Tumor heterogeneity and tumor-microglia interactions in primary and recurrent IDH1-mutant gliomas

Oncogene aberrations drive medulloblastoma progression, not initiation

Despite recent advances in understanding disease biology, treatment of group 3/4 medulloblastoma remains a therapeutic challenge in paediatric neuro-oncology1. Bulk-omics approaches have identified considerable intertumoural heterogeneity in group 3/4 medulloblastoma, including the presence of clear single-gene oncogenic drivers in only a subset of cases, whereas in most cases, large-scale copy number aberrations prevail2,3. However, intratumoural heterogeneity, the role of oncogene aberrations, and broad copy number variation in tumour evolution and treatment resistance remain poorly understood. To dissect this interplay, we used single-cell technologies (single-nucleus RNA sequencing (snRNA-seq), single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing (snATAC-seq) and spatial transcriptomics) on a cohort of group 3/4 medulloblastoma with known alterations in the oncogenes MYC, MYCN and PRDM6. We show that large-scale chromosomal aberrations are early tumour-initiating events, whereas the single-gene oncogenic events arise late and are typically subclonal, but MYC can become clonal upon disease progression to drive further tumour development and therapy resistance. Spatial transcriptomics shows that the subclones are mostly interspersed across tumour tissue, but clear segregation is also present. Using a population genetics model, we estimate medulloblastoma initiation in the cerebellar unipolar brush cell lineage starting from the first gestational trimester. Our findings demonstrate how single-cell technologies can be applied for early detection and diagnosis of this fatal disease.

Novel metabolic subtypes in IDH-mutant gliomas: implications for prognosis and therapy

BACKGROUND

Although IDH-mutant glioma generally has a better prognosis than their IDH-wildtype counterparts, considerable prognostic heterogeneity persists among patients with the same IDH mutation. Current study has primarily focused on the different IDH statuses or grades, while the metabolic heterogeneity within IDH-mutant gliomas remains insufficiently characterized. This study aims to identify transcriptomic metabolic subtypes and associated immune microenvironment differences to better understand survival variability and potential therapeutic targets in IDH-mutant glioma.

METHODS

Patients with IDH-mutant gliomas were included from four public datasets (TCGA, n = 373; CGGA325, n = 167; CGGA693, n = 333; GLASS, n = 100), supplemented by 22 cases from Beijing Tiantan Hospital as an independent cohort. Consensus clustering was used to define novel metabolic subtypes. Clinical features were assessed using chi-square tests and Kaplan-Meier analysis. Metabolic profiles were characterized through enrichment analysis and GSVA; immune infiltration was analyzed using CIBERSORTx and ESTIMATE. Tumor samples from the independent cohort underwent untargeted metabolomics for validation. LASSO regression was applied to select metabolic signatures, and the CGP2014 drug library was used for drug screening.

RESULTS

Three metabolic subtypes (C1-C3) with distinct prognoses (p < 0.05) were identified. C1 exhibited enhanced carbohydrate and nucleotide metabolism; C2 displayed upregulated amino acid and lipid metabolism; and C3 demonstrated elevated lipid, nucleotide, and vitamin metabolism. These patterns were validated in the independent cohort. Subtypes were also correlated with immune infiltration. A 13-gene metabolic signature was established to stratify prognostic risk and suggest subtype-specific drug sensitivities.

CONCLUSIONS

Our study provided a novel metabolic subtype for IDH-mutant glioma and highlighted these patients' metabolic heterogeneity and potential therapeutic strategies.

Single-Cell Profiling and Proteomics-Based Insights Into mTORC1-Mediated Angio+TAMs Polarization in Recurrent IDH-Mutant Gliomas

BACKGROUND

IDH mutant gliomas often exhibit recurrence and progression, with the mTORC1 pathway and tumor-associated macrophages potentially contributing to these processes. However, the precise mechanisms are not fully understood. This study seeks to investigate these relationships using proteomic, phosphoproteomic, and multi-dimensional transcriptomic approaches.

