H3K27M mutant glioma: Disease definition and biological underpinnings

Multi-omic landscape of human gliomas from diagnosis to treatment and recurrence

Gliomas are among the most lethal cancers, with limited treatment options. To uncover hallmarks of therapeutic escape and tumor microenvironment (TME) evolution, we applied spatial proteomics, transcriptomics, and glycomics to 670 lesions from 310 adult and pediatric patients. Single-cell analysis shows high B7H3+ tumor cell prevalence in glioblastoma (GBM) and pleomorphic xanthoastrocytoma (PXA), while most gliomas, including pediatric cases, express targetable tumor antigens in less than 50% of tumor cells, potentially explaining trial failures. Longitudinal samples of isocitrate dehydrogenase (IDH)-mutant gliomas reveal recurrence driven by tumor-immune spatial reorganization, shifting from T-cell and vasculature-associated myeloid cell-enriched niches to microglia and CD206+ macrophage-dominated tumors. Multi-omic integration identified N-glycosylation as the best classifier of grade, while the immune transcriptome best predicted GBM survival. Provided as a community resource, this study opens new avenues for glioma targeting, classification, outcome prediction, and a baseline of TME composition across all stages.

Machine learning radiomics for H3K27M mutation prediction in gliomas: A systematic review and meta-analysis

PURPOSE

Noninvasive prediction and identification of the H3K27M mutation play an important role in optimizing therapeutic strategies and improving outcomes in gliomas. In this systematic review and meta-analysis, we aimed to evaluate the performance of machine learning (ML)-based models in predicting H3K27M mutation in gliomas.

METHODS

Literature records were retrieved on September 16th, 2024, in PubMed, Embase, Scopus, and Web of Science. Records were screened according to the eligibility criteria, and the data from the included studies were extracted. The meta-analysis, sensitivity analysis, and meta-regression were conducted using R software.

RESULTS

A total of 15 studies were included in our study. Our meta-analysis demonstrated a pooled AUC, sensitivity, and specificity of 0.87 (95% CI: 0.77-0.97), 92% (95% CI: 83%-96%), and 89% (95% CI: 86%-91%)), respectively. The subgroup meta-analysis revealed that despite the higher sensitivity of the deep learning (DL) models, the sensitivity is not superior to ML (P = 0.6). In contrast, the ML-based pooled specificity was significantly higher (P < 0.01). The meta-analysis revealed a 78.1 (95% CI: 33.3 - 183.5). The SROC curve indicated an AUC of 0.921, and the estimated sensitivity is 0.898 concurrent with the false positive rate of 0.126, which indicates high sensitivity with a low false positive rate.

CONCLUSION

Our systematic review and meta-analysis demonstrated that ML-based magnetic resonance imaging (MRI) radiomics models are associated with promising diagnostic performance in predicting H3K27M mutation in gliomas.

Targeting GDF15 to enhance immunotherapy efficacy in glioblastoma through tumor microenvironment-responsive CRISPR-Cas9 nanoparticles

Despite the outstanding clinical success of immunotherapy, its therapeutic efficacy in glioblastoma (GBM) is still limited. To identify critical regulators of GBM immunity, we constructed a mouse single-guide RNA (sgRNA) library corresponding to all disease-related immune genes, and performed an in vivo CRISPR knockout (KO) screen in syngeneic GBM mouse models. We demonstrated that the deletion of GDF15 in GBM cells ameliorated the immunosuppressive tumor microenvironment (TME) and enhanced the antitumor efficacy of immune checkpoint blockade (ICB) response. Moreover, we designed unique nanoparticles for efficient encapsulation of CRISPR-Cas9, noninvasive brain delivery and tumor cell targeting, demonstrating an effective and safe strategy for GDF15 gene therapy. The CRISPR-Cas9 nanoparticles, known as ANPSS (Cas9/sgRNA), are easily created by enclosing a single Cas9/sgRNA complex in a polymer shell that is sensitive to glutathione. This shell also contains a dual-action ligand that aids in crossing the blood‒brain barrier, targeting tumor cells, and selectively releasing Cas9/sgRNA. Our encapsulating nanoparticles demonstrated promising GBM targeting, resulting in high GDF15 gene editing efficiency within brain tumors while showing minimal off-target gene editing in high-risk tissues. Treatment with ANPSS (Cas9/sgGDF15) effectively halted tumor growth, reversed immune suppression, and enhanced the efficacy of ICB therapy. These results emphasize the potential role of GDF15 in modulating the immune microenvironment and enhancing the effectiveness of current immunotherapy strategies for GBM.

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.

