Glioma progression is shaped by genetic evolution and microenvironment interactions

Cutting-edge technologies illuminate the neural landscape of cancer: Insights into tumor development

Neurogenesis constitutes a pivotal facet of malignant tumors, wherein cancer and its therapeutic interventions possess the ability to reconfigure the nervous system, establishing a pathologic feedback loop that exacerbates tumor progression. Recent strides in high-resolution imaging, single-cell analysis, multi-omics technologies, and experimental models have opened unprecedented avenues in cancer neuroscience. This comprehensive review summarizes the latest advancements of these emerging technologies in elucidating the biological mechanisms underlying tumor initiation, invasion, metastasis, and the dynamic heterogeneity of the tumor microenvironment(TME), with a specific focus on neuron-glial-tumor interactions in glioblastoma(GBM) and other neurophilic cancers. Moreover, we innovatively propose target screening processes based on sequencing technologies and database frameworks. It rigorously evaluates ongoing clinical trial drugs and efficacy while spotlighting characteristic cells in the central and peripheral TME, consolidating cancer biomarkers pivotal for future targeted therapies and management strategies. By integrating these cutting-edge findings, this review aims to offer fresh insights into tumor-nervous system interactions, establishing a robust foundation for forthcoming clinical advancements.

Machine learning-based prognostic subgrouping of glioblastoma: A multicenter study

BACKGROUND

Glioblastoma (GBM) is the most aggressive adult primary brain cancer, characterized by significant heterogeneity, posing challenges for patient management, treatment planning, and clinical trial stratification.

METHODS

We developed a highly reproducible, personalized prognostication, and clinical subgrouping system using machine learning (ML) on routine clinical data, magnetic resonance imaging (MRI), and molecular measures from 2838 demographically diverse patients across 22 institutions and 3 continents. Patients were stratified into favorable, intermediate, and poor prognostic subgroups (I, II, and III) using Kaplan-Meier analysis (Cox proportional model and hazard ratios [HR]).

RESULTS

The ML model stratified patients into distinct prognostic subgroups with HRs between subgroups I-II and I-III of 1.62 (95% CI: 1.43-1.84, P < .001) and 3.48 (95% CI: 2.94-4.11, P < .001), respectively. Analysis of imaging features revealed several tumor properties contributing unique prognostic value, supporting the feasibility of a generalizable prognostic classification system in a diverse cohort.

CONCLUSIONS

Our ML model demonstrates extensive reproducibility and online accessibility, utilizing routine imaging data rather than complex imaging protocols. This platform offers a unique approach to personalized patient management and clinical trial stratification in GBM.

Targeting the glioblastoma resection margin with locoregional nanotechnologies

Surgical resection is the first stage of treatment for patients diagnosed with resectable glioblastoma and is followed by a combination of adjuvant radiotherapy and systemic single-agent chemotherapy, which is typically commenced 4-6 weeks after surgery. This delay creates an interval during which residual tumour cells residing in the resection margin can undergo uninhibited proliferation and further invasion, even immediately after surgery, thus limiting the effectiveness of adjuvant therapies. Recognition of the postsurgical resection margin and peri-marginal zones as important anatomical clinical targets and the need to rethink current strategies can galvanize opportunities for local, intraoperative approaches, while also generating a new landscape of innovative treatment modalities. In this Perspective, we discuss opportunities and challenges for developing locoregional therapeutic strategies to target the glioblastoma resection margin as well as emerging opportunities offered by nanotechnology in this clinically transformative setting. We also discuss how persistent barriers to clinical translation can be overcome to offer a potential path forward towards broader acceptability of such advanced technologies.

Targeting mesenchymal monocyte-derived macrophages to enhance the sensitivity of glioblastoma to temozolomide by inhibiting TNF/CELSR2/p65/Kla-HDAC1/EPAS1 axis

INTRODUCTION

Temozolomide (TMZ) resistance poses a significant challenge to the treatment of aggressive and highly lethal glioblastomas (GBM). Monocyte-derived Macrophages (MDM) within the tumor microenvironment are key factors contributing to TMZ resistance in GBM. Lactate-mediated histone lysine lactylation (Kla) plays a crucial role in the regulation of tumor progression. However, the mechanism through which MDM-induced Kla expression promotes TMZ resistance in GBM remains unclear.

OBJECTIVES

The objective of this study s to identify a subtype of MDM with therapeutic potential target and to elucidate the mechanisms through which this subtype of MDM contributes to tumor malignant progression and TMZ resistance.

METHODS

We integrated single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data to evaluate whether mesenchymal (MES) MDM is associated with poor prognosis. By establishing a subtype model of GBM cells for the first time, we validated the mechanism by which MES-MDM promotes subtype conversion of tumor cells. Using patient-derived GBM organoids and an intracranial orthotopic GBM model, we demonstrated that targeting MES-MDMs increased GBM sensitivity to TMZ treatment.

RESULTS

We identified a novel MDM subtype, MES-MDM, in the hypoxic niches of the perinecrotic region characterized by high TREM1 expression, which fueled GBM progression. Hypoxia drived MES-MDM signatures by activating ATF3 transcription. MES-MDM facilitated the transition from the NPC to the MES subtype in GBM cells, in which Histone Deacetylase 1 (HDAC1) Kla, induced by the TNF-CELSR2/p65 signaling pathway, promoted this conversion, thereby promoting TMZ resistance. Targeting MES-MDM with TREM1 inhibitory peptides amplified TMZ sensitivity, offering a potential strategy for overcoming resistance to therapy in GBM. Targeting TREM1 enhanced the effectiveness of anti-PD-1 immunotherapy.

CONCLUSION

This study provides a potential therapeutic strategy for patients with MES-subtype GBM by targeting MES-MDMs in combination with TMZ or PD-1 antibody treatment.

Deciphering the dialogue between brain tumors, neurons, and astrocytes

Glioblastoma (GB) and brain metastases (BM) from peripheral tumors account for most cases of tumors in the central nervous system (CNS) while also being the deadliest. From a structural point of view, malignant brain tumors are classically characterized by hypercellularity of glioma and vascular endothelial cells. Given these atypical histological features, GB and BM have long been considered as "foreign" entities with few to no connections to the brain parenchyma. The identification of intricate connections established between GB cells and the brain parenchyma paired with the ability of peripheral metastatic cells to form functional synapses with neurons, challenged the concept of brain tumors disconnected from the CNS. In patients, tumor cell integration to the CNS alters brain functionality and accelerates cancer progression. Next generation precision medicine should therefore attempt to disconnect brain cancer cells from the brain. This review encompasses recent discoveries on the mechanisms underlying these relationships and discusses the impact of these connections on tumor progression, and summarizes the therapeutic opportunities of interrupting the dialogue between healthy and neoplastic brains.

Targeting Glioma Stem Cells: Therapeutic Opportunities and Challenges

Glioblastoma (GBM), or grade 4 glioma, is the most common and aggressive primary brain tumor in adults with a median survival of 15 months. Increasing evidence suggests that GBM's aggressiveness, invasiveness, and therapy resistance are driven by glioma stem cells (GSCs), a subpopulation of tumor cells that share molecular and functional characteristics with neural stem cells (NSCs). GSCs are heterogeneous and highly plastic. They evade conventional treatments by shifting their state and entering in quiescence, where they become metabolically inactive and resistant to radiotherapy and chemotherapy. GSCs can exit quiescence and be reactivated to divide into highly proliferative tumor cells which contributes to recurrence. Understanding the molecular mechanisms regulating the biology of GSCs, their plasticity, and the switch between quiescence and mitotic activity is essential to shape new therapeutic strategies. This review examines the latest evidence on GSC biology, their role in glioblastoma progression and recurrence, emerging therapeutic approaches aimed at disrupting their proliferation and survival, and the mechanisms underlying their resistance to therapy.

Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics

The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing and bulk DNA sequencing, assessing the longitudinal evolution of the GBM ecosystem across layers of cellular and molecular heterogeneity. The most consistent change was a lower malignant cell fraction at recurrence and a reciprocal increase in glial and neuronal cell types in the tumor microenvironment (TME). The predominant malignant cell state differed between most matched pairs, but no states were exclusive or highly enriched in either time point, nor was there a consistent longitudinal trajectory across the cohort. Nevertheless, specific trajectories were enriched in subsets of patients. Changes in malignant state abundances mirrored changes in TME composition and baseline profiles, reflecting the co-evolution of the GBM ecosystem. Our study provides a blueprint of GBM's diverse longitudinal trajectories and highlights the treatment and TME modifiers that shape them.

