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Keywords = O6-methylguanine-DNA-methyltransferase

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19 pages, 2933 KiB  
Article
Role of Amide Proton Transfer Weighted MRI in Predicting MGMTp Methylation Status, p53-Status, Ki-67 Index, IDH-Status, and ATRX Expression in WHO Grade 4 High Grade Glioma
by Faris Durmo, Jimmy Lätt, Anna Rydelius, Elisabet Englund, Tim Salomonsson, Patrick Liebig, Johan Bengzon, Peter C. M. van Zijl, Linda Knutsson and Pia C. Sundgren
Tomography 2025, 11(6), 64; https://doi.org/10.3390/tomography11060064 - 31 May 2025
Viewed by 693
Abstract
Objectives: To assess amide proton transfer weighted (APTw) MR imaging capabilities in differentiating high-grade glial tumors across alpha-thalassemia/mental retardation X-linked (ATRX) expression, tumor-suppressor protein p53 expression (p53), O6-methylguanine-DNA methyltransferase promoter (MGMTp) methylation, isocitrate dehydrogenase (IDH) status, and proliferation marker Ki-67 (Ki-67 index) as [...] Read more.
Objectives: To assess amide proton transfer weighted (APTw) MR imaging capabilities in differentiating high-grade glial tumors across alpha-thalassemia/mental retardation X-linked (ATRX) expression, tumor-suppressor protein p53 expression (p53), O6-methylguanine-DNA methyltransferase promoter (MGMTp) methylation, isocitrate dehydrogenase (IDH) status, and proliferation marker Ki-67 (Ki-67 index) as a preoperative diagnostic aid. Material & Methods: A total of 42 high-grade glioma WHO grade 4 (HGG) patients were evaluated prospectively (30 males and 12 females). All patients were examined using conventional MRI, including the following: T1w-MPRAGE pre- and post-contrast administration, conventional T2w and 3D FLAIR, and APTw imaging with a 3T MR scanner. Receiver operating characteristic (ROC) curves were calculated for the APTw% mean, median, and max signal for the different molecular biomarkers. A logistic regression model was constructed for combined mean and median APTw% signals for p53 expression. Results: The whole-tumor max APTw% signal could significantly differentiate MGMTp from non-MGMTp HGG, p = 0.035. A cutoff of 4.28% max APTw% signal yielded AUC (area under the curve) = 0.702, with 70.6% sensitivity and 66.7% specificity. The mean/median APTw% signals differed significantly in p53 normal versus p53-overexpressed HGG s: 1.81%/1.83% vs. 1.15%/1.18%, p = 0.002/0.006, respectively. Cutoffs of 1.25%/1.33% for the mean/median APTw% signals yielded AUCs of 0.786/0.757, sensitivities of 76.9%/76.9%, and specificities of 50%/66.2%, p = 0.002/0.006, respectively. A logistic regression model with a combined mean and median APTw% signal for p53 status yielded an AUC = 0.788 and 76.9% sensitivity and 66.2% specificity. ATRX-, IDH- wild type (wt) vs. mutation (mut), and the level of Ki-67 did not differ significantly, but trends were found: IDH-wt and low Ki-67 showed higher mean/median/max APTw% signals vs. IDH-mut and high Ki-67, respectively. ATRX-wt vs. mutation showed higher mean and median APTw% signals but lower max APTw% signal. Conclusions: APTw imaging can potentially be a useful marker for the stratification of p53 expression and MGMT status in high-grade glioma in the preoperative setting and potentially aid surgical decision-making. Full article
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13 pages, 1584 KiB  
Article
Radiomics and AI-Based Prediction of MGMT Methylation Status in Glioblastoma Using Multiparametric MRI: A Hybrid Feature Weighting Approach
by Erdal Tasci, Ying Zhuge, Longze Zhang, Holly Ning, Jason Y. Cheng, Robert W. Miller, Kevin Camphausen and Andra V. Krauze
Diagnostics 2025, 15(10), 1292; https://doi.org/10.3390/diagnostics15101292 - 21 May 2025
Cited by 1 | Viewed by 968
Abstract
Background/Objectives: Glioblastoma (GBM) is a highly aggressive primary central nervous system tumor with a median survival of 14 months. MGMT (O6-methylguanine-DNA methyltransferase) promoter methylation status is a key biomarker as a prognostic indicator and a predictor of chemotherapy response in GBM. Patients [...] Read more.
