bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMIC-60. BRATS-PATH: ASSESSING HETEROGENEOUS HISTOPATHOLOGIC REGIONS IN GLIOBLASTOMA
Authors: Thakur Siddhesh , Faghani Shahriar , Moassefi Mana , Baid Ujjwal , Chung Verena , Pati Sarthak , Innani Shubham , Baheti Bhakti , Albrecht Jacob , Karargyris Alexandros , Kassem Hasan , Nasrallah Maclean , Ahrendsen Jared , Barresi Valeria , Gubbiotti Maria , Lopez Giselle , Lucas Calixto-Hope , Miller Michael , Cooper Lee , Huse Jason , Bell William , Bakas Spyridon 
Published: November 2024

Abstract
Glioblastoma, the most common malignant primary adult brain tumor, poses significant diagnostic and treatment challenges due to its heterogeneous molecular and micro-environmental profiles. To this end, we organize the BraTS-Path challenge to provide a public benchmarking environment and a comprehensive dataset to develop and validate AI models for identifying distinct histopathologic glioblastoma sub-regions in H&E-stained digitized tissue sections. We identified 188 multi-institutional diagnostic slides of glioblastoma (IDH-wt, Gr.4) cases, from the TCGA-GBM and TCGA-LGG data collections, following their reclassification according to the 2021 WHO classification criteria. Sub-regions were selected according to distinctive morphology of histopathologic features and included aggressive tumor biology and areas consistent with potential treatment effect. Selected sub-region annotations included cellular tumor, geographic necrosis, cortical infiltration, pseudopalisading necrosis, microvascular proliferation, white matter penetration, regions dense with macrophages, leptomeningeal infiltration, and presence of lymphocytes. We obtained 107,340 patches of size 512x512 from the 9 sub-regions. A global network of board-certified expert neuropathologists defined and followed a systematic annotation protocol based on clinical definitions and only delineated sub-regions with high confidence, thus ensuring high-quality standardized data. Each tissue section was assigned to an annotator-approver pair, with the annotator delineating sub-regions and the approver ensuring the consistency of the annotations. By crowdsourcing annotations, the BraTS-Path challenge harnesses the collective expertise of clinical neuropathologists and fosters a collaborative environment to advance the neuro-oncology field. The anticipated developed algorithms are expected to integrate state-of-the-art computational methods, achieving high accuracy in identifying diverse histopathologic features and advancing clinical decision-making processes. The BraTS-Path challenge aims to bridge the gap between research and clinical practice by promoting the development of AI-driven tools for precise tumor characterization. This collaborative effort can significantly enhance our understanding of glioblastoma, improve diagnostic accuracy, and inform treatment strategies, thereby contributing to better patient outcomes.
TMIC-61. DEVELOPMENT OF A NOVEL NOTCH-TARGETING ONCOLYTIC HSV FOR GBM TUMORS
Authors: Vazquez-Arreguin Karina , Otani Yoshihiro , Rivera-Caraballo Kimberly , Kaur Balveen 
Published: November 2024

Abstract
Glioblastoma (GBM) is the most aggressive brain malignancy, which despite continuing worldwide efforts to develop new therapies, remains a deadly disease with limited treatment options. The NOTCH signaling pathway is often hyperactive in GBM tumors, and its activity contributes to tumor progression and resistance to treatment. The role of NOTCH signaling in tumor growth and resistance is well studied, but the significance of this pathway for immunotherapy of GBM is not very well understood. We have recently shown that NOTCH activation following virotherapy contributes to tumor regrowth and induces recruitment of monocytic MDSC cells into the tumor, which limit optimal immune activation to kill tumor cells. For this study, we have discovered a NOTCH interfering intracellular ligand (NIIL) that blocks NOTCH activation from inside glioma cells. RNA sequencing shows the expression of NIIL downregulates NOTCH signaling in vitro. To evaluate the effect of NIIL on virotherapy, we generated an oncolytic herpes simplex virus (oHSV) that also encodes for NIIL. This virus showed a slower spread in vitro but improved therapeutic efficacy in vivo in multiple models of intracranial tumors. In immune competent mice there was a significant improvement in the survival of mice treated with the NIIL-encoding virus, with a fraction of mice showing a complete response after a single treatment. Single-cell RNA sequencing analysis of immune infiltrates is ongoing to understand how NIIL impacts tumor microenvironment and anti-tumor immune therapy.
TMIC-81. AN IMMUNOSUPPRESSIVE MACROPHAGE NICHE MAY DRIVE T CELL DYSFUNCTION AND IMMUNOTHERAPY RESISTANCE IN MELANOMA BRAIN METASTASES
Authors: Sun Lu , Ding Lizhong , Shiuan Eileen , Lee Alexander , Kim Won , Trembath Dimitri , Moschos Stergios , Hugo Willy , Prins Robert 
Published: November 2024