The multilayered transcriptional architecture of glioblastoma ecosystems

In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.

Integrating Multiplex Immunohistochemistry and Machine Learning for Glioma Subtyping and Prognosis Prediction

Glioma subtyping is crucial for treatment decisions, but traditional approaches often fail to capture tumor heterogeneity. This study proposes a novel framework integrating multiplex immunohistochemistry (mIHC) and machine learning for glioma subtyping and prognosis prediction. 185 patient samples from the Huashan hospital cohort were stained using a multi-label mIHC panel and analyzed with an AI-based auto-scanning system to calculate cell ratios and determine the proportion of positive tumor cells for various markers. Patients were divided into two cohorts (training: N = 111, testing: N = 74), and a machine learning model was then developed and validated for subtype classification and prognosis prediction. The framework identified two distinct glioma subtypes with significant differences in prognosis, clinical characteristics, and molecular profiles. The high-risk subtype, associated with older age, poorer outcomes, astrocytoma/glioblastoma, higher tumor grades, elevated mesenchymal scores, and an inhibitory immune microenvironment, exhibited IDH wild-type, 1p19q non-codeletion, and MGMT promoter unmethylation, suggesting chemotherapy resistance. Conversely, the low-risk subtype, characterized by younger age, better prognosis, astrocytoma/oligodendroglioma, lower tumor grades, and favorable molecular profiles (IDH mutation, 1p19q codeletion, MGMT promoter methylation), indicated chemotherapy sensitivity. The mIHC-based framework enables rapid glioma classification, facilitating tailored treatment strategies and accurate prognosis prediction, potentially improving patient management and outcomes.

Multipronged SMAD pathway targeting by lipophilic poly(β-amino ester) miR-590-3p nanomiRs inhibits mesenchymal glioblastoma growth and prolongs survival

ASBSTRACT

Despite aggressive therapy, glioblastoma (GBM) recurs in almost all patients and treatment options are very limited. Despite our growing understanding of how cellular transitions associate with relapse in GBM, critical gaps remain in our ability to block these molecular changes and treat recurrent disease. In this study we combine computational biology, forward-thinking understanding of miRNA biology and cutting-edge nucleic acid delivery vehicles to advance targeted therapeutics for GBM. Computational analysis of RNA sequencing from clinical GBM specimens identified TGFβ type II receptor (TGFBR2) as a key player in the mesenchymal transition associated with worse outcome in GBM. Mechanistically, we show that elevated levels of TGFBR2 is conducive to reduced temozolomide (TMZ) sensitivity. This effect is, at least partially, induced by stem-cell driving events coordinated by the reprogramming transcription factors Oct4 and Sox2 that lead to open chromatin states. We show that blocking TGFBR2 via molecular and pharmacological approaches decreases stem cell capacity and sensitivity of clinical recurrent GBM (rGBM) isolates to TMZ in vitro. Network analysis uncovered miR-590-3p as a tumor suppressor that simultaneously inhibits multiple oncogenic nodes downstream of TGFBR2. We also developed novel biodegradable lipophilic poly(β-amino ester) nanoparticles (LiPBAEs) for in vivo microRNA (miRNAs) delivery. Following direct intra-tumoral infusion, these nanomiRs efficiently distribute through the tumors. Importantly, miR-590-3p nanomiRs inhibited the growth and extended survival of mice bearing orthotopic human rGBM xenografts, with an apparent 30% cure rate. These results show that miRNA-based targeted therapeutics provide new opportunities to treat rGBM and bypass the resistance to standard of care therapy.

A novel model of glioblastoma recurrence to identify therapeutic vulnerabilities

Glioblastoma remains incurable and recurs in all patients. Here we design and characterize a novel induced-recurrence model in which mice xenografted with primary patient-derived glioma initiating/stem cells (GIC) are treated with a therapeutic regimen closely recapitulating patient standard of care, followed by monitoring until tumours recur (induced recurrence patient-derived xenografts, IR-PDX). By tracking in vivo tumour growth, we confirm the patient specificity and initial efficacy of treatment prior to recurrence. Availability of longitudinally matched pairs of primary and recurrent GIC enabled patient-specific evaluation of the fidelity with which the model recapitulated phenotypes associated with the true recurrence. Through comprehensive multi-omic analyses, we show that the IR-PDX model recapitulates aspects of genomic, epigenetic, and transcriptional state heterogeneity upon recurrence in a patient-specific manner. The accuracy of the IR-PDX enabled both novel biological insights, including the positive association between glioblastoma recurrence and levels of ciliated neural stem cell-like tumour cells, and the identification of druggable patient-specific therapeutic vulnerabilities. This proof-of-concept study opens the possibility for prospective precision medicine approaches to identify target-drug candidates for treatment at glioblastoma recurrence.

Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial

This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.

Dissecting the immune landscape in pediatric high-grade glioma reveals cell state changes under therapeutic pressure

Pediatric high-grade gliomas (pHGGs) are among the most lethal childhood tumors. While therapeutic approaches were largely adapted from adult treatment regime, significant biological differences between pediatric and adult gliomas exist, which influence the immune microenvironment and may contribute to the limited response to current pHGG treatment strategies. We provide a comprehensive transcriptomic analysis of the pHGG immune landscape using single-cell RNA sequencing and spatial transcriptomics. We analyze matched malignant, myeloid, and T cells from patients with pediatric diffuse high-grade glioma (HGG) or high-grade ependymoma, examining immune microenvironment distinctions after chemo-/radiotherapy, immune checkpoint inhibition treatment, and by age. Our analysis reveals differences in the proportions of pediatric myeloid subpopulations compared to adult counterparts. Additionally, we observe significant shifts toward immune-suppressive environments following cancer therapy. Our findings offer valuable insights into potential immunotherapy targets and serve as a robust resource for understanding immune microenvironmental variations across HGG age groups and treatment regimens.

IDH status dictates oHSV mediated metabolic reprogramming affecting anti-tumor immunity

Identification of isocitrate dehydrogenase (IDH) mutations has uncovered the crucial role of metabolism in gliomagenesis. Oncolytic herpes virus (oHSV) initiates direct tumor debulking by tumor lysis and activates anti-tumor immunity, however, little is known about the role of glioma metabolism in determining oHSV efficacy. Here we identify that oHSV rewires central carbon metabolism increasing glucose utilization towards oxidative phosphorylation and shuttling glutamine towards reductive carboxylation in IDH wildtype glioma. The switch in metabolism results in increased lipid synthesis and cellular ROS. PKC induces ACSL4 in oHSV treated cells leading to lipid peroxidation and ferroptosis. Ferroptosis is critical to launch an anti-tumor immune response which is important for viral efficacy. Mutant IDH (IDHR132H) gliomas are incapable of reductive carboxylation and hence ferroptosis. Pharmacological blockade of IDHR132H induces ferroptosis and anti-tumor immunity. This study provides a rationale to use an IDHR132H inhibitor to treat high grade IDH-mutant glioma patients undergoing oHSV treatment.

Regulatory T Cell Mimicry by a Subset of Mesenchymal GBM Stem Cells Suppresses CD4 and CD8 Cells

Attempts to activate an anti-tumor immune response in glioblastoma (GBM) have been met with many challenges due to its inherently immunosuppressive tumor microenvironment. The degree and mechanisms by which molecularly and phenotypically diverse tumor-propagating glioma stem cells (GSCs) contribute to this state are poorly defined. In this study, our multifaceted approach combining bioinformatics analyses of clinical and experimental datasets, single-cell sequencing, and the molecular and pharmacologic manipulation of patient-derived cells identified GSCs expressing immunosuppressive effectors mimicking regulatory T cells (Tregs). We showed that this immunosuppressive Treg-like (ITL) GSC state is specific to the mesenchymal GSC subset and is associated with and driven specifically by TGFβ type II receptor (TGFBR2) in contrast to TGFBR1. Transgenic TGFBR2 expression in patient-derived GBM neurospheres promoted a mesenchymal transition and induced a six-gene ITL signature consisting of CD274 (PD-L1), NT5E (CD73), ENTPD1 (CD39), LGALS1 (galectin-1), PDCD1LG2 (PD-L2), and TGFB1. This TGFBR2-driven ITL signature was identified in clinical GBM specimens, patient-derived GSCs, and systemic mesenchymal malignancies. TGFBR2high GSCs inhibited CD4+ and CD8+ T cell viability and their capacity to kill GBM cells, effects reversed by pharmacologic and shRNA-based TGFBR2 inhibition. Collectively, our data identify an immunosuppressive GSC state that is TGFBR2-dependent and susceptible to TGFBR2-targeted therapeutics.

Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research

INTRODUCTION

Glioblastoma (GBM) progression and therapeutic resistance are significantly influenced by complex interactions between tumor cells and the brain microenvironment, particularly neurons. However, studying these interactions in physiologically relevant conditions has remained challenging due to limitations in existing model systems.

OBJECTIVES

Here, we present hGliCS (human glioma-cortical spheroid), a novel fully human brain tumor model that overcomes key limitations of current approaches by combining patient-derived GBM cells with mature human cortical neurons derived from induced pluripotent stem cells.

RESULTS

We demonstrate that GBM cells in hGliCS develop three critical hallmark features observed in patients: (i) formation of tumor microtubes enabling intercellular communication, (ii) establishment of neuron-glioma synapses, and (iii) development of an interconnected network with coordinated calcium signaling. Single-cell RNA sequencing reveals that tumor cells in hGliCS exhibit cellular heterogeneity and transcriptional profiles remarkably similar to those observed in mouse xenografts, including activation of key oncogenic pathways and neuronal-like features. Notably, while GBM cells showed substantial transcriptional adaptation to the neural environment, neurons maintained their core identity with only subtle alterations in glutamate signaling and structural gene expression. We validate hGliCS as a drug screening platform by demonstrating resistance patterns to standard chemotherapy and radiation similar to clinical observations. Furthermore, we show the model's utility in testing standard and novel therapeutic compounds targeting cell proliferation and tumor-specific neurobiological features, respectively.

CONCLUSION

This physiologically relevant human model system provides new opportunities for studying GBM biology and tumor-neuron interactions in a controlled environment. By bridging the gap between simplified in vitro systems and complex in vivo models, hGliCS represents a promising platform for therapeutic development and personalized medicine approaches in GBM treatment.

Programs, origins and immunomodulatory functions of myeloid cells in glioma

Gliomas are incurable malignancies notable for having an immunosuppressive microenvironment with abundant myeloid cells, the immunomodulatory phenotypes of which remain poorly defined1. Here we systematically investigate these phenotypes by integrating single-cell RNA sequencing, chromatin accessibility, spatial transcriptomics and glioma organoid explant systems. We discovered four immunomodulatory expression programs: microglial inflammatory and scavenger immunosuppressive programs, which are both unique to primary brain tumours, and systemic inflammatory and complement immunosuppressive programs, which are also expressed by non-brain tumours. The programs are not contingent on myeloid cell type, developmental origin or tumour mutational state, but instead are driven by microenvironmental cues, including tumour hypoxia, interleukin-1β, TGFβ and standard-of-care dexamethasone treatment. Their relative expression can predict immunotherapy response and overall survival. By associating the respective programs with mediating genomic elements, transcription factors and signalling pathways, we uncover strategies for manipulating myeloid-cell phenotypes. Our study provides a framework to understand immunomodulation by myeloid cells in glioma and a foundation for the development of more-effective immunotherapies.

Characterization of MRI findings by pTERT mutation status and the prognostic significance in GBM patients with recurrent lesions

AIM

To investigate the MRI characteristics of recurrent glioblastoma (GBM) in relation to telomerase reverse transcriptase-promoter (pTERT) mutation status and their prognostic significance.

MATERIALS AND METHODS

A retrospective analysis was conducted on 80 patients with primary IDH wild-type GBM. MRI features, including conventional and functional imaging, were compared between pTERT mutant and wild-type groups. Cox regression and receiver operating characteristic (ROC) analyses were performed to evaluate survival outcomes and predictive models.

RESULTS

Compared to patients with wild-type pTERT (n = 24), those with mutant pTERT (n = 56) were older (p = 0.008) and had shorter overall survival (OS) (p = 0.003). They also exhibited a higher incidence of massive-like enhancement (p = 0.036) and new subependymal enhancement (p = 0.034), lower relative apparent diffusion coefficient (rADC) (p = 0.006), and higher relative cerebral blood volume (rCBV) (p = 0.048) and choline/N-acetyl aspartate ratio (p = 0.033). Multivariate analysis identified new subependymal enhancement (HR = 2.348, p = 0.018) and massive-like enhancement (HR = 2.348, p = 0.018) as independent risk factors for shorter OS. The areas under the ROC curve (AUCs) for predicting poor OS using pTERT mutation status, conventional MRI, and combination models were 0.700, 0.695, and 0.764, respectively. Among the 31 patients with available functional MRI data, the AUCs for prediction using functional MRI, conventional MRI + pTERT mutation status, and the combination model were 0.783, 0.710, and 0.888, respectively.

CONCLUSIONS

MRI features, particularly subependymal and massive-like enhancements, along with pTERT mutation status, serve as valuable prognostic markers for survival outcomes in recurrent GBM patients. The combination model incorporating MRI characteristics and genetic status enhances predictive accuracy.

Molecular biology of the deadliest cancer - glioblastoma: what do we know?

Glioblastomas are the most prevalent primary brain tumors and are associated with a dramatically poor prognosis. Despite an intensive treatment approach, including maximal surgical tumor removal followed by radio- and chemotherapy, the median survival for glioblastoma patients has remained around 18 months for decades. Glioblastoma is distinguished by its highly complex mechanisms of immune evasion and pronounced heterogeneity. This variability is apparent both within the tumor itself, which can exhibit multiple phenotypes simultaneously, and in its surrounding microenvironment. Another key feature of glioblastoma is its "cold" microenvironment, characterized by robust immunosuppression. Recent advances in single-cell RNA sequencing have uncovered new promising insights, revealing previously unrecognized aspects of this tumor. In this review, we consolidate current knowledge on glioblastoma cells and its microenvironment, with an emphasis on their biological properties and unique patterns of molecular communication through signaling pathways. The evidence underscores the critical need for personalized poly-immunotherapy and other approaches to overcome the plasticity of glioblastoma stem cells. Analyzing the tumor microenvironment of individual patients using single-cell transcriptomics and implementing a customized immunotherapeutic strategy could potentially improve survival outcomes for those facing this formidable disease.

IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma

The glioblastoma tumor immune microenvironment (TIME) is an immunosuppressive barrier to therapy that encumbers glioblastoma responses to immune checkpoint inhibition (ICI). Immunosuppressive cytokines, pro-tumor myeloid cells, and exhausted T-cells are hallmarks of the glioblastoma TIME. Here we integrate spatial and single-cell analyses of patient-matched human glioblastoma samples before and after ICI with genetic, immunologic, single-cell, and pharmacologic studies in preclinical models to reveal that interleukin-6 (IL-6) inhibition reprograms the glioblastoma TIME to sensitize mouse glioblastoma to ICI and radiotherapy. Rare human glioblastoma patients who achieve clinical responses to ICI have lower pre-treatment IL-6 levels compared to glioblastomas who do not respond to ICI. Immune stimulatory gene therapy suppresses IL-6 tumor levels in preclinical murine models of glioblastoma. Furthermore, survival was longer in Il-6 knockout mice with orthotopic SB28 glioblastoma relative to wild-type mice. IL-6 blockade with a neutralizing antibody transiently sensitizes mouse glioblastoma to anti-PD-1 by increasing MHCII+ monocytes, CD103+ migratory dendritic cells (DCs), CD11b+ conventional DCs, and effector CD8+ T cells, and decreasing immunosuppressive Tregs. To translate these findings to a combination treatment strategy for recurrent glioblastoma patients, we show that IL-6 blockade plus ICI durably sensitizes mouse glioblastoma to high-dose radiotherapy.

Dynamic Tumor in Situ Fluid Circulating Tumor DNA Postsurgery Effectively Predicts Recurrence and Clinical Benefits for Glioblastomas

BACKGROUND AND OBJECTIVES

Glioblastoma (GBM) recurrence after surgery remains a significant clinical challenge because of limited early detection methods and effective molecular markers. This study investigates the potential of dynamic tumor in situ fluid circulating tumor DNA (TISF-ctDNA) as a tool for monitoring molecular residual disease and evaluating treatment efficacy in postsurgical patients with GBM.