The triple code model for advancing research in rare and undiagnosed diseases beyond the base pairs

Rare and undiagnosed diseases pose significant challenges for understanding their mechanisms, diagnosis, and treatment. The Triple Code Model, an integrative paradigm described here, considers the combined influence of the genetic code, epigenetic code, and nuclear structure (an emerging code), as fundamental biochemical mechanisms underlying many rare diseases. Studies demonstrate dysfunctional membrane and cytoplasmic signals instruct the epigenome to ultimately impact the 3D structure and dynamics of the nucleus, highlighting their close interrelationships. Consequently, this model offers a holistic perspective on rare and undiagnosed diseases by moving beyond a solely genetic view. We propose that this integrated framework will efficiently guide rare disease research by taking it 'Beyond the Base Pairs,' leading to improved diagnostics and personalized treatments.

Latest Advancements in the Management of H3K27M-Mutant Diffuse Intrinsic Pontine Glioma: A Narrative Review

Despite recent advancements in radiotherapy for Diffuse Intrinsic Pontine Glioma (DIPG), the prognosis of this disease remains poor, highlighting the need for new treatment strategies to improve outcomes. Adding stereotactic biopsy to the diagnostic process for children with DIPG has been crucial in improving the management of this disease. Indeed, the discovery of the H3K27M mutation as a key driver of DIPG has led to the development of new drugs that are more effective than traditional ones. These include nimotuzumab (an anti-EGFR drug) and vinorelbine (a semisynthetic vinca alkaloid) in combination, Panobinostat (a histone deacetylase inhibitor), ONC201 (a drug that blocks the dopamine receptor D2 and inactivates Akt and ERK kinases), and chimeric antigen receptor (CAR) T cells. In terms of local therapy, identifying the H3K27M mutation can help us explore how genetic changes affect treatment response, recurrence patterns, and survival. Beyond the time to first recurrence, specific patterns of tumor recurrence, like leptomeningeal spread, can influence treatment plans. For example, radiotherapy can be adjusted in terms of doses and volumes, based on tumor aggressiveness. Because the H3K27M mutation is linked to higher malignancy, a slightly higher dose could be used for the second round of local irradiation. Additionally, irradiating the entire craniospinal axis could help control both local and leptomeningeal disease.

GABA production induced by imipridones is a targetable and imageable metabolic alteration in diffuse midline gliomas

Diffuse midline gliomas (DMGs) are lethal primary brain tumors in children. The imipridones ONC201 and ONC206 induce mitochondrial dysfunction and have emerged as promising therapies for DMG patients. However, efficacy as monotherapy is limited, identifying a need for strategies that enhance response. Another hurdle is the lack of biomarkers that report on drug-target engagement at an early timepoint after treatment onset. Here, using 1 H-magnetic resonance spectroscopy, which is a non-invasive method of quantifying metabolite pool sizes, we show that accumulation of ψ-aminobutyric acid (GABA) is an early metabolic biomarker that can be detected within a week of ONC206 treatment, when anatomical alterations are absent, in mice bearing orthotopic xenografts. Mechanistically, imipridones activate the mitochondrial protease ClpP and upregulate the stress-responsive transcription factor ATF4. ATF4, in turn, upregulates glutamate decarboxylase, which synthesizes GABA, and downregulates ABAT , which degrades GABA, leading to GABA accumulation in DMG cells and tumors. Functionally, GABA secreted by imipridone-treated cells acts in an autocrine manner via the GABAB receptor to induce expression of superoxide dismutase (SOD1), which mitigates imipridone-induced oxidative stress and, thereby, curbs apoptosis. Importantly, blocking autocrine GABA signaling using the clinical stage GABAB receptor antagonist SGS-742 exacerbates oxidative stress and synergistically induces apoptosis in combination with imipridones in DMG cells and orthotopic tumor xenografts. Collectively, we identify GABA as a unique metabolic adaptation to imipridones that can be leveraged for non-invasive assessment of drug-target engagement and therapy. Clinical translation of our studies has the potential to enable precision metabolic therapy and imaging for DMG patients.

One Sentence Summary

Imipridones induce GABA accumulation in diffuse midline gliomas, an effect that can be leveraged for therapy and non-invasive imaging.

Epigenetic regulation of tumor-immune symbiosis in glioma

Glioma is a type of aggressive and incurable brain tumor. Patients with glioma are highly resistant to all types of therapies, including immunotherapies. Epigenetic reprogramming is a key molecular hallmark in tumors across cancer types, including glioma. Mounting evidence highlights a pivotal role of epigenetic regulation in shaping tumor biology and therapeutic responses through mechanisms involving both glioma cells and immune cells, as well as their symbiotic interactions in the tumor microenvironment (TME). In this review, we discuss the molecular mechanisms of epigenetic regulation that impacts glioma cell biology and tumor immunity in both a cell-autonomous and non-cell-autonomous manner. Moreover, we provide an overview of potential therapeutic approaches that can disrupt epigenetic-regulated tumor-immune symbiosis in the glioma TME.