Global hypo-methylation in a proportion of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape

Prognostic implications of DNA methylation machinery (DNMTs and TETs) expression in gliomas: correlations with tumor grading and patient survival

PURPOSE

DNA methylation is a crucial epigenetic modification that regulates gene expression and chromatin structure. Its dysregulation is linked to glioma progression and prognosis, particularly through alterations in methylation machinery. DNMTs and TETs play key roles in these processes, but their involvement in gliomagenesis remains complex, especially in the context of IDH mutations. This study examines the expression patterns of DNMT and TET family genes in gliomas to assess their prognostic significance and therapeutic potential.

MATERIALS AND METHODS

mRNA expression levels of DNMT1, DNMT3A, DNMT3B, DNMT3L, TET1, TET2, TET3, and TDG were analyzed in 75 glioma samples and 10 normal controls using real-time quantitative PCR (qPCR). Statistical analyses and graphical representation were performed using R (v3.3.2) and RStudio (v1.4.1717), with p-values < 0.05 considered significant. Findings were validated using publicly available databases, TCGA and CGGA.

RESULTS

Compared to normal controls, DNMTs and TETs were significantly downregulated in gliomas, with expression levels inversely correlated with histological grade. Survival analysis using the log-rank test demonstrated a significant association between lower TETs and DNMTs expression and an increased risk of mortality. However, multivariate Cox regression analysis indicated that DNMTs and TETs expression were not independent prognostic markers for patient survival, suggesting their impact may be influenced by other clinical and molecular factors. Validation through online databases (TCGA and CGGA) showed that TET family expression across histological grades was consistent with our samples, whereas TDG and DNMT family expression differed.

CONCLUSION

Our findings suggest that DNMTs and TETs may serve as therapeutic targets in glioma due to their downregulation and association with survival, with TET family members (TET1, TET2, and TET3) validated through online databases. However, their prognostic value is limited, as other clinical and molecular factors influence patient outcomes. The downregulation of DNMTs in our samples compared to online databases can be attributed to distinct epigenetic mechanisms: in IDH-mutant gliomas, DNMT suppression results from global hypermethylation (G-CIMP) due to 2-HG accumulation, which inhibits TET enzymes and disrupts DNA methylation homeostasis. In contrast, IDH-wildtype high-grade gliomas exhibit global hypomethylation, genomic instability, oncogenic signaling, and dedifferentiation, reducing the demand for active DNA methylation maintenance. These findings underscore the complex regulation of DNMTs and TETs in gliomas and their potential therapeutic implications.

The role of lncRNAs in the interplay of signaling pathways and epigenetic mechanisms in glioma

Gliomas, highly aggressive tumors of the central nervous system, present overwhelming challenges due to their heterogeneity and therapeutic resistance. Glioblastoma multiforme (GBM), the most malignant form, underscores this clinical urgency due to dismal prognosis despite aggressive treatment regimens. Recent advances in cancer research revealed signaling pathways and epigenetic mechanisms that intricately govern glioma progression, offering multifaceted targets for therapeutic intervention. This review explores the dynamic interplay between signaling events and epigenetic regulation in the context of glioma, with a particular focus on the crucial roles played by non-coding RNAs (ncRNAs). Through direct and indirect epigenetic targeting, ncRNAs emerge as key regulators shaping the molecular landscape of glioblastoma across its various stages. By dissecting these intricate regulatory networks, novel and patient-tailored therapeutic strategies could be devised to improve patient outcomes with this devastating disease.

Unravelling the mosaic: Epigenetic diversity in glioblastoma

Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.

Mechanistic Insights on Metformin and Arginine Implementation as Repurposed Drugs in Glioblastoma Treatment

As the most common and aggressive primary malignant brain tumor, glioblastoma is still lacking a satisfactory curative approach. The standard management consisting of gross total resection followed by radiotherapy and chemotherapy with temozolomide only prolongs patients' life moderately. In recent years, many therapeutics have failed to give a breakthrough in GBM treatment. In the search for new treatment solutions, we became interested in the repurposing of existing medicines, which have established safety profiles. We focused on the possible implementation of well-known drugs, metformin, and arginine. Metformin is widely used in diabetes treatment, but arginine is mainly a cardiovascular protective drug. We evaluated the effects of metformin and arginine on total DNA methylation, as well as the oxidative stress evoked by treatment with those agents. In glioblastoma cell lines, a decrease in 5-methylcytosine contents was observed with increasing drug concentration. When combined with temozolomide, both guanidines parallelly increased DNA methylation and decreased 8-oxo-deoxyguanosine contents. These effects can be explained by specific interactions of the guanidine group with m5CpG dinucleotide. We showed that metformin and arginine act on the epigenetic level, influencing the foreground and potent DNA regulatory mechanisms. Therefore, they can be used separately or in combination with temozolomide, in various stages of disease, depending on desired treatment effects.

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.

Role of Senescent Astrocytes in Health and Disease

For many decades after their discovery, astrocytes, the abundant glial cells of the brain, were believed to work as a glue, supporting the structure and metabolic functions of neurons. A revolution that started over 30 years ago revealed many additional functions of these cells, including neurogenesis, gliosecretion, glutamate homeostasis, assembly and function of synapses, neuronal metabolism with energy production, and others. These properties have been confirmed, limited however, to proliferating astrocytes. During their aging or following severe brain stress lesions, proliferating astrocytes are converted into their no-longer-proliferating, senescent forms, similar in their morphology but profoundly modified in their functions. The changed specificity of senescent astrocytes is largely due to their altered gene expression. The ensuing effects include downregulation of many properties typical of proliferating astrocytes, and upregulation of many others, concerned with neuroinflammation, release of pro-inflammatory cytokines, dysfunction of synapses, etc., specific to their senescence program. The ensuing decrease in neuronal support and protection by astrocytes induces the development, in vulnerable brain regions, of neuronal toxicity together with cognitive decline. Similar changes, ultimately reinforced by astrocyte aging, are also induced by traumatic events and molecules involved in dynamic processes. Senescent astrocytes play critical roles in the development of many severe brain diseases. The first demonstration, obtained for Alzheimer's disease less than 10 years ago, contributed to the elimination of the previously predominant neuro-centric amyloid hypothesis. The initial astrocyte effects, operating a considerable time before the appearance of known Alzheimer's symptoms evolve with the severity of the disease up to their proliferation during the final outcome. Involvement of astrocytes in other neurodegenerative diseases and cancer is now intensely investigated.

Epigenetics of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) arise from the epithelial cells of the thymus and consist in the 1% of all adult malignancies, despite the fact that they are the most common lesions of the anterior mediastinum. TETs can be divided mainly into thymomas, thymic carcinomas, and the rarest ad aggressive neuroendocrine forms. Despite the surgical resection is quite resolving, the diagnosis of TETs is complicated by the absence of symptoms and the clinical presentation aggravated by several paraneoplastic disorders, including myasthenia gravis. Thus, the heterogeneity of TETs prompts the search for molecular biomarkers that could be helpful for tumor characterization and clinical outcomes prediction. With these aims, several researchers investigated the epigenetic profiles of TETs. In this manuscript, we narratively review the works investigating the deregulation of epigenetic mechanisms in TETs, highlighting the need for further studies combining genetic, epigenetic, and expression data to better characterize the different molecular subtypes and identify, for each of them, the most relevant epigenetic biomarkers of clinical utility.