METHODS

In this prospective cohort study, 75 resectable glioma patients were enrolled between October 2019 to June 2023. Primary tumor tissues and postsurgical TISF samples were collected, along with cranial imaging. TISF-ctDNA was identified through targeted next-generation sequencing, with positivity defined by the presence of one or more variants in the TISF matching those of the primary tumors or an increase of ≥10 single-nucleotide variants across consecutive assessments.

RESULTS

TISF-ctDNA positivity was identified in 62.2% of patients in the early postsurgical period, indicating a high prevalence of molecular residual disease. Patients with positive TISF-ctDNA showed a significantly higher risk of recurrence (hazard ratio 2.512, 95% CI 1.264-4.993, P = .0054). Conversion to TISF-ctDNA negativity post-treatment was associated with improved overall survival, highlighting its role in evaluating treatment response. Multivariate analysis revealed that TISF-ctDNA positivity was an independent predictor of progression-free survival during adjuvant therapy, with high predictive accuracy (sensitivity 86.2%, specificity 100%). Importantly, TISF-ctDNA positivity preceded imaging signs of recurrence by a median of 71 days. In this study, no significant impact of specific tumor markers in each subcohort (EGFR, TP53, PTEN, NF1) on progression-free survival or overall survival was observed.

CONCLUSION

TISF-ctDNA is a promising biomarker for monitoring GBM recurrence and evaluating clinical benefit. It provides insight into tumor genomic evolution and identifies patients who may benefit from adjuvant chemotherapy. TISF-ctDNA positivity is a robust prognostic indicator for patient outcomes and a marker for molecular recurrence after frontline therapy.

The molecular history of IDH-mutant astrocytomas without adjuvant treatment

Hypermutation and malignant transformation are potential complications arising from temozolomide treatment of IDH-mutant gliomas. However, the natural history of IDH-mutant low-grade gliomas without temozolomide treatment is actually under-studied. We retrieved retrospectively from our hospitals paired tumors from 19 patients with IDH-mutant, 1p19q non-codeleted Grade 2 astrocytomas where no interim adjuvant treatment with either temozolomide or radiotherapy was given between primary resections and first recurrences. Tissues from multiple recurrences were available from two patients and radiotherapy but not temozolomide was given before the last specimens were resected. We studied the natural molecular history of these low-grade IDH-mutant astrocytomas without pressure of temozolomide with DNA methylation profiling and copy number variation (CNV) analyses, targeted DNA sequencing, TERTp sequencing, FISH for ALT and selected biomarkers. Recurrences were mostly higher grades (15/19 patients) and characterized by new CNVs not present in the primary tumors (17/19 cases). Few novel mutations were identified in recurrences. Tumors from 17/19 (89.5%) patients showed either CDKN2A homozygous deletion, MYC or PDGFRA focal and non-focal gains at recurrences. There was no case of hypermutation. Phylogenetic trees constructed for tumors for the two patients with multiple recurrences suggested a lack of subclone development in their evolution when under no pressure from temozolomide. In summary, our studies demonstrated, in contrast to the phenomenon of temozolomide-induced hypermutation, IDH-mutant, 1p19q non-codeleted Grade 2 astrocytomas which had not been treated by temozolomide, acquired new CNVs at tumor recurrences. These findings improve our understanding of the molecular life history of IDH-mutant astrocytomas.

Circulating biomarkers in high-grade gliomas: current insights and future perspectives

PURPOSE

High-grade gliomas (HGG) represent a challenging subset of brain tumors characterized by aggressive nature and poor prognosis. Histopathology remains to be the standard for diagnosis, however, it is invasive, prone to sampling errors, and may not capture the full tumor heterogeneity and evolution over time. In recent years, there has been a growing interest in the potential utility of circulating biomarkers, obtained through minimally-invasive liquid biopsies, providing an opportunity for diagnosis, prognostication, monitoring treatment response and developing targeted therapies.

METHODS

We have reviewed the literature on circulating biomarkers for HGG, including circulating tumor cells (CTCs), circulating tumor-derived exosomes/extracellular vesicles (ctEVs), circulating tumor-derived DNA (ctDNA), circulating tumor-derived miRNA (ctmiRNA), and circulating tumor-derived proteins.

RESULTS

CTCs provide real-time information about tumor characteristics for molecular profiling and monitoring treatment response, yet their low numbers in circulation makes detection challenging. ctEVs carry a range of biomolecules and are easily detectable. However, they are not exclusively released from tumor cells and heterogeneity in their content requires standardized isolation and analysis methods. ctDNA is another promising biomarker with its levels correlating with the disease stage. However, its low concentration in blood requires highly sensitive techniques for identification and differentiation from normal cell-free DNA. ctmiRNA and tumor-derived proteins show promise but are limited by their susceptibility to dilution and lack of specificity in current technology.

CONCLUSION

This review highlights the transformative potential of circulating biomarkers in the management of HGG, with implications for improving patient outcomes, optimizing treatment strategies, and advancing precision oncology in neuro-oncology practice.

Genetically Engineered Brain Organoids Recapitulate Spatial and Developmental States of Glioblastoma Progression

Glioblastoma (GBM) is an aggressive form of brain cancer that is highly resistant to therapy due to significant intra-tumoral heterogeneity. The lack of robust in vitro models to study early tumor progression has hindered the development of effective therapies. Here, this study develops engineered GBM organoids (eGBOs) harboring GBM subtype-specific oncogenic mutations to investigate the underlying transcriptional regulation of tumor progression. Single-cell and spatial transcriptomic analyses revealed that these mutations disrupt normal neurodevelopment gene regulatory networks resulting in changes in cellular composition and spatial organization. Upon xenotransplantation into immunodeficient mice, eGBOs form tumors that recapitulate the transcriptional and spatial landscape of human GBM samples. Integrative single-cell trajectory analysis of both eGBO-derived tumor cells and patient GBM samples reveal the dynamic gene expression changes in developmental cell states underlying tumor progression. This analysis of eGBOs provides an important validation of engineered cancer organoid models and demonstrates their utility as a model of GBM tumorigenesis for future preclinical development of therapeutics.

GNE-317 Reverses MSN-Mediated Proneural-to-Mesenchymal Transition and Suppresses Chemoradiotherapy Resistance in Glioblastoma via PI3K/mTOR

Glioblastoma (GBM) resistance to chemoradiotherapy is a major factor contributing to poor treatment outcomes. This resistance markedly affects the effectiveness of surgery combined with chemoradiotherapy and leads to post-surgical tumor recurrence. Therefore, exploring the mechanisms underlying chemoradiotherapy resistance in GBM is crucial for understanding its progression and improving therapeutic options. This study found that moesin (MSN) acts as a key promotor of chemoradiotherapy resistance in glioma stem cells (GSCs), enhancing their proliferation and stemness maintenance. Mechanistically, MSN activates the downstream PI3K/mTOR signaling pathway, driving the proneural-to-mesenchymal transition (PMT) in GSCs. This process enhances the repair of DNA damage caused by radiotherapy (RT) and temozolomide (TMZ), thereby increasing the resistance of GSCs to chemoradiotherapy. Additionally, GNE-317, a small molecule drug capable of crossing the blood-brain barrier, specifically inhibits MSN and suppresses the activation of downstream PI3K/mTOR signaling. Importantly, the combination of GNE-317 with RT and TMZ exhibits a strong synergistic effect both in vivo and in vitro, achieving better efficacy compared to the traditional combination of RT and TMZ. This study not only advances understanding of the mechanisms underlying chemoradiotherapy resistance in GBM but also provides a promising new approach for enhancing treatment outcomes.

Spatial omics shed light on the tumour organisation of glioblastoma

The glioblastoma tumour microenvironment is characterised by immense heterogeneity, with malignant and non-malignant cells that interact in a complex ecosystem. Emerging evidence suggests that the tumour microenvironment is key in facilitating rapid proliferation, invasion, migration and cancer cell survival, crucial for treatment resistance. Spatial omics technologies have enabled the molecular characterisation of regions or individual cells within their spatial context, providing previously unattainable insights into the complex organisation of the glioblastoma tumour microenvironment. Understanding this organisation is crucial for the development of new therapeutics and novel diagnostic tools that guide patient care. This review explores spatial omics technologies and how they have contributed to the development of a model outlining the architecture of the glioblastoma tumour microenvironment.

Dynamic Monitoring of Circulating Tumor DNA to Predict the Risk of Non In Situ Recurrence of Postoperative Glioma: A Prospective Cohort Study

BACKGROUND

Glioma recurrence can be divided into in situ recurrence and non-in situ recurrence, and the mutation evolution of gliomas with different recurrence patterns is still unknown. We used sequential sequencing of circulating tumor DNA (ctDNA) to compare the somatic mutation profile and clonal evolution of gliomas with different recurrence patterns. To investigate the value of ctDNA in predicting early postoperative tumor recurrence and guiding prognosis stratification in patients with glioma.

