bims-malgli Biomed News
on Biology of malignant gliomas
Issue of 2025–06–08
eleven papers selected by
Oltea Sampetrean, Keio University



  1. bioRxiv. 2025 May 21. pii: 2025.05.16.654515. [Epub ahead of print]
      Gliomas are aggressive and heterogeneous brain tumors with limited treatment options. While oncogenic mutations in gliomas have been well-characterized, their impact on the tumor microenvironment remains poorly understood. To investigate how genomic alterations may influence the glioma microenvironment, we performed an integrative multiomic and spatial transcriptomic analysis of 93 glioma samples (46 IDH-mutant gliomas and 47 IDH-wildtype glioblastoma) from 69 patients representing both primary and recurrent stages. Using whole-genome sequencing, chromatin conformation capture (Hi-C), RNA-seq, and single-cell spatial transcriptomics (Xenium), we defined how major driver mutations influence spatial tumor organization. We found that IDH-mutant gliomas frequently harbored inflammatory microglia expressing CX3CR1 specifically within their astrocyte-like malignant neighborhoods. In contrast, glioblastomas demonstrated relatively higher T-cell infiltration and enrichment of immunosuppressive myeloid cell populations. We further compared glioblastomas harboring EGFR amplifications due to extrachromosomal DNA (ecDNA) amplifications versus linear chromosomal 7 gains. Tumors with EGFR ecDNA displayed increased presence of mesenchymal-like malignant cells, and higher interactions between pericytes and mesenchymal-like malignant cells, likely driven by hypoxia-associated vascular proliferation. Our findings reveal that the mode of oncogene amplification-linear versus ecDNA-shapes distinct tumor architectures and transcriptional dynamics. Taken together, our study highlights the role of oncogenic drivers in shaping the glioma microenvironment, revealing subtype-specific cellular ecosystems that could inform targeted therapeutic strategies.
    DOI:  https://doi.org/10.1101/2025.05.16.654515
  2. bioRxiv. 2025 May 14. pii: 2025.05.09.653178. [Epub ahead of print]
      IDH -wildtype glioblastoma (GBM) is an aggressive brain tumor with poor survival and few therapeutic options. Transcriptionally-defined cell states coexist in GBM and occupy defined regions of the tumor. Evidence indicates that GBM cell states are plastic, but it remains unclear if they are determined by the underlying epigenetic state and/or by microenvironmental factors. Here, we present spatially-resolved epigenomic profiling of human GBM tissues that implicate chromatin structure as a key enabler of cell plasticity. We report two epigenetically-defined and spatially-nested tumor niches. Each niche activates short-range molecular signals to maintain its own state and, surprisingly, long-range signals to reinforce the state of the neighboring niche. The position of a cell along this gradient-like system of opposing signals determines its likelihood to be in one state or the other. Our results reveal an intrinsic system for cell plasticity that is encoded in the chromatin profiles of two adjacent niches that dot the topological architecture of GBM in cartesian space.
    DOI:  https://doi.org/10.1101/2025.05.09.653178
  3. bioRxiv. 2025 May 22. pii: 2025.05.17.654526. [Epub ahead of print]
       BACKGROUND: Glioblastoma (GBM) is the deadliest primary brain tumor in adults, where current therapies fail to meaningfully extend survival. Available animal GBM tumor models, especially therapy-resistant and recurrent ones with unique immunological aspects, are restricted, impeding innovative treatment research. To confront this critical obstacle we established a unique GBM mouse model that utilizes patient-derived xenografts (PDXs) within humanized mice.
    METHODS: We selected two immune-deficient mouse models to facilitate the reconstitution of myeloid lineage cells. After undergoing myeloablation, mice received CD34+ hematopoietic stem progenitor cells derived from human umbilical cord blood for humanization. Upon confirming the reconstitution of human blood cells, mice were xenografted with PDXs resistant to radiation. Tumor profiles and immune cell infiltration were analyzed via flow cytometry, immunohistochemistry, and single-cell RNA sequencing (scRNA-seq). The findings were evaluated against scRNA-seq data from recurrent human GBM.
