bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMIC-52. DECODING METABOLIC INTERACTIONS IN GLIOBLASTOMA TUMOR MICROENVIRONMENT THROUGH COMPREHENSIVE SPATIAL TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS
Authors: Chakraborty Avirup , Yang Changlin , Feier Diana , Silver Aryeh , Anica Miruna , Pittu Avinash , West Illeana , Sobanjo Olusegun , Hodge Ethan , Engelbart Mia , Sengupta Srabasti , Thomas Nagheme , Von Roemeling Christina , Rahman Maryam , Sarkisian Matthew , Huang Jianping , Harrison Jeffrey , Mitchell Duane , Deleyrolle Loic 
Published: November 2024

Abstract

INTRODUCTION
Within the GBM microenvironment, distinct micro-niches arise from independent cancer cell lineages with unique metabolic needs, characterized as Fast Cycling Cells (FCCs) and Slow Cycling Cells (SCCs). FCCs preferentially utilize aerobic glycolysis for energy, whereas treatment-resistant SCCs depend on lipid metabolism. Our study decodes the molecular and spatial heterogeneity within the GBM microenvironment, focusing on the dichotomy of immune infiltrates and the metabolic interactions between SCCs and the immune compartment in human GBM patients.

METHODS
We performed spatial transcriptomics and proteomics combined with geospatially resolved single-cell neighborhood analysis of IHC-stained GBM tissues using CellProfiler and the SNAQ algorithm that we developed to investigate the specific immune microenvironment of SCCs and FCCs. Holotomography and fluorescence-based time-lapse imaging coupled with flow cytometry were used to study lipid transfer between immune cells and GBM cells. Finally, the effects of pharmacological and genetic targeting of lipid transfer were investigated both in vitro and in vivo.

RESULTS
Our study establishes a connection between spatial metabolic heterogeneity and immune diversity, highlighting how specific tumor cell lineages correlate with characteristic immune micro-niches. In particular, SCCs exploit the metabolic properties of recruited immunosuppressive myeloid-derived cells, which metabolically support tumor cells by facilitating lipid transport and supporting SCC metabolism. Our results show that inhibiting lipid transfer affect SCCs, remodels the immune microenvironment, delays tumor growth and improves disease outcome. Our study also demonstrates a correlation between predicted sensitivity to lipid-modifying drugs, such as statins, and the SCC phenotype. This correlation could enable stratification and selection of patients most likely to benefit from such treatments.

CONCLUSIONS
This study establishes critical connections between the TME, cellular metabolism, anti-tumor immunity, and treatment vulnerabilities. Our research provides novel insights into how metabolic exchanges contribute to tumor progression and suggests that targeting metabolic interactions could be an effective therapeutic strategy for GBM.
TMIC-57. EFFECT OF HYPOXIA ON SPHINGOSINE-1-PHOSPHATE (S1P) METABOLIZING ENZYMES IN DIFFUSE INTRINSIC PONTINE GLIOMA CELL LINES
Authors: Russell Hanna , Fillmore Helen 
Published: November 2024

Abstract
Diffuse Midline Glioma H3K27 altered (DMG) is a devastating and incurable paediatric brain tumour. Previously a bioinformatic approach was taken to evaluate genes involved in the sphingosine-1-phosphate (S1P) biosynthesis pathway in diffuse intrinsic pontine gliomas (DIPG). S1P is known to interact with epigenetic partners (HDAC1) as well as play a role in proliferation, immune cell trafficking, angiogenesis and apoptosis. As a part of a broad bioinformatic approach evaluating the expression of genes associated with the sphingomyelin (SM) biosynthesis pathway, S1P metabolism, S1P receptors and downstream targets, 14 of 25 genes were found to be dysregulated in DIPG relative to normal brain (p&lt;0.0002). Herein we focus on the imbalance of the S1P metabolic enzymes sphingosine kinase 2 (SPHK2) and sphingosine-1-phosphate lyase (SGPL1). Bioinformatic data revealed higher levels of SGPL1 and lower levels of SPHK2 compared with normal brain. DIPG cell lines (SU-DIPG-IV, VUMC-DIPG-08, VUMC-DIPG-A) were used to validate gene and protein expression and to evaluate changes following exposure to hypoxic conditions. Confocal images reveal an increase in nuclear SPHK2 staining in cells cultured for 24- and 48-hours under hypoxic conditions. HDAC1 immunostaining was localised in the nucleus. SGPL1 immunostaining, while mostly cytoplasmic, nuclear staining was observed. qRT-PCR assays were used to evaluate changes in mRNA expression in SPHK2, SGPL1 and HDAC1 in DIPG cell lines incubated under hypoxic conditions. The Pfaffl method was used to analyse gene expression relative to the housekeeping gene TBP. Under hypoxic conditions, the levels of SPHK2 and HDAC1 were higher in DIPG cells cultured in hypoxic conditions for 48 hours compared to DIPG cells cultured in normoxic conditions, whereas SGPL1 expression was lower in hypoxic treated cells. Current experiments targeting the modulation of these S1P-metabolizing enzymes are underway to determine the role of the S1P signalling pathway and determine the potential advantage of targeting this pathway in DIPG.
TMIC-68. DEEP LEARNING OF THE SPATIAL IMMUNE ENGAGEMENT IN GLIOBLASTOMA UNDER TEMOZOLOMIDE TREATMENT
Authors: Castillo Simon , Jahedi Afrooz , Gupta Pravesh , Huse Jason , Kannan Kasthuri , Yuan Yinyin , Bhat Krishna 
Published: November 2024