Abstract
Nearly half of metastatic melanoma patients develop brain metastases (MBM). Local therapies like surgery and radiotherapy provide limited survival benefit. While targeted therapies and immune checkpoint inhibitors (ICI) improved outcomes in patients with asymptomatic MBM, the prognosis is still grim for the majority of patients. To decipher resistance mechanism to immunotherapy in MBM, we integrated datasets from both single-cell RNAseq (scRNAseq) and spatial transcriptomics (Visium). Our scRNAseq analysis of 25 MBM patients (7 treated pre-surgery with ICI) showed that lymphoid cells increased by 8.1-fold post-ICI (p=0.006). Notably, 34% of these were CXCL13+CXCR6+ putative tumor-reactive T cells (TR-T), known for their critical role as tumor-killing effectors. This led us to investigate why, despite their prevalence, TR-T don’t translate to effective immunotherapy in MBM. Our scRNAseq interactome analysis revealed that ICI intensified IFN-II interactions between TR-T and interferon-stimulated macrophage/microglia (Mφ.ISG). However, it also boosted immunosuppressive interactions, like the TIGIT-NECTIN2 interaction, which increased 20 fold, potentially diminishing TR-T’s effectiveness. To overcome the lack of spatial context in scRNAseq, we applied spatial transcriptomics on 27 MBM sections, including 12 post-ICI treatments. Remarkably, TR-T were primarily found (63%) in proximity with Mφ.ISG cells—not with tumor cells. These TR-T-Mφ.ISG niches were 1.7 times more prevalent in ICI-treated samples; these niches are rich in chemokine receptors like CCR1 and immunosuppressive molecules like NECTIN2. This suggests that Mφ.ISG cells are chemotactically attracted to TR-T, forming a barrier that impedes TR-T’s tumor interaction and impairs their functionality. Our current efforts focus on pinpointing key pathways enriched within TR-T-Mφ.ISG niches, particularly in ICI-treated MBM. We are also assessing the clinical impact of these niches in relation to patient survival. Our goal is to elucidate how specific immunosuppressive subsets and molecules within the MBM microenvironment restrict TR-T effectiveness, with the ultimate objective of enhancing ICI efficacy for these patients.
TMOD-01. EGFR AMPLIFICATION ACCOMPANIES ADAPTATION TO MITOGEN-INDUCED DEFECTIVE MITOSIS IN PDGFA
Authors: Meode Mathieu , Omairi Hiba , Sait Sarah , Black Sophie , Cairncross J Gregory 
Published: November 2024

Abstract
Using a newly described in vitro murine model of GBM [Bohm et al., Neuro-Oncol 2020 and Omairi et al., Neuro-Oncol 2023] in which P53 null neural progenitor cells (NPCs) divide abnormally and evolve a GBM-like genome during exposure to Platelet-Derived Growth Factor-AA (PDGFA), we asked how a brain-abundant mitogen could transform NPCs. By analyzing gene and protein expression over time, we found that PDGFA fails to induce the transcription of kinetochore and spindle assembly checkpoint genes, while simultaneously driving NPCs to enter mitosis. These dual effects caused chromosome miss-segregation in continuously dividing NPCs; moreover, they occurred in both WT and null NPCs, although only null cells survived defective mitosis. These surviving cells gradually expanded in PDGFA accumulating both random and clonal chromosomal re-arrangements. Transcriptome analysis of NPCs in PDGFA revealed significant under-expression of Foxm1, the major regulator of kinetochore transcription, together with over-expression and phosphorylation of the immediate early response gene, FOS. Analysis of signalling downstream of PDGFRα identified the Ras-MAPK pathway, especially ERK, as responsible for FOS activation. As surviving null cells gradually expanded, they accumulated random and recurrent chromosomal rearrangements. Expansion and subsequent PDGFA-independent proliferation and tumorigenicity were associated with re-expression of Foxm1 and kinetochore proteins, and accompanied by over-expression of Egfr, an RTK-signature that defines human GBM. By stimulating proliferation without setting the stage for error-free mitosis, exposure to PDGFA transforms p53 null NPCs and generates Egfr amplified GBM-like cancer cells.
TMOD-02. PATIENT-DERIVED GLIOBLASTOMA ORGANOIDS AS REAL-TIME AVATARS FOR ASSESSING RESPONSES TO CLINICAL CAR-T CELL THERAPY
Authors: Wang Xin , Logun Meghan , Sun Yusha , Bagley Stephen J , Li Nannan , Desai Arati , Zhang Daniel Y , Nasrallah MacLean P , Pai Emily Ling-Lin , Oner Bike Su , Plesa Gabriela , Siegel Donald , Binder Zev A , Ming Guo-li , Song Hongjun , O’Rourke Donald M 
Published: November 2024