METHODS

We prospectively recruited 92 patients with near-total resection of gliomas from our center. Two hundred and thirty-four postoperative tissue and Tumor In Situ Fluid (TISF) samples from 69 eligible patients were included in ctDNA analysis.

RESULTS

Among the 69 patients, 37 glioblastoma (GBM) patients experienced recurrence, and the median progression-free survival (mPFS) was not significantly different between the situ recurrence group and the non-in situ recurrence group (8.6 vs. 6.1 months). The ctDNA of recurrent tissue and TISF were significantly consistent. Before and after initial treatment, TISF-ctDNA mutant allele fraction (MAF), subclonal mutation, and alterations in related pathways (lysine degradation and PI3K pathway) were negatively correlated with treatment response and PFS. Among recurrent GBM patients, EGFR mutations were the most common. Mutations related to the RTK-RAS pathway (NF1) were most common in patients with situ recurrent GBM, while mutations in the MUC family and TP53 pathway (MUC16, CHEK2) were prevalent and continuously increased in patients with non-in situ recurrent GBM.

CONCLUSIONS

In glioma patients undergoing primary surgery, dynamic monitoring of ctDNA and genotyping can be used for early risk stratification, efficacy monitoring, and early recurrence detection, and provide a basis for clinical research to evaluate early therapeutic intervention.

A pathogenic subpopulation of human glioma associated macrophages linked to glioma progression

Malignant gliomas follow two distinct natural histories: de novo high grade tumors such as glioblastoma, or lower grade tumors with a propensity to transform into high grade disease. Despite differences in tumor genotype, both entities converge on a common histologically aggressive phenotype, and the basis for this progression is unknown. Glioma associated macrophages (GAM) have been implicated in this process, however GAMs are ontologically and transcriptionally diverse, rendering isolation of pathogenic subpopulations challenging. Since macrophage contextual gene programs are orchestrated by transcription factors acting on cis -acting promoters and enhancers in gene regulatory networks (GRN), we hypothesized that functional populations of GAMs can be resolved through GRN inference. Here we show via parallel single cell RNA and ATAC sequencing that a subpopulation of human GAMs can be defined by a GRN centered around the Activator Protein-1 transcription factor FOSL2 preferentially enriched in high grade tumors. Using this GRN we nominate ANXA1 and HMOX1 as surrogate cell surface markers for activation, thus permitting prospective isolation and functional validation in human GAMs. These cells, termed malignancy associated GAMs (mGAMs) are pro-invasive, pro-angiogenic, pro-proliferative, possess intact antigen presentation but skew T-cells towards a CD4+FOXP3+ phenotype under hypoxia. Ontologically, mGAMs share somatic mitochondrial mutations with peripheral blood monocytes, and their presence correlates with high grade disease irrespective of underlying tumor mutation status. Furthermore, spatio-temporally mGAMs occupy distinct metabolic niches; mGAMs directly induce proliferation and mesenchymal transition of low grade glioma cells and accelerate tumor growth in vivo upon co-culture. Finally mGAMs are preferentially enriched in patients with newly transformed regions in human gliomas, supporting the view that mGAMs play a pivotal role in glioma progression and may represent a plausible therapeutic target in human high-grade glioma.

An integrated perspective on single-cell and spatial transcriptomic signatures in high-grade gliomas

High-grade gliomas (HGG) are incurable brain malignancies in children and adults. Breakthrough advances in transcriptomic technologies unveiled the intricate diversity of cellular states and their spatial organization within HGGs. We qualitatively integrated 55 neoplastic transcriptomic signatures described in 17 single-cell and spatial RNA sequencing-based studies. Our review delineates a spectrum of cellular states, represented by the expression of specific genes, which can be conceptualized along a "reactive-developmental programs" axis. Additionally, we discussed the potential cues influencing these cellular states, including how spatial organization may impact transcriptomic dynamics. Leveraging these insightful discoveries, we discussed a novel, evolutive way to integrate the different transcriptomic signatures in two or three dimensions, incorporating developmental states, their proliferative capacity, and their possible transition towards reactive states. This integrated analysis illuminates the diverse cellular landscape of HGGs and provides a valuable resource for further elucidation of malignant mechanisms, and for the design of therapeutic endeavors.

EZH2 functional dichotomy in reactive oxygen species-stratified glioblastoma

BACKGROUND

Enhancer of zeste homolog 2 (EZH2), well known for its canonical methyltransferase activity in transcriptional repression in many cancers including glioblastoma (GBM), has an understudied noncanonical function critical for sustained tumor growth. Recent GBM consortial efforts reveal complex molecular heterogeneity for which therapeutic vulnerabilities correlated with subtype stratification remain relatively unexplored. Current enzymatic EZH2 inhibitors (EZH2inh) targeting its canonical su(var)3-9, enhancer-of-zeste and trithorax domain show limited efficacy and lack durable response, suggesting that underlying differences in the noncanonical pathway may yield new knowledge. Here, we unveiled dual roles of the EZH2 CXC domain in therapeutically distinct, reactive oxygen species (ROS)-stratified tumors.

METHODS

We analyzed differentially expressed genes between ROS classes by examining cis-regulatory elements as well as clustering of activities and pathways to identify EZH2 as the key mediator in ROS-stratified cohorts. Pull-down assays and CRISPR knockout of EZH2 domains were used to dissect the distinct functions of EZH2 in ROS-stratified GBM cells. The efficacy of NF-κB-inducing kinase inhibitor (NIKinh) and standard-of-care temozolomide was evaluated using orthotopic patient-derived GBM xenografts.

RESULTS

In ROS(+) tumors, CXC-mediated co-interaction with RelB drives constitutive activation of noncanonical NF-κB2 signaling, sustaining the ROS(+) chemoresistant phenotype. In contrast, in ROS(-) subtypes, Polycomb Repressive Complex 2 methyltransferase activity represses canonical NF-κB. Addressing the lack of EZH2inh targeting its nonmethyltransferase roles, we utilized a brain-penetrant NIKinh that disrupts EZH2-RelB binding, consequently prolonging survival in orthotopic ROS(+)-implanted mice.

CONCLUSIONS

Our findings highlight the functional dichotomy of the EZH2 CXC domain in governing ROS-stratified therapeutic resistance, thereby advocating for the development of therapeutic approaches targeting its noncanonical activities and underscoring the significance of patient stratification methodologies.

Sex differences in the molecular profile of adult diffuse glioma are shaped by IDH status and tumor microenvironment

BACKGROUND

Sex differences in adult diffuse glioma (ADG) are well established clinically, yet the underlying molecular mechanisms remain inadequately understood. Here, we aim to reveal molecular features and cellular compositions unique to each sex in ADG to comprehend the role of sex in disease etiology.

METHODS

We quantified sex differences in the transcriptome of ADG using multiple independent glioma patient datasets. Next, we delved into the single-cell landscape to examine sex differences in gene expression and cellular composition. To explore how sex influences disease progression, we analyzed paired samples from primary and recurrent ADG cases, aiming to identify sex-specific differences in molecular and cellular features.

RESULTS

Our analysis revealed that mutations in isocitrate dehydrogenase (IDH) genes and the tumor microenvironment emerged as primary influencers of sex-differential molecular enrichments. In IDHwt tumors, genes in the neuronal signaling pathway are found to be enriched in male tumors, while genes in hypoxia and inflammatory response pathways are enriched in female tumors. This pattern was reversed in IDHmut gliomas. We hypothesized that these distinctions could be attributed to heterogeneous cellular composition between sexes. Using single-cell data, we observed distinctive patterns of sex differences in cell states, cell composition, and cell-cell interaction in IDHwt and IDHmut tumors separately. Further, by comparing molecular changes in paired primary and recurrent ADG samples, we identified sex-specific differences in molecular characteristics and cellular compositions of recurrent tumors.

CONCLUSIONS

Our results provide a comprehensive multilevel characterization of sex differences in ADG; such findings provide novel insights into glioma disease progression in each sex.