Abstract
Effective immune synapses are a prerequisite for desirable immune surveillance and control of tumour growth. Cell-to-cell interactions form the basis of immune synapses, resulting in either immunoprotected or immunosuppressed manifestations in the tumour brain that could explain glioblastoma (GBM) recurrence. Using state-of-the-art multiplex imaging, spatial statistics, and spatially aware deep learning tools in 14 patient-matching tissues from primary and recurrent GBM, we detected spatial immune networks (SINets). SINets across 105 regions of interest comprising 2.3 million cells show stronger spatial engagement between myeloid and lymphoid lineages at recurrence. SINets’ architecture in primary tumours is associated with relapse timing. Patients, where the SINets are more modular, recur sooner than patients with denser SiNets. In addition, this association presents sexual dimorphism in our cohort (N=3 females, and N=4 males). Phenotype-to-phenotype spatial coexistence also contributes to enhancing phenotype prediction. A spatial-aware deep learning model trained with single-cell data from primary tumours reaches an average balanced accuracy of 0.76 in primary tumour cellular communities unseen during training, compared to a spatial-agnostic model that reached an average balanced accuracy of 0.69. In summary, we detected a distinct spatial engagement in glioblastoma undergoing chemo-radiation treatment. The spatial patterns of coexistence represent ecological niches that contribute to defining cell occurrence and may underpin effective immune synapses. Overall, the spatiotemporal elements provide a newer approach for dissecting glioblastoma’s complexity and discovering opportunities for stratifying patients by harnessing spatial information encoded in multicellular niches.
TMIC-71. ELUCIDATING IMMUNE MICROENVIRONMENTAL DISTINCTIONS BETWEEN IDH-MUTANT ASTROCYTOMA AND OLIGODENDROGLIOMA USING SINGLE-CELL TRANSCRIPTIONAL PROFILING
Authors: Whitfield Benjamin , Liu Yang , Gupta Pravesh , Oberai Shivangi , Bhat Krishna , Huse Jason 
Published: November 2024

Abstract
Despite exhibiting longer overall survival that IDH-wt counterparts, IDH-mutant gliomas remain uniformly deadly and impact patients in the prime of adult life. The immune microenvironment of IDH-mutant gliomas remains incompletely characterized, particularly with regard to distinctions between IDH-mutant astrocytoma and IDH-mutant, 1p/19q codeleted oligodendroglioma. To address this knowledge gap, we subjected dissociated tumor suspensions derived from 7 astrocytoma and 7 oligodendroglioma clinical samples to flow cytometry-based sorting for the pan-immune marker, CD45, and the microglial marker, P2RY12. This process yielded both microglial and non-microglial immune cell populations, which were then analyzed by scRNA sequencing. This workflow revealed a single large cluster of microglia, characterized by expression of Galectin-1 and lysosomal Lipase A, which was present at a significantly higher level in oligodendroglioma. While the biological significance of this cluster is unclear, gene set enrichment analysis exploring phenotypic differences between microglia in astrocytoma and oligodendroglioma revealed significant increases in expression of gene sets related to antigen presentation in astrocytoma. Parallel analysis of the non-microglial immune fraction showed an increase in the expression of pro-inflammatory gene sets, such as genes related to cytokine secretion, within the CD8 T-cell compartment of astrocytomas. We also observed upregulation of the expression of inflammatory gene sets within the dendritic cells of astrocytomas. Taken together, these changes suggest that the immune compartment of astrocytoma is more active and inflamed, and targeting the immune system in these tumors may represent a potential therapeutic avenue.
TMOD-05. GLIOMA-ASSOCIATED OLIGODENDROCYTE PROGENITOR CELLS’ DYNAMIC PATTERNS SUGGEST FUNCTIONAL ADAPTATIONS DURING GLIOMA PROGRESSION IN A UNIQUE MOUSE MODEL
Authors: K Petritsch Claudia , Xing Lulu , Bui Brandon 
Published: November 2024

