively correlated with MGMT gene body methylation. We defined an MGMT score as the difference between the average MGMT DNA methylation in negatively correlated promoter probes and the average methylation in positively correlated gene body probes. This score was prognostic in the TCGA (OS HR=1.6, p=0.003, PFS HR=1.6, p=0.001) and GLASS (OS HR=3.1, p=0.01, PFS HR=3.9, p=0.004) and was also superior to the MGMT-STP27 classifiers in multivariate analyses (TCGA p=0.03).

CONCLUSION
Overall, we defined an MGMT methylation score that considers promoter and gene body methylation and may be a superior predictor of glioblastoma response to alkylating agents compared to MGMT-STP27.