Neuro-oncology最新文献

Background: Cellular heterogeneity is a defining feature of glioblastoma (GBM), shaping tumor progression and therapeutic response. While single-cell profiling resolves this heterogeneity, it remains impractical for large-cohort studies and clinical implementation. Conversely, DNA methylation-based classification is widely used for GBM diagnostics but does not provide cellular resolution.

Methods: We introduce a hierarchical non-negative matrix factorization approach (ITHresolveGBM) to deconvolute bulk DNA methylation profiles, inferring the abundance of glial, immune, and neuronal cells of the microenvironment, and further distinguishing differentiation states of malignant cells.

Results: Using ITHresolveGBM, we find that low tumor cell content impairs methylation-based classification, most notably linking the mesenchymal subtype with high immune cell infiltration. By integrating multi-omic single-cell data, we show that epigenetic deconvolution captures a malignant differentiation continuum ranging from stem-like to more differentiated tumors. This continuum aligns prior GBM classification systems and is associated with distinct molecular drivers (e.g., PDGFRA, TP53, EGFR) and survival outcomes.

Conclusions: Our framework reconciles DNA methylation- and RNA-based classification systems and provides a blueprint for unifying bulk tumor profiles with single-cell biology, thereby refining molecular stratification and enhancing GBM diagnostics.

Background: Neuroblastoma (NB) is the most common extracranial solid tumor in children and accounts for 15% of childhood cancer death. The nucleosome remodeling and deacetylase (NuRD) complex is a major chromatin remodeling complex that regulates chromatin accessibility and gene transcription. However, its role in the pathogenesis of neuroblastoma remains poorly understood.

Methods: The genetic dependency and clinical significance of MBD3 in neuroblastoma was evaluated by analysis of public datasets. The function of MBD3 in neuroblastoma cell growth was evaluated by shRNA knockdown experiment. Cleavage under targets and tagmentation sequencing (CUT&Tag-seq), coupled with RNA-sequencing, was employed to explore the mechanisms involved in the epigenetic regulation executed by NuRD decommissioning following MBD3 deficiency.

Results: Here we find that MBD3 is the most lineage-selective dependency among the non-enzymatic subunits of the NuRD complex in neuroblastoma. Knockdown of MBD3 induces cell cycle arrest and apoptosis, and inhibits neuroblastoma growth in vivo. Mechanistically, MBD3 deficiency leads to decommissioning of the NuRD complex and dissociation of the EZH2-PRC2 complex from chromatin, thereby orchestrating the epigenetic regulation of gene expression by modulating the balance between histone acetylation and methylation. NuRD decommissioning upon MBD3 deficiency selectively downregulates the expression of core regulatory transcription factors and upregulates a tumor suppressor SRCIN1, collectively suppressing neuroblastoma progression.

Conclusions: Our data identify MBD3 and the NuRD complex as potential therapeutic targets in neuroblastoma, highlighting the critical role of epigenetic regulation in tumor maintenance. Targeting this pathway may offer a novel strategy to selectively impair neuroblastoma cell survival and improve outcomes.

Background: Although the genetic evolution of IDHwt glioblastomas has extensively been investigated, limited studies have addressed the epigenetic evolution. Understanding the epigenetic evolution is particularly relevant as demethylation of the MGMT promoter may form a means of treatment resistance.

Methods: We generated whole genome DNA methylation data of 64 matched primary-recurrent samples from IDHwt glioblastoma patients. Data were combined with three publicly available datasets into a cohort consisting of 418 samples. MGMT promoter methylation was determined using the MGMT-STP27 algorithm. CoxPH regression was used to investigate the impact of identified changes on survival.

Results: Our analysis demonstrate that the methylome of IDHwt glioblastomas was highly stable (93%). Changes that occur could mostly be allocated to differences in tumor purity. Conversion from a methylated MGMT promoter to unmethylated status at progression occurred infrequently (9/66, 13.6%), but significantly more often than the converse (4/113, 3.5%). Conversion was associated with worse overall- and progression-free survival compared to patients whose tumors remained MGMT methylated. Despite a large survival difference between patients with MGMT promoter-methylated and unmethylated tumors, very few CpGs were differentially methylated between samples from MGMT methylated and unmethylated tumors. Of the ones that were, the vast majority were located within the MGMT gene body and were inversely correlated with MGMT promoter methylation status.