    RESULTS: A diverse range of human immune cells, including T, NK, and myeloid lineage cells, infiltrated PDX tumors in humanized mice. Notably, gene expression profiles in these immune cells resembled that of recurrent human GBM. Unlike conventional xenograft models, this model highlighted enhanced tumor diversity, particularly a high fraction of neural progenitor-like cells.
    CONCLUSIONS: Our humanized GBM mouse model displayed an immune cell signature similar to recurrent GBM. This model is a valuable resource for analyzing the tumor immune landscape and assessing new therapies, particularly immunotherapies. By enabling effective evaluation of novel treatments, our model has the potential to significantly advance GBM research.
    DOI:  https://doi.org/10.1101/2025.05.17.654526
  4. Neurooncol Adv. 2025 Jan-Dec;7(1):7(1): vdaf078
       Background: Telomerase reverse transcriptase (TERT) promoter mutations are observed in most glioblastoma (GBM) tumors, leading to TERT expression, which is crucial for tumor growth. Accordingly, inhibiting TERT or its upstream tumor-specific transcription factor GA-binding protein transcription factor subunit beta 1 (GABPB1) was shown to inhibit tumor growth. In addition, epidermal growth factor receptor (EGFR) was shown to signal upstream of TERT and GABPB1 and to control TERT expression, and EGFR inhibition also inhibits GBM growth.
    Methods: This study investigated the individual as well as combined effects of EGFR, TERT, and GABPB1 inhibition on cell and orthotopic rat models. We assessed cell proliferation, animal survival, tumor size, 1H magnetic resonance spectroscopy (MRS)-detectable steady-state lactate, and 13C MRS-detectable hyperpolarized (HP) lactate production.
    Results: When TERT or GABPB1 were inhibited simultaneously with EGFR, the combination treatment resulted in enhanced inhibition of cell and tumor growth as well as animal survival compared not only to controls but also to any of the single treatments. Our study also found that steady-state 1H MRS-detectable lactate and HP 13C MRS-detectable lactate production dropped following every treatment, and the drop was significantly greater following combination treatments. Furthermore, the metabolic changes occurred prior to changes in tumor size, and a reversal of these metabolic biomarkers was associated with tumor recurrence.
    Conclusion: Our study points to the value of steady-state 1H MRS-detectable lactate and HP 13C MRS-detectable lactate as potential biomarkers of response to combination EGFR/TERT inhibition.
    Keywords:  1H MRS; EGFR; TERT; glioblastoma; hyperpolarized 13C MRS
    DOI:  https://doi.org/10.1093/noajnl/vdaf078
  5. bioRxiv. 2025 May 21. pii: 2025.05.16.654616. [Epub ahead of print]
      Although progress has been made in treating glioblastoma (GBM), with fewer than 5% of patients surviving more than 5 years after diagnosis. For reasons that are not well understood, females are roughly 60% as likely as males to develop GBM, and female patients consistently respond better to treatment than do males. Understanding the molecular etiology of these sex differences in tumor progression and resiliency to treatment could reveal potent new therapeutic targets, ultimately improving survival of both male and female GBM patients. Here we show that the transcription factor Egr1 is a primary mediator of sex differences in multiple GBM tumorigenic phenotypes. In multivariate analysis, high levels of EGR1 expression are correlated with shortened survival for male GBM patients only. To investigate the molecular mechanisms underlying this sex difference, we performed a genomic analysis in our established ex vivo murine model of sex differences, which showed that the transcription factors Egr1 and Klf5 preferentially recruit the transcriptional activator Brd4 to enhancers in male cells relative to female cells, explaining a previously made observation that Brd4 inhibitors reverse sex differences in GBM. Next, using murine and human primary GBM cells, we demonstrated that the small molecule compound SR18662, which downregulates Egr1 and its downstream target Klf5, abrogates GBM growth, migration, invasion, clonogenicity, and response to radiation in a sex-biased fashion. Finally, we knocked down Egr1 and Klf5 via CRISPRi in both untreated and SR18662-treated GBM cells to reveal the sex-biased anti-tumorigenic effects of SR18662 were largely due to Egr1 downregulation, independent of Klf5 downregulation. This result was replicated in vivo. Our results strongly indicate that an Egr1 regulon is a key determinant of sex differences in GBM. As EGR1 is implicated in the cancer biology of many cancers that also display sex differences in incidence and treatment response, our results are likely to be broadly applicable in oncology.