GBMPurity: A Machine Learning Tool for Estimating Glioblastoma Tumour Purity from Bulk RNA-seq Data

BACKGROUND

Glioblastoma (GBM) presents a significant clinical challenge due to its aggressive nature and extensive heterogeneity. Tumour purity, the proportion of malignant cells within a tumour, is an important covariate for understanding the disease, having direct clinical relevance or obscuring signal of the malignant portion in molecular analyses of bulk samples. However, current methods for estimating tumour purity are non-specific and technically demanding. Therefore, we aimed to build a reliable and accessible purity estimator for GBM.

METHODS

We developed GBMPurity, a deep-learning model specifically designed to estimate the purity of IDH-wildtype primary GBM from bulk RNA-seq data. The model was trained using simulated pseudobulk tumours of known purity from labelled single-cell data acquired from the GBmap resource. The performance of GBMPurity was evaluated and compared to several existing tools using independent datasets.

RESULTS

GBMPurity outperformed existing tools, achieving a mean absolute error of 0.15 and a concordance correlation coefficient of 0.88 on validation datasets. We demonstrate the utility of GBMPurity through inference on bulk RNA-seq samples and observe reduced purity of the Proneural molecular subtype relative to the Classical, attributed to the increased presence of healthy brain cells.

CONCLUSIONS

GBMPurity provides a reliable and accessible tool for estimating tumour purity from bulk RNA-seq data, enhancing the interpretation of bulk RNA-seq data and offering valuable insights into GBM biology. To facilitate the use of this model by the wider research community, GBMPurity is available as a web-based tool at: https://gbmdeconvoluter.leeds.ac.uk/.

Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing

Glioblastomas are invasive brain tumors with high therapeutic resistance. Neuron-to-glioma synapses have been shown to promote glioblastoma progression. However, a characterization of tumor-connected neurons has been hampered by a lack of technologies. Here, we adapted retrograde tracing using rabies viruses to investigate and manipulate neuron-tumor networks. Glioblastoma rapidly integrated into neural circuits across the brain, engaging in widespread functional communication, with cholinergic neurons driving glioblastoma invasion. We uncovered patient-specific and tumor-cell-state-dependent differences in synaptogenic gene expression associated with neuron-tumor connectivity and subsequent invasiveness. Importantly, radiotherapy enhanced neuron-tumor connectivity by increased neuronal activity. In turn, simultaneous neuronal activity inhibition and radiotherapy showed increased therapeutic effects, indicative of a role for neuron-to-glioma synapses in contributing to therapeutic resistance. Lastly, rabies-mediated genetic ablation of tumor-connected neurons halted glioblastoma progression, offering a viral strategy to tackle glioblastoma. Together, this study provides a framework to comprehensively characterize neuron-tumor networks and target glioblastoma.

Potassium ion channel modulation at cancer-neural interface enhances neuronal excitability in epileptogenic glioblastoma multiforme

The central nervous system (CNS) is increasingly recognized as a critical modulator in the oncogenesis of glioblastoma multiforme (GBM), with interactions between cancer and local neuronal circuits frequently leading to epilepsy; however, the relative contributions of these factors remain unclear. Here, we report a coordinated intratumor shift among distinct cancer subtypes within progenitor-like families of epileptic GBM patients, revealing an accumulation of oligodendrocyte progenitor (OPC)-like subpopulations at the cancer-neuron interface along with heightened electrical signaling activity in the surrounding neuronal networks. The OPC-like cells associated with epilepsy express KCND2, which encodes the voltage-gated K+ channel KV4.2, enhancing neuronal excitability via accumulation of extracellular K+, as demonstrated in patient-derived ex vivo slices, xenografting models, and engineering organoids. Together, we uncovered the essential local circuitry, cellular components, and molecular mechanisms facilitating cancer-neuron interaction at peritumor borders. KCND2 plays a crucial role in mediating nervous system-cancer electrical communication, suggesting potential targets for intervention.

Mechanism analysis and targeted therapy of IDH gene mutation in glioma

Isocitrate dehydrogenase (IDH) is a pivotal enzyme responsible for catalyzing the oxidative decarboxylation of isocitrate into α-ketoglutarate (α-KG). This enzyme serves as a crucial regulator in the tricarboxylic acid cycle (TCA cycle), acting as a rate-limiting step. Its role extends beyond mere metabolic function, influencing cellular homeostasis and overall cell function. In the past decade, prominent research in cancer genetics has revealed that genes responsible for encoding isocitrate dehydrogenase are commonly mutated across various human malignancies. Significant research in the field has shown that these mutations are commonly found in diseases like glioma, acute myeloid leukemia (AML), cholangiocarcinoma (CCA), chondrosarcoma, and thyroid cancer (TC). As research on IDH progresses, deeper insights into the biological effects of IDH mutations have been gained, unveiling their potential role in tumorigenesis. In addition, IDH mutants' unique activities creates new pathways in tumor metabolism, gene rearrangement, and therapeutic resistance. Currently, innovative molecular targeting strategies for genes bearing mutations in IDH have been devised to enhance the therapeutic efficacy against cancers harboring IDH mutations. These methods represent a promising avenue for improving treatment outcomes in IDH-mutated malignancies. This article mainly summarizes the related research on glioma caused by IDH mutation, and focuses on the biological characteristics and transformation of IDH.

Cancer Neuroscience of Brain Tumors: From Multicellular Networks to Neuroscience-Instructed Cancer Therapies

Deepening our understanding of neuro-cancer interactions can innovate brain tumor treatment. This mini review unfolds the most relevant and recent insights into the neural mechanisms contributing to brain tumor initiation, progression, and resistance, including synaptic connections between neurons and cancer cells, paracrine neuro-cancer signaling, and cancer cells' intrinsic neural properties. We explain the basic and clinical-translational relevance of these findings, identify unresolved questions and particularly interesting future research avenues, such as central nervous system neuro-immunooncology, and discuss the potential transferability to extracranial cancers. Lastly, we conceptualize ways toward clinical trials and develop a roadmap toward neuroscience-instructed brain tumor therapies. Significance: Neural influences on brain tumors drive their growth and invasion. Herein, we develop a roadmap to use these fundamentally new insights into brain tumor biology for improved outcomes.

Longitudinal multimodal profiling of IDH-wildtype glioblastoma reveals the molecular evolution and cellular phenotypes underlying prognostically different treatment responses

BACKGROUND

Despite recent advances in the biology of IDH-wildtype glioblastoma, it remains a devastating disease with median survival of less than 2 years. However, the molecular underpinnings of the heterogeneous response to the current standard-of-care treatment regimen consisting of maximal safe resection, adjuvant radiation, and chemotherapy with temozolomide remain unknown.

METHODS

Comprehensive histopathologic, genomic, and epigenomic evaluation of paired initial and recurrent glioblastoma specimens from 106 patients was performed to investigate the molecular evolution and cellular phenotypes underlying differential treatment responses.

RESULTS

While TERT promoter mutation and CDKN2A homozygous deletion were early events during gliomagenesis shared by initial and recurrent tumors, most other recurrent genetic alterations (eg, EGFR, PTEN, and NF1) were commonly private to initial or recurrent tumors indicating acquisition later during clonal evolution. Furthermore, glioblastomas exhibited heterogeneous epigenomic evolution with subsets becoming more globally hypermethylated, hypomethylated, or remaining stable. Glioblastoma that underwent sarcomatous transformation had shorter interval to recurrence and were significantly enriched in NF1, TP53, and RB1 alterations and the mesenchymal epigenetic class. Patients who developed somatic hypermutation following temozolomide treatment had significantly longer interval to disease recurrence and prolonged overall survival, and increased methylation at 4 specific CpG sites in the promoter region of MGMT was significantly associated with this development of hypermutation. Finally, an epigenomic evolution signature incorporating change in DNA methylation levels across 347 critical CpG sites was developed that significantly correlated with clinical outcomes.

CONCLUSIONS

Glioblastoma undergoes heterogeneous genetic, epigenetic, and cellular evolution that underlies prognostically different treatment responses.