Conclusion: The methylome of IDHwt glioblastomas is highly stable at tumor progression. In this series, only 7% of tumors showed change in MGMT promoter methylation status at progression.

Background: Glioblastoma (GBM) is a highly aggressive brain tumor with profound metabolic heterogeneity. However, a clinically actionable classification based on metabolic gene expression remains undefined.

Methods: We conducted a comprehensive multi-omics analysis of IDH-wildtype GBMs from three publicly available datasets. Prognostic metabolism-related genes were used to define transcriptional subtypes, which were validated in independent datasets and patient-derived cell (PDC) models. Functional assays and drug sensitivity studies were performed to explore therapeutic relevance.

Results: We identified three distinct metabolic subtypes: M1, enriched for synaptic signaling and amino acid metabolism, exhibited leading-edge anatomical features; M2, characterized by mitochondrial metabolism and cell cycle activity, was associated with favorable survival; and M3, marked by hypoxia, immune activation and suppression, and broad metabolic pathway engagement, correlated with poor prognosis. These subtypes were reproducible across cohorts and faithfully recapitulated in PDC models. Metabolomic profiling confirmed distinct subtype-specific metabolic signatures. Notably, M3 cells showed high sensitivity to inhibitors targeting glycosaminoglycan degradation, nicotinamide metabolism, and retinoic acid pathways in both in vitro and in vivo models.

Conclusion: Our study defines three biologically and clinically relevant metabolic subtypes of IDH-wildtype GBM. This classification reveals distinct metabolic programs and therapeutic vulnerabilities, providing a framework for precision metabolism-targeted strategies in glioblastoma.

Background: Meningioma brain invasion encumbers surgical resection and increases the risk of tumor recurrence, but the molecular mechanisms underlying this process are poorly understood.

Methods: To identify molecular and cellular features of brain-invasive meningiomas, we (1) analyzed bulk RNA sequencing data from 199 meningiomas, including 33 brain-invasive tumors, (2) analyzed patient-matched single-cell RNA sequencing data of spatially mapped meningioma samples from the tumor core or brain-tumor interface (BTI), and (3) performed spatial transcriptomic sequencing of brain-invasive meningioma samples. Multiplexed immunofluorescence (IF) was used to validate bioinformatic spatial expression patterns. Functional interactions between meningioma cells and neurons were studied in meningioma/neuron co-cultures using confocal microscopy, multi-electrode array recordings, and live cell calcium imaging.

Results: Transcriptomic analyses showed conserved enrichment of TGM2, S100A11, ZYX, and PDGFRA at the BTI across bulk, single-cell, and spatial RNA sequencing datasets. The expression of these genes at the BTI was confirmed using multiplexed IF, and single-cell bioinformatic and microscopy analyses further demonstrated enrichment of macrophages at the BTI. Co-culture assays showed neuronal hyperexcitability and increased proliferation of meningioma cells, suggesting functional communication between meningioma cells and the tumor microenvironment may contribute to meningioma growth in cases with brain invasion.

Conclusions: Meningioma brain invasion is defined by molecular remodeling of tumor cells and functional interactions within the tumor microenvironment.

Background: Glioblastoma (GBM) is characterized by extensive tissue hypoxia. This hypoxic microenvironment drives chemoresistance and promotes aberrant vascularization, critically limiting the efficacy of temozolomide (TMZ) and bevacizumab (BEV). Here, we report EPIC-0502, a novel small-molecule competitive antagonist that inhibits hypoxia signaling while sensitizing GBM to both TMZ and BEV.