Abstract
Patient-derived tumor organoids have been increasingly leveraged for disease modeling and preclinical studies, but rarely in real-time to aid with the interpretation of patient treatment responses in the clinical setting. Whether tumor organoids can be applied to mirror clinical activity in patients and even to predict responses for personalized medicine remains uncertain. We recently demonstrated promising early efficacy signals in a first-in-human, phase 1 study of dual-targeting chimeric antigen receptor T cells (EGFR-IL13Rα2 CAR-T cells) in patients with recurrent glioblastoma (clinical trial identifier: NCT05168423). Determination of meaningful clinical efficacy, in particular for CAR-T cell therapy, may take months to manifest. Given this challenge, real-time analysis of patient-derived glioblastoma organoids (GBOs) could help to provide early assessment of clinical efficacy and guide patient management. We analyzed six sets of GBOs generated on the same timeline as the production of patients’ CAR-T cell products. GBOs demonstrated the presence and retention of both targeted tumor-associated antigens EGFR and IL13Rα2 by immunohistochemistry. These GBOs were then treated with the same autologous CAR-T cell products received by patients in our phase 1 study in parallel with patient treatment. CAR-T cell treatment led to target antigen reduction assessed by immunohistochemistry and flow cytometry. Furthermore, we confirmed cytolysis of tumor cells in GBOs by cleaved caspase-3 immunostaining and by co-culture in the Axion Maestro Cellular Impedance platform. Importantly, the degree of cytolysis ex vivo significantly correlated with CAR-T cell engraftment detected in patients’ cerebrospinal fluid (CSF) for all six patients. Furthermore, cytotoxic activity of CAR-T cells as measured by TNFα, IL-2, and IFNγ release kinetics in GBOs mirrored cytokine levels in patient CSF samples over time. Our findings highlight a unique trial design and suggest GBOs as a valuable platform for real-time assessment of CAR-T cell bioactivity and for insights into immunotherapy efficacy.
TMOD-04. SAFETY AND EFFICACY DATA FROM A CLINICAL TRIAL OF SONODYNAMIC THERAPY WITH 5-ALA HCL ORAL SOLUTION AND CV-01 DELIVERED WHOLE HEMISPHERIC LOW-INTENSITY NON-ABLATIVE ULTRASOUND IN PET FRENCH BULLDOGS WITHDE NOVO NATURALLY OCCURRING HIGH-GRADE GLIOMA
Authors: Elizabeth Pluhar G , Arnold Susan , Ling Jeremy , Hunt Matthew , Agarwal Vijay 
Published: November 2024

Abstract
To date, no animal model has been able to accurately test emerging therapeutics for high-grade glioma. Pet dogs’ high-grade gliomas closely mimic human tumors histopathologically and radiologically as well as with poor clinical survival. Dogs with these tumors have notably shorter survival than humans, with French Bulldogs showing the shortest survival of all breeds affected, aiding swift therapeutic evaluations. We report the first use of the novel CV-01 device delivering non-ablative low-intensity diffuse ultrasound (LIDU) with oral 5-ALA as a recurrent high-grade glioma treatment in a veterinary safety and efficacy trial. This Phase 1 study focused on safety, with secondary outcomes assessing histopathological efficacy markers (CC3, Iba1) and overall survival. After one SDT treatment pre-resection, treatments every 3-4 weeks were administered to eight French Bulldogs, totaling 60 administrations (average of 7.5 total treatments/patient). The control group matched breed, age, and histopathologic diagnosis. Average age was 6.35 years (range: 4.8 – 7.8 years), slightly older than controls (5.9 years, range: 3.0 - 9.9 years). No complications or toxicities were noted, and MRI scans showed no damage to the normal brain. Histopathologic analysis from four canine tumor samples revealed increased apoptosis and immune activation markers post-SDT (e.g. cleaved caspase 3 [CC3] and ionized calcium-binding adaptor molecule 1 [Iba1]), indicating selective tumor cell death. Median overall survival in the treatment group reached 205.5 days (6.8 months) compared to 55 days (1.8 months) in controls, with the longest survival at 587 days (versus 213 in controls). Although preliminary, these results affirm the safety of 5-ALA-mediated SDT in canine glioma patients. A multi-center, First-In-Human trial in recurrent high-grade glioma recently completed enrollment, aiming to further validate canine trials for emerging high-grade glioma therapeutics.
TMOD-06. ESTABLISHMENT OF PITUITARY NEUROENDOCRINE TUMOR (PITNET) ORGANOID MODELS
Authors: Maeda Sachi , Ohka Fumiharu , Kanamori Fumiaki , Okumura Yuka , Takeuchi Kazuhito , Nagata Yuichi , Yamaguchi Junya , Harada Hideyuki , Shimizu Hiroki , Takido Yuhei , Saito Ryuta 
Published: November 2024