Background/Objectives: Glioblastoma (GBM) is a highly aggressive primary central nervous system tumor with a median survival of 14 months. MGMT (O6-methylguanine-DNA methyltransferase) promoter methylation status is a key biomarker as a prognostic indicator and a predictor of chemotherapy response in GBM. Patients with MGMT methylated disease progress later and survive longer (median survival rate 22 vs. 15 months, respectively) as compared to patients with MGMT unmethylated disease. Patients with GBM undergo an MRI of the brain prior to diagnosis and following surgical resection for radiation therapy planning and ongoing follow-up. There is currently no imaging biomarker for GBM. Studies have attempted to connect MGMT methylation status to MRI imaging appearance to determine if brain MRI can be leveraged to provide MGMT status information non-invasively and more expeditiously. Methods: Artificial intelligence (AI) can identify MRI features that are not distinguishable to the human eye and can be linked to MGMT status. We employed the UPenn-GBM dataset patients for whom methylation status was available (n = 146), employing a novel radiomic method grounded in hybrid feature selection and weighting to predict MGMT methylation status. Results: The best MGMT classification and feature selection result obtained resulted in a mean accuracy rate value of 81.6% utilizing 101 selected features and five-fold cross-validation. Conclusions: This compared favorably with similar studies in the literature. Validation with external datasets remains critical to enhance generalizability and propagate robust results while reducing bias. Future directions include multi-channel data integration with radiomic features and deep and ensemble learning methods to improve predictive performance. Full article
(This article belongs to the Special Issue The Applications of Radiomics in Precision Diagnosis)
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13 pages, 1045 KiB  
Article
All-Trans Retinoic Acid Induces Differentiation and Downregulates Stemness Markers and MGMT Expression in Glioblastoma Stem Cells
by Justin Tang and Raymond Yang
Cells 2025, 14(10), 746; https://doi.org/10.3390/cells14100746 - 20 May 2025
Viewed by 740
Abstract
Background: Glioblastoma (GBM) remains almost uniformly fatal, owing in part to therapy-resistant cancer stem-like cells (CSCs) and to temozolomide (TMZ) resistance driven by O6-methylguanine-DNA methyltransferase (MGMT). Differentiation therapy with all-trans retinoic acid (ATRA) has the potential to attenuate stemness and sensitize [...] Read more.
Background: Glioblastoma (GBM) remains almost uniformly fatal, owing in part to therapy-resistant cancer stem-like cells (CSCs) and to temozolomide (TMZ) resistance driven by O6-methylguanine-DNA methyltransferase (MGMT). Differentiation therapy with all-trans retinoic acid (ATRA) has the potential to attenuate stemness and sensitize GBM to TMZ. We therefore asked whether ATRA reduces expression of key CSC markers and MGMT in established GBM lines. Methods: Two established human GBM cell lines, U87-MG and A172, were cultured under neurosphere-promoting conditions to enrich for potential stem-like subpopulations. Cells were treated with either 1 µM ATRA or vehicle control (DMSO) for 5 days. Total RNA was extracted, and cDNA was synthesized. Quantitative Real-Time PCR (qPCR) assessed relative mRNA expression levels of key stemness transcription factors (SOX2, NES) and the DNA repair gene MGMT and corresponding protein levels were measured by an Enzyme-Linked Immunosorbent Assay (ELISA). Gene expression was normalized to the geometric mean of two validated housekeeping genes (GAPDH, ACTB). Relative quantification was calculated using the ΔΔCt method, and statistical significance was determined using Student’s t-tests. Results: ATRA markedly suppressed stemness and MGMT in both lines. In U87-MG, SOX2 mRNA fell 3.7-fold (p = 0.0008) and protein 2.99-fold (148.3 ± 6.0 → 49.7 ± 2.7 pg µg−1; p = 0.0002); Nestin dropped 4.1-fold (p = 0.0005) and 3.51-fold (450.0 ± 17.3 → 128.3 ± 4.4 pg µg−1; p = 0.00008). MGMT decreased 2.6-fold at transcript level (p = 0.0065) and 2.11-fold at protein level (81.7 ± 4.4 → 38.7 ± 1.8 pg µg−1; p = 0.0005). In A172, SOX2 was reduced 2.9-fold (p = 0.0041) and 2.31-fold (p = 0.0007); Nestin 3.3-fold (p = 0.0028) and 2.79-fold (p = 0.00009). MGMT declined 2.2-fold (p = 0.0132) and 1.82-fold (p = 0.0015), respectively. Conclusions: Five-day exposure to ATRA diminishes SOX2, Nestin, and MGMT at both mRNA and protein levels in stem-enriched GBM cultures, supporting the premise that ATRA-induced differentiation can concurrently blunt CSC traits and TMZ-resistance mechanisms. These data provide a molecular rationale for testing ATRA in combination regimens aimed at improving GBM therapy. Full article
(This article belongs to the Special Issue The Pivotal Role of Tumor Stem Cells in Glioblastoma)
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16 pages, 8017 KiB  
Article
A Novel Squalenoylated Temozolomide Nanoparticle with Long Circulating Properties Reverses Drug Resistance in Glioblastoma
by Jiao Feng, Chengyong Wen, Xiao Zhang, Xiaolong Zhu, Mengmeng Ma, Xiaohong Zhao and Xinbing Sui
Int. J. Mol. Sci. 2025, 26(10), 4723; https://doi.org/10.3390/ijms26104723 - 15 May 2025
Viewed by 574
Abstract
Temozolomide (TMZ) remains the frontline chemotherapy for gliomas; yet its clinical efficacy is significantly compromised by inherent instability and the emergence of resistance mechanisms. To surmount these challenges, we engineered a squalenoylated TMZ nanoparticle (SQ-TMZ NPs) via conjugation of TMZ with squalene, enabling [...] Read more.