TGFBR2 High mesenchymal glioma stem cells phenocopy regulatory T cells to suppress CD4+ and CD8+ T cell function

Attempts to activate an anti-tumor immune response in glioblastoma (GBM) have been met with many challenges due to its inherently immunosuppressive tumor microenvironment. The degree and mechanisms by which molecularly and phenotypically diverse tumor-propagating glioma stem cells (GSCs) contribute to this state are poorly defined. In this study, our multifaceted approach combining bioinformatics analyses of clinical and experimental datasets, single-cell sequencing, and molecular and pharmacologic manipulation of patient-derived cells identified GSCs expressing immunosuppressive effectors mimicking regulatory T cells (Tregs). We show that this I mmunosuppressive T reg- L ike (ITL) GSC state is specific to the mesenchymal GSC subset and is associated with and driven specifically by TGF-β type II receptor (TGFBR2) in contrast to TGFBR1. Transgenic TGFBR2 expression in patient-derived GBM neurospheres promoted a mesenchymal transition and induced a 6-gene ITL signature consisting of CD274 (PD-L1), NT5E (CD73), ENTPD1 (CD39), LGALS1 (galectin-1), PDCD1LG2 (PD-L2), and TGFB1. This TGFBR2-driven ITL signature was identified in clinical GBM specimens, patient-derived GSCs and systemic mesenchymal malignancies. TGFBR2 High GSCs inhibited CD4+ and CD8+ T cell viability and their capacity to kill GBM cells, effects reversed by pharmacologic and shRNA-based TGFBR2 inhibition. Collectively, our data identify an immunosuppressive GSC state that is TGFBR2-dependent and susceptible to TGFBR2-targeted therapeutics.

Comprehensive Analysis Identifies THEMIS2 as a Potential Prognostic and Immunological Biomarker in Glioblastoma

Glioblastoma (GBM) is a highly aggressive brain tumor characterized by its ability to evade the immune system, hindering the efficacy of current immunotherapies. Recent research has highlighted the important role of immunosuppressive macrophages in the tumor microenvironment (TME) in driving this immune evasion. In this study, we are the first to identify THEMIS2 as a key regulator of tumor-associated macrophage (TAM)-mediated immunosuppression in GBM. We found that a high THEMIS2 expression is associated with poor patient outcomes and increased infiltration of immune cells, particularly macrophages. Functional analyses revealed THEMIS2's critical involvement in immune-related pathways, including immune response activation, mononuclear cell differentiation, and the positive regulation of cytokine production. Additionally, single-cell RNA sequencing data demonstrated that macrophages with a high THEMIS2 expression were associated with increased phagocytosis, immune suppression, and enhanced tumor growth. These findings suggest that THEMIS2 could serve as both a prognostic marker and a therapeutic target for enhancing anti-tumor immunity in GBM.

Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas

Isocitrate dehydrogenase (IDH) mutants define a class of gliomas that are initially slow-growing but inevitably progress to fatal disease. To characterize their malignant cell hierarchy, we profiled chromatin accessibility and gene expression across single cells from low-grade and high-grade IDH-mutant gliomas and ascertained their developmental states through a comparison to normal brain cells. We provide evidence that these tumors are initially fueled by slow-cycling oligodendrocyte progenitor cell-like cells. During progression, a more proliferative neural progenitor cell-like population expands, potentially through partial reprogramming of 'permissive' chromatin in progenitors. This transition is accompanied by a switch from methylation-based drivers to genetic ones. In low-grade IDH-mutant tumors or organoids, DNA hypermethylation appears to suppress interferon (IFN) signaling, which is induced by IDH or DNA methyltransferase 1 inhibitors. High-grade tumors frequently lose this hypermethylation and instead acquire genetic alterations that disrupt IFN and other tumor-suppressive programs. Our findings explain how these slow-growing tumors may progress to lethal malignancies and have implications for therapies that target their epigenetic underpinnings.

Multidimensional analysis of matched primary and recurrent glioblastoma identifies contributors to tumor recurrence influencing time to relapse

Glioblastoma (GBM) is a lethal brain tumor without effective treatment options. This study aimed to characterize longitudinal tumor changes in order to find potentially actionable targets to prevent GBM relapse. We extracted RNA and proteins from fresh frozen tumor samples from patient-matched IDHwt WHO grade 4 primary (pGBM) and recurrent (rGBM) tumors for transcriptomics and proteomics analysis. A tissue microarray containing paired tumor samples was processed for spatial transcriptomics analysis. Differentially expressed genes and proteins between pGBM and rGBM were involved in synapse development and myelination. By categorizing patients into short (STTR) and long (LTTR) time-to-lapse, we identified genes/proteins whose expression levels positively or negatively correlated with TTR. In rGBM, expressions of Fcγ receptors (FCGRs) and complement system genes were negatively correlated with TTR, whereas expression of genes involved in DNA methylation was positively correlated with TTR. Spatial transcriptomics of the tumor cells showed enrichment of oligodendrocytes in rGBM. Besides, we observed changes in the myeloid compartment such as a switch from quiescent to activated microglia and an enrichment in B and T cells in rGBM with STTR. Our results uncover a role for activated microglia/macrophages in GBM recurrence and suggest that interfering with these cells may hinder GBM relapse.

Longitudinal profiling of IDH-mutant astrocytomas reveals acquired RAS-MAPK pathway mutations associated with inferior survival

Background

Isocitrate dehydrogenase (IDH)-mutant astrocytomas represent the most frequent primary intraparenchymal brain tumor in young adults, which typically arise as low-grade neoplasms that often progress and transform to higher grade despite current therapeutic approaches. However, the genetic alterations underlying high-grade transformation and disease progression of IDH-mutant astrocytomas remain inadequately defined.

Methods

Genomic profiling was performed on 205 IDH-mutant astrocytomas from 172 patients from both initial treatment-naive and recurrent post-treatment tumor specimens. Molecular findings were integrated with clinical outcomes and pathologic features to define the associations of novel genetic alterations in the RAS-MAPK signaling pathway.

Results

Likely oncogenic alterations within the RAS-MAPK mitogenic signaling pathway were identified in 13% of IDH-mutant astrocytomas, which involved the KRAS, NRAS, BRAF, NF1, SPRED1, and LZTR1 genes. These included focal amplifications and known activating mutations in oncogenic components (e.g. KRAS, BRAF), as well as deletions and truncating mutations in negative regulatory components (e.g. NF1, SPRED1). These RAS-MAPK pathway alterations were enriched in recurrent tumors and occurred nearly always in high-grade tumors, often co-occurring with CDKN2A homozygous deletion. Patients whose IDH-mutant astrocytomas harbored these oncogenic RAS-MAPK pathway alterations had inferior survival compared to those with RAS-MAPK wild-type tumors.

Conclusions

These findings highlight novel genetic perturbations in the RAS-MAPK pathway as a likely mechanism contributing to the high-grade transformation and treatment resistance of IDH-mutant astrocytomas that may be a potential therapeutic target for affected patients and used for future risk stratification.

Breed-Associated Differences in Differential Gene Expression Following Immunotherapy-Based Treatment of Canine High-Grade Glioma

Canine high-grade glioma (HGG) is among the deadliest and most treatment-resistant forms of canine cancer. Successful, widespread treatment is challenged by heterogeneity in tumor cells and the tumor microenvironment and tumor evolution following treatment. Immunotherapy is theoretically a strong novel therapy, since HGG-generated immunosuppression is a substantial malignancy mechanism. Immunotherapy has improved survival times overall, but has been associated with extremely poor outcomes in French bulldogs. Given this breed-specific observation, we hypothesized that within the French bulldog breed, there are key transcriptomic differences when compared to other breeds, and that their tumors change differently in response to immunotherapy. Using bulk RNA sequencing, French bulldog tumors were confirmed to differ substantially from boxer and Boston terrier tumors, with only 15.9% overlap in significant differentially expressed genes (DEGs). In upregulated DEGs, the magnitude of changes in expression post-treatment compared to pre-treatment was markedly greater in French bulldogs. Gene set enrichment analysis confirmed that following treatment, French bulldog tumors showed enrichment of key immune-associated pathways previously correlated with poor prognosis. Overall, this study confirmed that French bulldog HGG transcriptomes differ from boxer and Boston terrier transcriptomes, further refining description of the canine glioma transcriptome and providing important information to guide novel therapy development, both for specific dog breeds and for possible correlative variants of human glioblastoma.

Radiomic Consensus Clustering in Glioblastoma and Association with Gene Expression Profiles

BACKGROUND/OBJECTIVES

Glioblastoma (GBM) is the most common malignant primary central nervous system tumor with extremely poor prognosis and survival outcomes. Non-invasive methods like radiomic feature extraction, which assess sub-visual imaging features, provide a potentially powerful tool for distinguishing molecular profiles across groups of patients with GBM. Using consensus clustering of MRI-based radiomic features, this study aims to investigate differential gene expression profiles based on radiomic clusters.