    DOI:  https://doi.org/10.1101/2025.05.16.654616
  6. bioRxiv. 2025 May 15. pii: 2025.05.15.654044. [Epub ahead of print]
      Glioblastoma (GBM) remains the most common and lethal adult malignant primary brain cancer with few treatment options. A significant issue hindering GBM therapeutic development is intratumor heterogeneity. GBM tumors contain neoplastic cells within a spectrum of different transcriptional states. Identifying effective therapeutics requires a platform that predicts the differential sensitivity and resistance of these states to various treatments. Here, we developed a novel framework, ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures), to quantify the cellular drug sensitivity and resistance landscape. Using single-cell RNA sequencing of newly diagnosed and recurrent GBM tumors, we identified compounds from the LINCS L1000 database with transcriptional response signatures selectively discordant with distinct GBM cell states. We validated the significance of these findings in vitro, ex vivo, and in vivo, and identified a novel combination of an OLIG2 inhibitor and Depatux-M for GBM. Our studies suggest that ISOSCELES identifies cell states sensitive and resistant to targeted therapies in GBM and that it can be applied to identify new synergistic combinations.
    Keywords:  Drug Resistance; Glioblastoma; Pharmacology; Pharmacotranscriptomics; Single-Cell RNA Sequencing
    DOI:  https://doi.org/10.1101/2025.05.15.654044
  7. bioRxiv. 2025 May 15. pii: 2025.05.12.653429. [Epub ahead of print]
       Background: Malignant gliomas (MG) are the most common primary brain malignancies and are considered universally fatal. Oncolytic HSVs (oHSV) are promising immunotherapeutics capable of selectively lysing cancer cells, eliciting anti-tumor immunity, and providing local delivery of immune-activating transgenes. IL-27 is a pleiotropic cytokine capable of enhancing tumor-reactive cytotoxic T cell (CTL) function while also possessing neuroprotective properties. We hypothesized that IL-27 expression by oHSV would enhance CTL function and improve anti-glioma therapeutic activity.
    Methods: We developed an oncolytic herpes simplex virus (oHSV) that expresses IL-27 (C027). The anti-glioma efficacy of C027 was tested in three syngeneic orthotopic glioma models derived from both chemical (CT-2A) and genetic (SB28, KR158) glioma lines. Spectral flow cytometry was used to assess immunophenotypic and functional changes in the tumor infiltrates and systemically. To further investigate the C027-related CTL activity, we employed in vivo cell specific depletion and IL-27 blockade alongside in vitro T cell stimulation assays. Local and systemic antitumor memory was evaluated by both orthotopic and flank tumor rechallenge of C027-treated long-term survivors.
    Results: C027 significantly prolonged survival in syngeneic orthotopic glioma models derived from both chemical (CT-2A) and genetic (KR158, SB28) glioma lines. In the CT-2A model, IL-27-expressing oHSV treatment was associated with increased intratumoral multifunctional effector cytotoxic T lymphocytes (CTL) and functional T cell populations systemically. Mechanistically, both CD8 T cells and IL-27 were required for the C027 survival benefit in vivo and IL-27 enhanced CTL function in vitro . C027-treated mice that survived their initial tumors had local and systemic anti-glioma memory rejecting tumors on rechallenge.
    Conclusions: Our findings demonstrate that IL-27 expression by oHSV significantly improves anti-glioma therapeutic efficacy, enhances CTL effector function, and induces durable immune memory. Thus, IL-27-oHSV may provide a promising therapeutic approach for malignant gliomas. What is already known on this topic - Malignant gliomas are highly aggressive tumors largely resistant to current immunotherapies. Oncolytic herpes simplex viruses (oHSV) are promising immunotherapy agents for malignant gliomas and provide a platform for immunomodulatory gene expression. What this study adds - In this study, we present a novel IL-27 expressing oHSV (C027) that improves survival in syngeneic glioma-bearing mice through a CD8 T cell and IL-27 dependent mechanism and induces durable immune memory. How this study might affect research, practice or policy - Our study demonstrates that IL-27-expression by oHSV enhances anti-tumor immunity and glioma efficacy suggesting its potential as a novel therapeutic.