Abstract
Gliomas account for more than one-third of brain tumors in children, with high fatality rate despite aggressive adjuvant treatment. Two-thirds of survivors suffer from health conditions due to the toxicity of conventional therapies. Notably, gliomas with the BRAFV600E mutation, occurring in ~20% of all glioma cases, are difficult to treat and have a high risk for progression, especially when combined with CDKN2A deletion. The mechanisms for glioma progression remain unclear and unraveling them could lead to therapies that inhibit glioma progression, preventing high-grade gliomas. Objectives: To gain mechanistic insights into glioma progression and exploit therapeutically for preventing progression. We developed two novel mouse models for BRAFV600E mutant progressive gliomas – one at high genetic risk for progression and one at intermediate genetic risk for progression. Expression of genetic alterations were induced by injecting compound transgenic mice with adenovirus-Cre. Our new mouse models therefore more faithfully recapitulated the genetic changes accompanying glioma formation and progression from low- to high-grade than earlier mouse models which used the RCAS system to overexpress the oncogene (PMCID: PMC11112369 ). Glioma formation was followed non-invasively by magnetic resonance imaging. Single cell RNA sequencing and spatial transcriptomics were performed and immunofluorescence was used for validation (PMCID: PMC10619673 ). We present new data showing that animal subject survival is significantly shorter in the high risk model than in the low risk model. Our two models with distinct latency can be used for preclinical studies and studies of the changes associated with progression, including in the glioma microenvironment. Analyses revealed temporal, functional, and spatial changes in glioma-associated oligodendrocyte progenitor cells (GA-OPCs) at distinct stages (initiation, expansion, progression) and grades. Our findings that GA-OPCs closely interact with glioma cells and their morphological transformation as gliomas progress, suggest changing functions, including potential roles in phagocytosis and immunomodulation. Understanding the unclear role of glioma microenvironment OPCs in promoting glioma progression could reveal an Achilles heel for targeted therapies.
TMOD-09. NEWLY DESIGNED TUMOR TREATING FIELDS (TTFIELDS) ARRAYS FOR THE MOUSE HEAD DEMONSTRATE EFFICACY FOR TREATMENT OF GLIOBLASTOMA
Authors: Zbidat Sewar , Blatt Roni , Sellevoll Mariell , Gabay Martin , Schlachet Inbar , Cahal Shay , Davidi Shiri , Tzchori Itai , Haber Adi , Giladi Moshe , Palti Yoram 
Published: November 2024

Abstract
Tumor Treating Fields (TTFields) therapy is a cancer treatment modality based on continuous, non-invasive delivery of electric fields. TTFields therapy is approved for treatment of glioblastoma (GBM), delivered to the patient’s brain by two array pairs placed on the scalp. Further research in animals to expand the knowledge regarding TTFields treatment of GBM is limited, as this is mainly performed in mouse models and arrays for application of TTFields to the mouse head are lacking. The small dimensions and specific geometries of the mouse head make the development of such arrays challenging. The aim of this study was to design arrays that will allow efficient and stable delivery of TTFields to the mouse head. To overcome the small head size, we developed a layout with two arrays situated on the head of the mouse, each divided into two smaller disks, and positioned opposite two arrays on the torso. We identified a thin and transparent adhesive tape (facilitating correct array positioning) with good tackiness and easy removal (without leaving residual adhesive on the skin). The arrays met the minimum treatment requirements: current ≥ 50 mA, usage ≥ 75%, field intensity ≥ 1 V/cm RMS. We then conducted an efficacy study with the new arrays, using GL-261 GBM cells intracranially injected into C57BL/6 mice. Treatment with sham-heat (control) or TTFields was initiated 11 days following tumor inoculation and maintained continuously for 12 days. Efficacy was measured via magnetic resonance imaging (MRI) of tumor volume, showing a decrease of 31% at treatment end in TTFields-treated mice versus the control. Overall, the new arrays are flexible, strongly adherent, deliver TTFields at a sufficient intensity, and showed efficacy for treating GBM in mice.
TMOD-14. ESTABLISHING A CLINICALLY RELEVANT MOUSE MODEL TO STUDY NECROSIS AS A PRIMARY VARIABLE IN GLIOBLASTOMA
Authors: Li Jiabo , Shih Ling-kai , Markwell Steven , Olson Cheryl , Sullivan David , Lam Nicholas , Brat Daniel 
Published: November 2024