Methods: EPIC-0502 was identified through molecular dynamics simulation. Its target blocking effect was validated via non-targeted metabolomics, stable isotope tracing-based metabolic flux analysis, and pull-down assays. The mechanisms underlying EPIC-0502 activity were elucidated by Western Blot (WB), Co-Immunoprecipitation (Co-IP), ELISA, Seahorse assays, and Immunofluorescence (IF). The sensitizing effects of EPIC-0502 on TMZ and BEV were evaluated in orthotopic GBM models.

Results: EPIC-0502 inhibited α-ketoglutarate (α-KG) to succinate conversion, depleting cytoplasmic succinate levels and inhibiting phosphoglycerate kinase 1 (PGK1) succinylation and phosphorylation, which significantly attenuated glycolysis. Furthermore, EPIC-0502 destabilized HIF1α by promoting hydroxylation-dependent ubiquitination, while impairing its transcriptional activity. Through HIF1α degradation, EPIC-0502 enhanced GBM sensitivity to TMZ via E2F1 downregulation and reversed hypoxia-induced vascular endothelial growth factor A (VEGFA) overexpression, potentiating the antiangiogenic efficacy of BEV. Collectively, these actions enable EPIC-0502 to synergistically enhance the therapeutic efficacy of TMZ/BEV combination.

Conclusion: Based on EPIC-0502-driven HIF1α degradation that overcomes BEV resistance and synergizes with TMZ, we propose the novel VITA-GBM regimen comprising: Vascular targeting (BEV), Inhibition of hypoxia signaling (EPIC-0502), TMZ chemotherapy, and Alignment of synergistic mechanisms. This strategy enhances the efficacy of first-line therapies and provides a promising approach to improve overall survival in GBM patients.

Background: Scarce T cell infiltration, immunosuppressive tumor-associated macrophages and ineffective drug delivery drive glioma progression and limit treatment efficacy. Mapping immunotherapy distribution by multimodality imaging might be a biomarker that could aid tumor monitoring and guide therapy development.

Methods: To assess drug delivery, we developed a MRI-lightsheet microscopy platform (MR-LSM) to monitor immunotherapy at the cellular level in two immunocompetent glioma models (Gl261, SB28). The atezolizumab (PD-L1 inhibitor) subgroup of the multicenter N2M2/NOA20 trial in MGMT unmethylated GBM patients was assessed by CNN analysis and correlated to progression free survival.

Results: In contrast to the conventional Gl261 glioma model, SB28 gliomas are characterized by poor immunogenicity and resistance to Toll-like receptor (TLR) 7 targeted therapy delivered by CDNP-R848 nanoparticles. SB28 resistance is driven by microvascular pathology, vasogenic edema and drug off-targeting to peritumoral edema and white matter tracts. Vascular endothelial growth factor (VEGF) inhibition in conjunction with irradiation and dual immunotherapy (DIR) targeting innate (CDNP-R848) and adaptive immunity (anti-CTLA-4) breaks resistance, increases survival and reverses drug off-targeting. Mechanistically, tumor control is orchestrated by vascular normalization, enhanced CD8+ T cell influx and a proinflammatory shift of myeloid cells along with strong IL-12/IL-13 upregulation. In a translational analysis of the multicenter N2M2/NOA20 trial we validate that edema and microvascular pathology are associated with poor prognosis in glioblastoma patients treated with checkpoint immunotherapy and that patients without edema have increased PFS.

Conclusions: We develop a customizable imaging platform to map drug delivery to glioma with broad applicability in neuroscience and neurooncology.

Background: The life expectancy of patients with diffuse IDH-mutant low-grade gliomas (IDHmt LGG) ranges from 5 to over 20 years. Tumor behavior, including spontaneous growth rate, varies even within homogeneously classified subtypes of oligodendroglioma and astrocytoma. Risk-adjusted treatment strategies are needed to avoid therapy-related toxicities, without compromising outcome. The spontaneous tumor volume growth rate (TVGR) serves as a prognostic marker and predicts response to therapy. Accurate prediction of TVGR through biomarkers would enable an improved evidence-based risk management.