METHODS

Patients from the TCGA and CPTAC datasets (n = 114) were included in this study. Radiomic features including T1, T1 with contrast, T2, and FLAIR MRI sequences were extracted using PyRadiomics. Selected radiomic features were then clustered using ConsensusClusterPlus (k-means base algorithm and Euclidean distance), which iteratively subsamples and clusters 80% of the data to identify stable clusters by calculating the frequency in which each patient is a member of a cluster across iterations. Gene expression data (available for n = 69 patients) was analyzed using differential gene expression (DEG) and gene set enrichment (GSEA) approaches, after batch correction using ComBat-seq.

RESULTS

Three distinct clusters were identified based on the relative consensus matrix and cumulative distribution plots (Cluster 1, n = 25; Cluster 2, n = 46; Cluster 3, n = 43). No significant differences in patient demographic characteristics, MGMT methylation status, tumor location, or overall survival were identified across clusters. Differentially expressed genes were identified in Cluster 1, which have been previously associated with GBM prognosis, recurrence, and treatment sensitivity. GSEA of Cluster 1 showed an enrichment of genes upregulated for immune-related and DNA metabolism pathways and genes downregulated in pathways associated with protein and histone deacetylation. Clusters 2 and 3 exhibited fewer DEGs which failed to reach significance after multiple testing corrections.

CONCLUSIONS

Consensus clustering of radiomic features revealed unique gene expression profiles in the GBM cohort which likely represent subtle differences in tumor biology and radiosensitivity that are not visually discernible, underscoring the potential of radiomics to serve as a non-invasive alternative for identifying GBM molecular heterogeneity. Further investigation is still required to validate these findings and their clinical implications.

Genetic and microenvironmental evolution of colorectal liver metastases under chemotherapy

Drug resistance limits the efficacy of chemotherapy for colorectal cancer liver metastasis (CRLM). However, the evolution of CRLM during drug treatment remains poorly elucidated. Multi-omics and treatment response data from 115 samples of 49 patients with CRLM undergoing bevacizumab (BVZ)-based chemotherapy show little difference in genomic alterations in 92% of cases, while remarkable differences are observed at the transcriptomic level. By decoupling intrinsic and acquired resistance, we find that hepatocyte and myeloid cell infiltration contribute to 38.5% and 23.1% of acquired resistance, respectively. Importantly, SMAD4 mutations and chr20q copy-number gain are associated with intrinsic chemoresistance. Gene interference experiments suggest that SMAD4R361H/C mutations confer BVZ and 5-fluorouracil (5-FU) resistance through STAT3 signaling. Notably, supplementing BVZ and 5-FU with the STAT3 inhibitor GB201 restores therapeutic efficacy in SMAD4R361H/C cancer cells. Our study uncovers the evolutionary dynamics of CRLM and its microenvironment during treatment and offers strategies to overcome drug resistance.

Comprehensive Transcriptomic Analysis Reveals Cell-Type-Specific Roles of Human Odorant Receptors in Glioblastoma and the Tumor Microenvironment

Odorant receptors (ORs), which constitute approximately 50% of all human G protein-coupled receptors, are increasingly recognized for their diverse roles beyond odor perception, including functions in various pathological conditions like brain diseases and cancers. However, the roles of ORs in glioblastoma (GBM), the most aggressive primary brain tumor with a median survival of only 15 months, remain largely unexplored. Here, we performed an integrated transcriptomic analysis combining The Cancer Genome Atlas RNA-seq and single-cell RNA sequencing data from GBM patients to uncover cell-type-specific roles of ORs within the tumor and its microenvironment. Our findings reveal that ORs display distinct expression patterns, with OR51E1 enriched in pericytes linked to vascular remodeling and angiogenesis, OR2B11 associated with tumor-associated macrophages supporting immunosuppressive phenotypes, and OR2L13 correlated with synaptic activity in recurrent tumors, potentially mediating treatment-induced neuronal adaptations. These results highlight ORs as potential therapeutic targets, offering new insights into their regulatory roles in GBM progression, immune modulation, and treatment resistance.

Decoding ferroptosis: transforming orthopedic disease management

As a mechanism of cell death, ferroptosis has gained popularity since 2012. The process is distinguished by iron toxicity and phospholipid accumulation, in contrast to autophagy, apoptosis, and other cell death mechanisms. It is implicated in the advancement of multiple diseases across the body. Researchers currently know that osteosarcoma, osteoporosis, and other orthopedic disorders are caused by NRF2, GPX4, and other ferroptosis star proteins. The effective relief of osteoarthritis symptoms from deterioration has been confirmed by clinical treatment with multiple ferroptosis inhibitors. At the same time, it should be reminded that the mechanisms involved in ferroptosis that regulate orthopedic diseases are not currently understood. In this manuscript, we present the discovery process of ferroptosis, the mechanisms involved in ferroptosis, and the role of ferroptosis in a variety of orthopedic diseases. We expect that this manuscript can provide a new perspective on clinical diagnosis and treatment of related diseases.

Immune landscape of isocitrate dehydrogenase-stratified primary and recurrent human gliomas

BACKGROUND

Human gliomas are classified using isocitrate dehydrogenase (IDH) status as a prognosticator; however, the influence of genetic differences and treatment effects on ensuing immunity remains unclear.

METHODS

In this study, we used sequential single-cell transcriptomics on 144 678 and spectral cytometry on over 2 million immune cells encompassing 48 human gliomas to decipher their immune landscape.

RESULTS

We identified 22 distinct immune cell types that contribute to glioma immunity. Specifically, brain-resident microglia (MG) were reduced with a concomitant increase in CD8+ T lymphocytes during glioma recurrence independent of IDH status. In contrast, IDH-wild type-associated patterns, such as an abundance of antigen-presenting cell-like MG and cytotoxic CD8+ T cells, were observed. Beyond elucidating the differences in IDH, relapse, and treatment-associated immunity, we discovered novel inflammatory MG subpopulations expressing granulysin, a cytotoxic peptide that is otherwise expressed in lymphocytes only. Furthermore, we provide a robust genomic framework for defining macrophage polarization beyond M1/M2 paradigm and reference signatures of glioma-specific tumor immune microenvironment (termed GlioTIME-36) for deconvoluting transcriptomic datasets.

CONCLUSIONS

This study provides advanced optics of the human pan-glioma immune contexture as a valuable guide for translational and clinical applications.

Genomic Profiling in Glioma Patients to Explore Clinically Relevant Markers

Gliomas are a heterogeneous group of brain tumors, among which the most aggressive subtype is glioblastoma, accounting for 60% of cases in adults. Available systemic treatment options are few and ineffective, so new approaches to therapies for glioblastoma are in high demand. In total, 131 patients with diffuse glioma were studied. Paired tumor–normal samples were sequenced on the Illumina platform; the panel included 812 genes associated with cancer development. Molecular profiles in clinically distinct groups were investigated. In low-grade glioma (LGG) patients (n = 18), the most common mutations were IDH1/2 (78%), ATRX (33%), TP53 (44%), PIK3CA (17%), and co-deletion 1p/19q (22%). In high-grade glioma (HGG) patients (n = 113), more frequently affected genes were CDKN2A/B (33%), TERTp (71%), PTEN (60%), TP53 (27%), and EGFR (40%). The independent predictors of better prognosis were tumor grade and IDH1/2 mutations. In IDH—wildtype glioblastoma patients, a history of other precedent cancer was associated with worse overall survival (OS), while re-operation and bevacizumab therapy increased OS. Also, among genetic alterations, TERTp mutation and PTEN deletion were markers of poor prognosis. Nine patients received molecular targeted therapy, and the results were evaluated. The search for molecular changes associated with tumor growth and progression is important for diagnosis and choice of therapy.

Co-evolution of glioma and immune microenvironment

Glioma evolution is governed by a multitude of dynamic interactions between tumor cells and heterogenous neighboring, non-cancerous cells. This complex ecosystem, termed the tumor microenvironment (TME), includes diverse immune cell types that have gained increasing attention for their critical and paradoxical roles in tumor control and tumorigenesis. Recent work has revealed that the cellular composition and functional state of immune cells in the TME can evolve extensively depending on the tumor stage and intrinsic features of surrounding glioma cells. Concurrently, adaptations to the glioma cellular phenotype, including activation of various cellular states, occur in the context of these immune cell alterations. In this review, we summarize important features of the immune TME that play key roles during each stage of glioma progression, from initiation to immune escape, invasion and recurrence. Understanding the complex interplay between tumor and immune cells is critical for the development of effective immunotherapies for glioma treatment.