    DOI:  https://doi.org/10.1101/2025.05.12.653429
  8. Clin Cancer Res. 2025 Jun 03.
       PURPOSE: Clinical trials have shown limited efficacy of anti-programmed cell death protein 1 (PD-1) treatment for glioblastoma (GBM). In this study, we examined the expression of TGFbRI in GBM-infiltrating CD8+ T cells and the characteristics of TGFbRI+CD8+ T cells. We examined the ex vivo effects of co-blockade of PD-1 and TGFb on the functions of GBM-infiltrating CD8+ T cells.
    EXPERIMENTAL DESIGN: Using flow cytometry, we examined the phenotypes of tumor-infiltrating CD8+ T cells from newly diagnosed GBM patients. We performed single-cell RNA/TCR-sequencing to characterize the tumor-infiltrating TGFbRI+CD8+ T cells. We also examined the effects of co-blockade of PD-1 and TGFb on the functions of tumor-infiltrating CD8+ T cells in ex vivo assays.
    RESULTS: GBM-infiltrating CD8+ T cells expressed significantly increased levels of TGFβRI compared to peripheral blood CD8+ T cells. Among tumor-infiltrating CD8+ T cells, TGFbRI+CD8+ T cells exhibited increased expression of immune checkpoint inhibitory receptors, and tumor antigen-specific cells were enriched in TGFbRI+CD8+ T cells. Single-cell profiling revealed that tumor-infiltrating TGFBR1+CD8+ T cells demonstrated more clonal expansion and upregulation of TCR signaling genes compared to TGFBR1-CD8+ T cells. In vitro, anti-CD3 stimulation upregulated TGFbRI expression on CD8+ T cells. GBM patients with a high frequency of TGFbRI+CD8+ T cells presented with increased TGFb signaling intensity. Importantly, combined blockade of PD-1 and TGFb significantly enhanced the functions of tumor-infiltrating CD8+ T cells ex vivo.
    CONCLUSIONS: Our findings provide a basis for further investigation of co-blockade of PD-1 and TGFβ for the treatment of patients with GBM.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-24-2184
  9. Nat Med. 2025 Jun 01.
      Glioblastoma (GBM) is the most common primary brain cancer in adults and carries a median overall survival (OS) of 12-15 months. Effective therapy for recurrent GBM (rGBM) following frontline chemoradiation is a major unmet medical need. Here we report the dose escalation and exploration phases of a phase 1 trial investigating intracerebroventricular delivery of bivalent chimeric antigen receptor (CAR) T cells targeting epidermal growth factor receptor (EGFR) epitope 806 and interleukin-13 receptor alpha 2 (IL-13Rα2), or CART-EGFR-IL13Rα2 cells, in patients with EGFR-amplified rGBM. Primary endpoints included dose-limiting toxicity, determination of the maximum tolerated dose and recommended dose for expansion, and occurrence of adverse events. Secondary endpoints included objective radiographic response, duration of response, progression-free survival and OS. A total of 18 patients received CART-EGFR-IL13Rα2 cells. The maximum tolerated dose was determined to be 2.5 × 107 cells. Of the 18 patients, 10 (56%) experienced grade 3 neurotoxicity; none had grade 4-5 neurotoxicity. Of 13 patients, 8 (62%) with measurable disease at the time of CAR T cell infusion experienced tumor regression, with one confirmed partial response by Modified Response Assessment in Neuro-Oncology criteria (objective radiographic response, 8%; 90% confidence interval, 0-32%) and one patient with ongoing durable stable disease lasting over 16 months. Median progression-free survival was 1.9 months (90% confidence interval, 1.1-3.4 months), and median OS was not yet reached at the time of data cut-off (median follow-up time, 8.1 months). These findings indicate that intracerebroventricular delivery of bivalent CART-EGFR-IL13Rα2 is feasible and appears safe. CART-EGFR-IL13Rα2 cells are bioactive and exhibit a signal of antitumor effect in rGBM. ClinicalTrials.gov registration: NCT05168423 .