Abstract
Pituitary neuroendocrine tumors (PitNETs) are tumors that originate from the anterior pituitary gland. While they are mostly benign, they can cause various clinical symptoms due to hormonal secretion abnormalities. PitNET can be broadly categorized into three lineages, each of which has its differentiation controlled by specific transcription factors. Treatment options for PitNET include surgical resection and pharmacotherapy, but available drugs are limited, and their efficacy markers remain unclear. To develop novel drugs for PitNET and identify their efficacy markers, it is necessary to develop new research models. In recent years, organoid models have garnered attention as novel research models for various cancer types. In this study, we established novel organoid models derived from PitNET patients and analyzed their histological and endocrinological characteristics. Surgical specimens from 4 cases of somatotroph adenoma, 1 case of double adenoma, 1 case of gonadotroph adenoma, and 1 case of corticotroph adenoma were minced in dissection medium and embedded in Matrigel basement membrane matrix respectively. The organoids were cultured under 5% CO2 at 37°C using media supplemented with various growth factors. After 28 days of culture, formalin-fixed paraffin-embedded sections were prepared to examine histological homology with patient tumors. Hematoxylin and eosin staining results showed that all organoids maintained cell morphology and tissue structure similar to the original tumors. Immunohistochemical staining for markers specific to each PitNET revealed similar staining patterns between the organoids and the original tumors. Furthermore, analysis of hormone levels in the culture medium showed that hormone production capabilities, such as growth hormone and follicle stimulating hormone, were maintained even after long-term culture. In this study, we successfully established PitNET organoid models that retain histological and endocrinological characteristics. These models are expected to serve as useful research tools for elucidating the molecular mechanisms of PitNET and developing novel therapies targeting critical molecular abnormalities.
TMOD-10. ESTABLISHMENT OF ADULT AND PEDIATRIC BRAZILIAN PRE-CLINICAL MODELS FOR HIGH-GRADE GLIOMAS
Authors: Baroni Mirella , Megid Raquel , Tshikawa Leticia , Martin Ana Carolina , Duarte Terence , Escremim Flavia , Gomes Izabela , Moreno Daniel , Garcia Felipe , Teixeira Gustavo , Lopes Luiz Fernando , Mançano Bruna , Polverini Allan , Lombardi Ismael , Júnior Carlos , Reis Rui , Teixeira Silvia 
Published: November 2024

Abstract
High-grade gliomas (HGG) are the most aggressive brain tumors, necessitating robust and representative preclinical models for therapeutic research. We established primary cultures and patient-derived xenograft models from three pediatric high-grade gliomas (pHGG) and one adult IDH wild-type glioblastoma (GBM IDHwt) Brazilian patients. The first pHGG case, from an 11-year-old with PDGFRA (c.1977C&gt;G) and TP53 (c.637C&gt;T) mutations, led to the development of the HCB570 primary culture, PDX and patient-derived orthotopic xenograft (PDOX) OXP9. The second pHGG, from an 11-year-old with CMMRD syndrome and MSH6 germline mutation, resulted in the HCB589 primary culture, PDX and PDOX OXP22. The third pHGG case, from a 14-year-old with diffuse midline glioma harboring an H3F3A mutation, established the HCB604 primary culture and PDX OXP32. The HCB612 primary culture and PDX GBM1, were established from an adult patient with GBM IDHwt, TERT mutated, with no MGMT promoter methylated. The primary cultures showed varied proliferative rates, with an average doubling time of 55 hours. All cultures demonstrated colony-formating capability, with an average IC50 of 750µM for temozolomide (TMZ) exposure. Immunohistochemical and EPIC methylation profiles confirmed that the PDX models closely resemble the patient features. Our establishment of diverse preclinical models, including those derived from patients with rare genetic conditions such as CMMRD, provides valuable insights into HGG pathogenesis and potential therapeutic strategies. The present Brazilian patient-derived models enrich glioma research inclusion diversity and foster future personalized treatment approaches.
TMOD-11. ADVANCED MRI ANALYSIS TO ASSESS CHEMO-RADIATION RESPONSE IN PEDIATRIC EPENDYMOMA MODELS
Authors: Eggers Lucas , Song Jane , Steiner Jenna , Pierce Angela , Griesinger Andrea , Foreman Nicholas , Serkova Natalie 
Published: November 2024