METHODS

This study established a matched transcriptomic, proteomic, and phosphoproteomic cohort of IDH-mutant gliomas with recurrence and progression, incorporating multiple glioma-related datasets. We first identified the genomic landscape of recurrent IDH-mutant gliomas through multi-dimensional differential enrichment, GSVA, and deconvolution analyses. Next, we explored tumor-associated macrophage subpopulations using single-cell sequencing in mouse models of IDH-mutant and wild-type gliomas, analyzing transcriptional changes via AddmodelScore and pseudotime analysis. We then identified these subpopulations in matched primary and recurrent IDH-mutant datasets, investigating their interactions with the tumor microenvironment and performing deconvolution to explore their contribution to glioma progression. Finally, spatial transcriptomics was used to map these subpopulations to glioma tissue sections, revealing spatial co-localization with mTORC1 and angiogenesis-related pathways.

RESULTS

Multi-dimensional differential enrichment, GSVA, and deconvolution analyses indicated that the mTORC1 pathway and the proportion of M2 macrophages are upregulated during the recurrence and progression of IDH-mutant gliomas. CGGA database analysis showed that mTORC1 activity is significantly higher in recurrent IDH-mutant gliomas compared to IDH-wildtype, with a correlation to M2 macrophage infiltration. KSEA revealed that AURKA is enriched during progression, and its inhibition reduces mTORC1 pathway activity. Single-cell sequencing in mouse models identified a distinct glioma subpopulation with upregulated mTORC1, exhibiting both M2 macrophage and angiogenesis transcriptional features, which increased after implantation of IDH-mutant tumor cells. Similarly, human glioma single-cell data revealed the same subpopulation, with cell-cell communication analysis showing active VEGF signaling. Finally, spatial transcriptomics deconvolution confirmed the co-localization of this subpopulation with mTORC1 and VEGFA in high-grade IDH-mutant gliomas.

CONCLUSIONS

Our findings suggest mTORC1 activation and Angio-TAMs play key roles in the recurrence and progression of IDH-mutant gliomas.

Targeting gut microbiota: a potential therapeutic approach for tumor microenvironment in glioma

Glioma, being one of the malignant tumors with the highest mortality rate globally, has an unclear pathogenesis, and the existing treatment effects still have certain limitations. The tumor microenvironment (TME) plays an important role in the occurrence, development, and recurrence of glioma. As one of the important regulatory factors of TME, the gut microbiota can regulate the progression of glioma not only by interacting with the brain through the brain-gut axis but also by influencing the tumor immune microenvironment (TIME) and inflammatory microenvironment. Recent studies have identified the gut microbiota and TME as potential therapeutic targets for glioma. This paper aims to summarize the role of the gut microbiota in TME, the association between them and glioma, and the potential of developing new intervention measures by targeting the gut microbiota. Understanding the involvement process of the gut microbiota in glioma may pave the way for the development of effective treatment methods that can regulate TME and prevent disease progression.

Microenvironmental Drivers of Glioma Progression

Gliomas, particularly glioblastoma (GBM), are among the most challenging brain tumors due to their complex and dynamic tumor microenvironment (TME). The TME plays a pivotal role in tumor progression, immune evasion, and resistance to therapy through intricate interactions among glioma cells, immune components, neurons, astrocytes, the extracellular matrix, and the blood-brain barrier. Targeting the TME has demonstrated potential, with immunotherapies such as checkpoint inhibitors and neoadjuvant therapies enhancing immune responses. Nonetheless, overcoming the immunosuppressive landscape and metabolic adaptations continues to pose significant challenges. This review explores the diverse cellular and molecular mechanisms that shape the glioma TME. A deeper understanding of these mechanisms holds promise for providing novel therapeutic opportunities to improve glioma treatment outcomes.

Single-cell sequencing elucidates the mechanism of NUSAP1 in glioma and its diagnostic and prognostic significance

Background

Personalized precision medicine (PPPM) in cancer immunology and oncology is a rapidly advancing field with significant potential. Gliomas, known for their poor prognosis, rank among the most lethal brain tumors. Despite advancements, there remains a critical need for precise, individualized treatment strategies.