    DOI:  https://doi.org/10.1038/s41591-025-03745-0
  10. Neurooncol Adv. 2025 Jan-Dec;7(1):7(1): vdaf076
       Background: Microstructural tumor characteristics discriminate metastases, glioblastoma, meningioma, and primary CNS lymphoma. We aimed to assess these intracranial neoplasms utilizing multiparametric diffusion imaging as a translational measure of morphology.
    Methods: We investigated 101 newly diagnosed intracranial tumors (35 metastases, 34 glioblastomas [GB], 21 meningiomas, 11 primary CNS lymphomas [PCNSL]) with advanced diffusion MRI including Diffusion Tensor Imaging (DTI), Neurite Orientation and Dispersion Density Imaging (NODDI), and Diffusion Microstructure Imaging (DMI). Beyond DTI-derived metrics (aD, fractional anisotropy [FA], mD, rD), we extracted the NODDI and DMI intra-axonal (NODDI intra-cellular volume fraction, DMI V-intra), extra-axonal cellular (DMI V-extra), and free water (NODDI ISO-VF, DMI V-CSF) fractions using a multi-compartment model. These metrics were read from contrast-enhancing tumor portions and compared across the entities.
    Results: Various microstructural parameters served as effective discriminators in pairwise comparisons: ISO-VF demonstrated high accuracy in distinguishing metastases from PCNSL (accuracy 90.13%) and meningiomas (accuracy 80.69%). aD was most accurate in discriminating GB from PCNSL (accuracy 89.57%) and meningioma from PCNSL (accuracy 74.03%), similar to MD which distinguished GB from meningiomas (accuracy 77.73%). FA performed best in discriminating GB from metastases (accuracy 83.11%). Discrimination on two axes of directionality and compartmentalization illustrate the comprehensive approach to tumor assessment.
    Conclusion:  Advanced microstructural imaging facilitates discrimination of four common intracranial neoplasms. Features such as cell density, extent of free water, and directional cellular elements are reflected in the diffusion metrics to varying degrees. As part of a first non-invasive assessment, they may direct early diagnostic and therapeutic procedures.
    Keywords:  DMI; DTI; NODDI; brain tumor; diffusion microstructure imaging
    DOI:  https://doi.org/10.1093/noajnl/vdaf076
  11. iScience. 2025 May 16. 28(5): 112404
      Gallium based therapeutic strategies are thought to be an effective means to promote tumor cell killing that are currently being investigated in glioblastoma. Gallium is a group IIIa metal that is redox inactive, however, its atomic similarity to iron allows it to serve as an iron mimic that may disrupt Fe metabolism. The current understanding of its mechanism of action is related to its ability to inhibit ribonucleotide reductase and the electron transport chain, however, its effects on other iron-dependent metabolic processes (e.g., lipid metabolism) are unknown. Ferroptosis is a unique iron-dependent form of cell death, thus, the goal of this study is to evaluate the effects of Ga(NO3)3 on the induction of ferroptosis. Despite its redox inactivity, Ga(NO3)3 promotes the formation of oxidized lipid droplets. Moreover, Ga(NO3)3 enhances the toxicity of the ferroptosis inducer, erastin, and decreases cell stiffness, indicating an exacerbation of ferroptosis. Ga(NO3)3 also enhances the toxicity of the stearoyl CoA desaturase (SCD) inhibition, and its toxicity can be reversed by oleic acid supplementation, suggesting that Ga(NO3)3 can potentially inhibit SCD. Lipidomic analysis revealed a significant increase in oxidizable triglycerides following Ga(NO3)3 treatment. Thus, it appears that Ga(NO3)3 exacerbates ferroptosis in glioblastoma cells by disrupting the di-ferric lipid metabolic regulator SCD and warrants further investigation as an alternate mechanism of action for Ga-based therapy.
    Keywords:  Biochemistry; Immunology; Molecular biology; Neuroscience
    DOI:  https://doi.org/10.1016/j.isci.2025.112404