Abstract
All glioblastoma (GBM) molecular subsets share the common trait of accelerated progression following necrosis, which cannot be adequately explained by cellular proliferation arising from accumulated genetic alterations. We suggest that necrosis is much more than a passive phenomenon related to rapid growth but rather is a driving force causing tumor microenvironment (TME) restructuring and biologic progression. yet mechanisms remain poorly understood due to a lack of animal models to study necrosis as a primary variable. In GBM, the most malignant primary brain tumor, vascular pathology and central necrosis precede rapid, radial expansion. To reveal spatio-temporal changes directly following vascular damage in the brain, we developed methodology to induce clinically relevant thrombosis vaso-occlusion within GBMs in immunocompetent RCAS/tv-a mouse model to study TME restructuring by intravital microscopy and demonstrate its impact on glioma progression in real-time. We found that following Rose Bengal photothrombosis, GBMs rapidly expanded radially, with glioma migration away from central necrosis and tumor-associated macrophages (TAMs) and glioma stem cells (GSCs) increased dramatically in the peri-necrotic zones. Through the single cell tracking analysis, we found that TAMs displaying increased displacement toward necrosis and greater overall migration distances. Collectively, this model introduces necrosis as the primary variable and captures glioma growth dynamics and TME restructuring in a manner that will facilitate the development of therapies that antagonize these mechanisms to improve outcomes.
TMOD-16. ZUCLOPENTHIXOL REDUCES ACTIVITY-DEPENDENT GLIOBLASTOMA PROLIFERATION
Authors: Negussie Mikias , Krishna Saritha , Daniel Andy , Gonzales Cesar Nava , Hervey-Jumper Shawn 
Published: November 2024

Abstract
A major challenge in modeling glioblastoma in the laboratory is the complex microenvironment in which tumors evolve in humans. The varied architecture and immune privilege of the brain limits the external validity of many experiments performed in modern cell biology laboratories. Organotypic human cortical slices present an opportunity to model glioblastoma and test the effect of drugs against glioma in ex-vivo human tissue. Cortical slice cultures maintain the cellular organization of the human brain, more closely approximating glioblastoma proliferation in patients. In this study, we test the effect zuclopenthixol, a repurposed antipsychotic inhibitor of glioblastoma-induced neuronal hyperexcitability, on the proliferation of glioblastoma cells in an organotypic human cortical slice culture. Primary patient-derived glioblastoma cultures were established, and human cortical tissues were emersed in oxygenated ACSF agarose gel before preparing 250 µm thick slices. Slices were either exogenously seeded with glioblastoma cells or stained for endogenous tumor infiltration. Slices with either endogenous or exogenous seeding were then treated with zuclopenthixol or regular media change and cultured for 10 days. Proliferation was measured with Ki67 staining and quantified via automated pixel summation using the Pillow library in Python. 0.1 µM zuclopenthixol treated slices had significantly lower proliferation index in both the endogenous tumor condition (0.04 vs 0.30, P &lt; 0.05) and the exogenous seeding condition (0.0013 vs 0.028, P = 0.033). Reduced tissue integrity was observed beginning day 8 of culture, as tissue surrounding tumor seeding sites eroded. Here, we model glioblastoma proliferation in live human tissue and quantify the anti-proliferative effect of zuclopenthixol. We show that zuclopenthixol treatment significantly reduced the proliferation index. Our experimental model allowed the optimization of organotypic human cortical slice cultures for immunofluorescence studies and live-cell imaging.
TMOD-17. FOXR2-ACTIVATED CNS NEUROBLASTOMA ORIGINATES FROM THE MEDIAL GANGLIONIC EMINENCE LINEAGE
Authors: Royston Hitomi , Hampton Autumn , Bhagat Dhruv , Pinto Evonne , Emerson Miriam , Funato Kosuke 
Published: November 2024