Methods

We conducted a comprehensive analysis of RNA-seq and microarray data from the TCGA and GEO databases, supplemented by single-cell RNA sequencing (scRNA-seq) data from glioma patients. By integrating single-cell sequencing analysis with foundational experiments, we investigated the molecular variations and cellular interactions within neural glioma cell subpopulations during tumor progression.

Results

Our single-cell sequencing analysis revealed distinct gene expression patterns across glioma cell subpopulations. Notably, differentiation trajectory analysis identified NUSAP1 as a key marker for the terminal subpopulation. We found that elevated NUSAP1 expression correlated with poor prognosis, prompting further investigation of its functional role through both cellular and animal studies.

Conclusions

NUSAP1-based risk models hold potential as predictive and therapeutic tools for personalized glioma treatment. In-depth exploration of NUSAP1's mechanisms in glioblastoma could enhance our understanding of its response to immunotherapy, suggesting that targeting NUSAP1 may offer therapeutic benefits for glioma patients.

Epigenetic Regulation of Stromal and Immune Cells and Therapeutic Targets in the Tumor Microenvironment

The tumor microenvironment (TME) plays a pivotal role in neoplastic initiation and progression. Epigenetic machinery, governing the expression of core oncogenes and tumor suppressor genes in transformed cells, significantly contributes to tumor development at both primary and distant sites. Recent studies have illuminated how epigenetic mechanisms integrate external cues and downstream signals, altering the phenotype of stromal cells and immune cells. This remolds the area surrounding tumor cells, ultimately fostering an immunosuppressive microenvironment. Therefore, correcting the TME by targeting the epigenetic modifications holds substantial promise for cancer treatment. This review synthesizes recent research that elucidates the impact of specific epigenetic regulations-ranging from DNA methylation to histone modifications and chromatin remodeling-on stromal and immune cells within the TME. Notably, we highlight their functional roles in either promoting or restricting tumor progression. We also discuss the potential applications of epigenetic agents for cancer treatment, envisaging their ability to normalize the ecosystem. This review aims to assist researchers in understanding the dynamic interplay between epigenetics and the TME, paving the way for better epigenetic therapy.

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.

Single-nucleus RNA-seq dissection of choroid plexus tumor cell heterogeneity

The genomic, genetic and cellular events regulating the onset, growth and survival of rare, choroid plexus neoplasms remain poorly understood. Here, we examine the heterogeneity of human choroid plexus tumors by single-nucleus transcriptome analysis of 23,906 cells from four disease-free choroid plexus and eleven choroid plexus tumors. The resulting expression atlas profiles cellular and transcriptional diversity, copy number alterations, and cell-cell interaction networks in normal and cancerous choroid plexus. In choroid plexus tumor epithelial cells, we observe transcriptional changes that correlate with genome-wide methylation profiles. We further characterize tumor type-specific stromal microenvironments that include altered macrophage and mesenchymal cell states, as well as changes in extracellular matrix components. This first single-cell dataset resource from such scarce samples should be valuable for divising therapies against these little-studied neoplasms.

IDH Mutations in Glioma: Molecular, Cellular, Diagnostic, and Clinical Implications

In 2021, the World Health Organization classified isocitrate dehydrogenase (IDH) mutant gliomas as a distinct subgroup of tumors with genetic changes sufficient to enable a complete diagnosis. Patients with an IDH mutant glioma have improved survival which has been further enhanced by the advent of targeted therapies. IDH enzymes contribute to cellular metabolism, and mutations to specific catalytic residues result in the neomorphic production of D-2-hydroxyglutarate (D-2-HG). The accumulation of D-2-HG results in epigenetic alterations, oncogenesis and impacts the tumor microenvironment via immunological modulations. Here, we summarize the molecular, cellular, and clinical implications of IDH mutations in gliomas as well as current diagnostic techniques.