Abstract
Pediatric Ependymoma (EPN) is an aggressive brain tumor for which the benefits of chemo-radiation (CR) therapy have yet to be established. Our team has previously reported behavior patterns of EPN, including high tumor cellularity, cytological anaplasia, high mitotic index, tumor necrosis, and the presence of inflammatory cells such as M2-type macrophages. Recently, we have established advanced MRI protocols and computational algorithms for cell- and vessel-size imaging. The goal of this study is to develop advanced MRI analysis for CR response biomarkers (including tumor size, cell- and vessel-size correlates, and texture analysis) in mice with patient-derived xenografts (PDX) of pediatric EPN. Female severely immune deficient (SCID) mice were used for intracranial orthotopical inoculation of disaggregated tumors from pediatric EPN patients. All multi-parametric MRI sequences (fast spin echo, FLAIR, diffusion weighted, quantitative T2- and r2*-maps) were acquired on a Bruker 9.4 Tesla MRI scanner prior to CR, followed by 2 days and 2 weeks after CR treatment. All radiation treatment was performed using an animal image-guided precision XRAD irradiator (2Gyx5days), using MRI and CT guided EPN localization with added 30 mg/kg 5-fluoracil. All MRI analysis was performed using Bruker ParaVision software and MATLAB based modeling. The sensitivity of T2w-MRI scans was 0.2 mm for the smallest tumor detected; the median tumor volume at baseline was 2.5 mm3. Untreated mice showed rapid progression of tumor growth from small to intermediate to large EPN. The increased tumor sizes in untreated EPN were characterized by low ADC, highly elevated blood vessel density and large tumor cell size. A significant decrease in vessel size density and an increase in inflammatory cells were seen as soon as 2 days after CR therapy. The late response (2 weeks post CR) is characterized by increased ADC values and decreased cell size, resulting in significantly decreased tumor volumes.
TMOD-13. IDENTIFYING MOLECULAR SIGNATURES OF PPM1D-MUTANT DIPGS
Authors: Kundu Ipsita , Kebede Adam , Morin Eric , Langhnoja Jaldeep , Arounleut Phonepasong , Bandopadhayay Pratiti , Phoenix Timothy 
Published: November 2024

Abstract
Diffuse Intrinsic Pontine Glioma (DIPGs) are universally fatal pediatric tumors with a median survival of only 9-12 months. PPM1D-truncating mutations (PPM1Dtr), which promote its phosphatase activity and suppress TP53 function, are found in approximately 15% of DIPG tumors. PPM1Dtr are mutually exclusive to TP53 mutations, and present unique therapeutic opportunities to reactivate wild-type TP53. Another distinct feature of PPM1Dtr DIPGs is the co-occurrence of PI3K/AKT/mTOR pathway alterations, such as PIK3CA. There is an unmet need to elucidate the underlying molecular mechanisms of DIPG and identify novel therapeutic vulnerabilities that will improve outcomes of this devastating tumor. We hypothesize that PPM1D-mutant DIPGs can be therapeutically targeted by reactivating the p53 signaling pathway and other complementary pathways which cooperate with PPM1Dtr. To investigate this, we have generated Trp53- and Ppm1d-mutant isogenic DIPG murine models to determine how specific oncogenic alterations function in DIPG formation, growth and treatment sensitivity. Current studies aim to examine differences in sensitivity to standard of care treatment modalities and leverage next generation sequencing techniques to uncover additional vulnerabilities. We found notable differences upon addition of PIK3CA mutations in the context of PPM1Dtr DIPG tumor formation, growth, survival, and lineage identity. Ongoing studies using whole genome transcriptomics to compare tumor models will provide insight into the molecular signals and cell state changes driven by individual genetic alterations. Furthermore, by comparing isogenic TP53 and PPM1Dtr mutant DIPG models, we aim to further delineate the molecular mechanisms that drive differential sensitivity of TP53 wild-type tumors. The immune-competent nature of our murine models also provides us with a unique opportunity to delineate tumor immune microenvironment changes. Leveraging this information and our novel murine models, our long-term goal is to develop combinatorial therapeutic strategies to improve outcomes for this deadly disease.