Patients & methods: A cohort of 77 patients treated in Montpellier, France, for IDHmt LGG grade II (WHO 2016) (29 oligodendrogliomas, 48 astrocytomas) was constituted (age >18 years; MRI scans, frozen tumor tissue). The DNA methylome (Illumina, EPIC array) and transcriptome (RNAseq) were established. TVGR was determined based on serial MRIs collected over the "watch & wait" period before first treatment beyond surgery. Transcriptomic and methylome data were analyzed for signatures associated with TVGR using rank-rank regression followed by preranked gene set enrichment analysis.

Results: : The median TVGR was lower in IDHmt codeleted compared to non-codeleted LGG, (0.241 year-1 range 0.082-0.366 vs 0.424 year-1 range 0.264-0.609, p < 0.001). In codeleted IDHmt LGG, TVGR was associated with upregulated gene signatures for neuronal systems, synaptic activity, and activation of repressed or poised signatures of neural progenitor cells; while the TVGR in non-codeleted IDHmt LGG was dominanted by upregulated proliferation-related signatures, including DNA replication and repair.

Conclusion: Spontaneous TVGR of codeleted and non-codeleted IDHmt LGG involve distinct biological processes, suggesting possible differences in response to therapies.

Background: Poly ADP-ribose polymerase-1 (PARP1) is a key enzyme in DNA damage repair and an established target for cancer drug treatment. Although the emergence of non-invasive imaging of PARP using PET has opened new opportunities in cancer diagnosis and drug development, subtype selective imaging of the enzyme, and particularly in brain, remains an unmet need.

Methods: The potent and selective novel PARP inhibitor AZ14193391 was labeled with carbon-11 and evaluated as a candidate PET radioligand for PARP1 through a series of translational in vitro and in vivo molecular imaging studies. These studies encompassed PET in non-human primates, healthy volunteers and patients with glioblastoma.

Results: Robust radioligand binding to PARP1 was observed in the healthy non-human primate and human brain both in vitro and in vivo. Elevated tumor binding with high contrast was also demonstrated in patients with glioblastoma.

Conclusions: The novel PET radioligand, [11C]AZ14193391 enables subtype selective imaging of PARP1 binding. Its ability to image this protein in the human brain paves the way for accelerated research, diagnosis and drug development in neuro-oncology.

Background: Astroblastomas are rare brain tumors predominantly affecting children and young adults, for which molecular subtypes and clinical management remain undefined.

Methods: We analyzed tumor samples, molecular profiles, and clinical data from 200 patients, classified as "Astroblastoma, MN1-altered" under WHO criteria, using DNA methylation profiling, DNA/RNA profiling/sequencing, and survival analyses.

Results: DNA methylation analyses identified three groups: Group A (n = 143, characterized by MN1::BEND2 fusions, predominantly supratentorial location, with striking female predominance and favorable survival); Group B (n = 37, epigenetically and transcriptionally closely related to Group A, but characterized by EWSR1::BEND2 fusions, with spinal and infratentorial locations and poor prognosis); and Group C (n = 20, epigenetically and transcriptionally distinct, characterized by MN1::CXXC5 fusions, exclusively supratentorially located, with favorable survival). Progression-free and overall survival were significantly shorter in Group B (5-year PFS 14%; 10-year OS 54%) compared to A (5-year PFS 47%; 10-year OS 89%) and C (5-year PFS 75%; 10-year OS 89%). Radiotherapy improved PFS in Group B (hazard ratio 0.25), while no clear benefit was identified for Group A and C.

Conclusions: Astroblastoma, MN1-altered, comprises three molecularly and clinically distinct groups, characterized by different fusion genes, including those without MN1. These new insights, including identification of potential predictive biomarkers like 14q/16q loss, provide a framework for development of risk-stratified therapeutic approaches. Importantly, we identified a molecularly defined high-risk group that benefits from radiation therapy. Our findings redefine Astroblastoma as a molecularly diverse tumor type, propose a refined classification, support the development of risk-adapted therapeutic strategies and provide a rational standard of care.