HOXD12 defines an age-related aggressive subtype of oligodendroglioma

Oligodendroglioma, IDH-mutant and 1p/19q-codeleted has highly variable outcomes that are strongly influenced by patient age. The distribution of oligodendroglioma age is non-Gaussian and reportedly bimodal, which motivated our investigation of age-associated molecular alterations that may drive poorer outcomes. We found that elevated HOXD12 expression was associated with both older patient age and shorter survival in the TCGA (FDR < 0.01, FDR = 1e-5) and the CGGA (p = 0.03, p < 1e-3). HOXD12 gene body hypermethylation was associated with older age, higher WHO grade, and shorter survival in the TCGA (p < 1e-6, p < 0.001, p < 1e-3) and with older age and higher WHO grade in Capper et al. (p < 0.002, p = 0.014). In the TCGA, HOXD12 gene body hypermethylation and elevated expression were independently prognostic of NOTCH1 and PIK3CA mutations, loss of 15q, MYC activation, and standard histopathological features. Single-nucleus RNA and ATAC sequencing data showed that HOXD12 activity was elevated in neoplastic tissue, particularly within cycling and OPC-like cells, and was associated with a stem-like phenotype. A pan-HOX DNA methylation analysis revealed an age and survival-associated HOX-high signature that was tightly associated with HOXD12 gene body methylation. Overall, HOXD12 expression and gene body hypermethylation were associated with an older, atypically aggressive subtype of oligodendroglioma.

Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma

In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.

The inactive X chromosome drives sex differences in microglial inflammatory activity in human glioblastoma

Biological sex is an important risk factor in cancer, but the underlying cell types and mechanisms remain obscure. Since tumor development is regulated by the immune system, we hypothesize that sex-biased immune interactions underpin sex differences in cancer. The male-biased glioblastoma multiforme (GBM) is an aggressive and treatment-refractory tumor in urgent need of more innovative approaches, such as considering sex differences, to improve outcomes. GBM arises in the specialized brain immune environment dominated by microglia, so we explored sex differences in this immune cell type. We isolated adult human TAM-MGs (tumor-associated macrophages enriched for microglia) and control microglia and found sex-biased inflammatory signatures in GBM and lower-grade tumors associated with pro-tumorigenic activity in males and anti-tumorigenic activity in females. We demonstrated that genes expressed or modulated by the inactive X chromosome facilitate this bias. Together, our results implicate TAM-MGs, specifically their sex chromosomes, as drivers of male bias in GBM.

Extracellular vesicles in glioblastoma: a challenge and an opportunity

Glioblastoma is a highly heterogeneous tumor whose pathophysiological complexities dictate both the diagnosis of disease severity as well as response to therapy. Conventional diagnostic tools and standard treatment regimens have only managed to achieve limited success in the management of patients suspected of glioblastoma. Extracellular vesicles are an emerging liquid biopsy tool that has shown great promise in resolving the limitations presented by the heterogeneous nature of glioblastoma. Here we discuss the contrasting yet interdependent dual role of extracellular vesicles as communication agents that contribute to the progression of glioblastoma by creating a heterogeneous microenvironment and as a liquid biopsy tool providing an opportunity to accurately identify the disease severity and progression.

Potential roles for efferocytosis in glioblastoma immune evasion

Glioblastoma is an aggressive and incurable brain cancer. This cancer establishes both local and systemic immunosuppression that creates a major obstacle to effective immunotherapies. Many studies point to tumor-resident myeloid cells (primarily microglia and macrophages) as key mediators of this immunosuppression. Myeloid cells exhibit a high level of plasticity with respect to their phenotype and are capable of both stimulating and repressing immune responses. How glioblastomas recruit myeloid cells and exploit them to avoid the immune system is an active area of research. Macrophages can acquire an immunosuppressive phenotype as a consequence of exposure to cytokines such as TGFB1 or IL4; in addition, macrophages can acquire an immunosuppressive phenotype as a consequence of the engulfment of apoptotic cells, a process referred to as efferocytosis. There is substantial evidence that glioblastoma cells are able to secrete cytokines and other factors that induce an immunosuppressive phenotype in macrophages and microglia. However, less is known about the contribution of efferocytosis to immunosuppression in glioblastoma. Here I review the literature in this area and discuss the potential of efferocytosis inhibition to improve glioblastoma response to immunotherapy.