Abstract
FOXR2-activated CNS neuroblastoma is a rare subtype of pediatric brain tumor characterized by the elevated expression of the transcription factor FOXR2 due to genomic rearrangement. However, the precise pathogenic mechanisms, including the cell type of origin and the function of FOXR2, are not fully understood. An expression profile analysis of patient tumors showed increased expression of the marker genes associated with the Medial Ganglionic Eminence (MGE) in the ventral forebrain such as NKX2.1 and SOX6. Based on this result, we hypothesized that FOXR2-activated CNS neuroblastoma originates from the MGE lineage. To test this hypothesis, we overexpressed FOXR2 in human embryonic stem cell-derived MGE progenitors and, as a control cell type, cortical progenitors. Our data showed that FOXR2 overexpression resulted in a significantly increased proliferation in the MGE progenitors but not in the cortical progenitors, indicating a cell-type-specific effect of FOXR2. When injected into the brain of immunodeficient mice, FOXR2-expressing MGE progenitors formed tumors that molecularly resemble patient tumors, while FOXR2-expressing cortical progenitors did not. To further dissect the underlying molecular mechanisms, we conducted an RNA-seq experiment and found that FOXR2 overexpression activated the MEK/ERK signaling pathway through a suppression of the endogenous RAS inhibitor DIRAS3. Moreover, the FDA-approved MEK inhibitor trametinib significantly suppressed the proliferation and induced cell death in FOXR2-expressing MGE progenitors in vitro with the IC50 value of 30 nM. Collectively, our study has revealed the cell type of origin of FOXR2-activated CNS neuroblastoma and identified the MEK/ERK pathway as a critical downstream of FOXR2 that can be targeted therapeutically.
TMOD-18. FUNCTIONAL DISSECTION OF RECURRENT COPY-NUMBER-ALTERATIONS INFORMS MECHANISMS OF LOW-GRADE-GLIOMA PROGRESSION
Authors: Haider Shahan , Drucker Kristen , Kollmeyer Thomas , Tsai Ricky , Al-Zahrani Khalid , Chiu Cynthia H , Elia Andrew , Jenkins Robert , Schramek Daniel 
Published: November 2024

Abstract
Low-grade gliomas (LGG) are slowly growing brain cancers that ultimately undergo a malignant progression to lethal secondary glioblastomas with a dismal prognosis. Despite intensive research, very little progress has been made in our understanding of this transformation. Hence, outside of known alternations in well-characterized driver genes CDKN2A, PTEN and PDGFRA, genetic drivers that underlie LGG transformation are largely unknown. Contrary to other types of cancer, LGGs exhibit very few driver mutations (30-40 mutations) as they progress. Interestingly, LGGs also exhibit a highly prevalent and heterogenous pattern of copy-number-alterations (CNAs) suggesting that they might be driven by changes in gene dosages that result from widespread chromosomal instability observed within these tumors. Through analysis of the human Mayo Clinic and TCGA LGG datasets (~1500 patients), we have identified eleven highly recurrent CNAs affecting LGG patients, many of which correlate with patient survival. We hypothesized that these CNAs contain driver genes that confer a growth advantage resulting in the highly recurrent CNA pattern and prognostic associations. To investigate the tumor suppressive potential of the ~1800 genes located in recurrently deleted regions and the oncogenic potential of the ~1200 genes located in recurrently amplified regions, our lab developed a novel in vivo ‘CRISPR-Knock Out and Activation Linked Assay’ (CRISPR-KOALA). Stereotaxic delivery of arm-level CNA lentiviral gRNA libraries targeting the mouse orthologs of genes in CNAs into the brain of our animal model (rs557mut;IDHmut;P53KO;AtrxKO;Cas9GFP: Yanchus et. al Science 2022) resulted in rapid formation of tumors compared to animals injected with control libraries. Deconvoluting the screen revealed enrichment of immune modulators such as Them6 as well as a modulator of NMDA receptors (Grina) implicating immune system and glutamate dysregulation in LGG malignant transformation. Taken together, our study provides insights into mechanisms underlying LGG progression which may serve to inform intervention strategies for this lethal disease.