Temozolomide (TMZ) remains the frontline chemotherapy for gliomas; yet its clinical efficacy is significantly compromised by inherent instability and the emergence of resistance mechanisms. To surmount these challenges, we engineered a squalenoylated TMZ nanoparticle (SQ-TMZ NPs) via conjugation of TMZ with squalene, enabling enhanced drug stability and improved therapeutic potency against glioblastoma cells. The resulting SQ-TMZ NPs exhibited a precisely controlled nanoscale architecture (~126 nm), demonstrating exceptional stability under physiological and storage conditions, with minimal hemolytic toxicity (<5%). Notably, these nanoparticles conferred superior cytotoxicity in TMZ-resistant glioblastoma T98G cells, attributed to the amplification of intracellular reactive oxygen species (ROS) and DNA damage, along with MGMT (O-6-methylguanine-DNA methyltransferase) expression suppression. Furthermore, in vivo imaging confirmed their efficient blood–brain barrier (BBB) penetration and selective tumor accumulation. This study presents a transformative approach by integrating prodrug self-assembly with targeted drug delivery to not only enhance TMZ stability but also decisively reverse glioblastoma resistance, offering a compelling therapeutic advancement. Full article
(This article belongs to the Section Molecular Nanoscience)
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23 pages, 7158 KiB  
Article
Positive Prognostic Overall Survival Impacts of Methylated TGFB2 and MGMT in Adult Glioblastoma Patients
by Sanjive Qazi, Michael Potts, Scott Myers, Stephen Richardson and Vuong Trieu
Cancers 2025, 17(7), 1122; https://doi.org/10.3390/cancers17071122 - 27 Mar 2025
Cited by 1 | Viewed by 1274
Abstract
(1) Background: Glioblastoma (GBM) is the most aggressive and common primary malignant brain tumor in adults, constituting 45.6% of tumors. We explored the impact of gene methylation of the O-6-Methylguanine-DNA Methyltransferase (MGMT) and the Transforming Growth Factor Beta (TGFB) gene [...] Read more.
(1) Background: Glioblastoma (GBM) is the most aggressive and common primary malignant brain tumor in adults, constituting 45.6% of tumors. We explored the impact of gene methylation of the O-6-Methylguanine-DNA Methyltransferase (MGMT) and the Transforming Growth Factor Beta (TGFB) gene complex using the TCGA dataset for GBM patients. (2) Methods: We implemented a multivariate Cox proportional hazards model to directly compare hazard ratios for TGFB1/2/3 and MGMT methylation in relation to OS, considering male versus female, age at diagnosis, and age interactions with TGFB2 gene methylation and sex variables. Reactome analysis was performed to identify enriched pathways negatively correlated with TGFB2 methylation. (3) Results: The GBM patients had high levels of TGFB2 gene methylation; this primarily benefited the young adult male patients, and multivariate analysis exhibited a significantly improved OS prognosis HR (95% CI range) = 0.04 (0.006–0.274); p = 0.001) relative to the TGFB1highMe (HR (95% CI range) = 0.657 (0.454–0.951); p = 0.026) and MGMThighMe (HR (95% CI range) = 0.667 (0.475–0.936); p = 0.019) groups of GBM patients. The Reactome pathways collectively represented T-cell activation, differentiation, effector functions, antigen presentation, and Toll-like receptor pathways. Gene level mRNA expression highlighted four positive prognostic genes upregulated in tumor tissues, and their expression was validated in independent single-cell RNA-seq experiments. These genes were highly expressed in macrophages (HIF1A, TRIM22, IRAK4, PARP9). In contrast, MALT1 mRNA expression was the only gene product with a negative prognostic impact on OS in GBM patients (HR (95% CI range) = 1.997 (1.1–3.625); p = 0.023). (4) Conclusions: Increased levels of TGFB2 gene methylation predict improved OS, especially in young adult male GBM patients, above that of MGMT gene methylation, and should be considered during the administration of mRNA-based TGFB2 therapies. Full article
(This article belongs to the Section Cancer Survivorship and Quality of Life)
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16 pages, 3545 KiB  
Article
Cortical Origin-Dependent Metabolic and Molecular Heterogeneity in Gliomas: Insights from 18F-FET PET
by Huantong Diao, Xiaolong Wu, Xiaoran Li, Siheng Liu, Bingyang Shan, Ye Cheng, Jie Lu and Jie Tang
Biomedicines 2025, 13(3), 657; https://doi.org/10.3390/biomedicines13030657 - 7 Mar 2025
Viewed by 818
Abstract
Objectives: The objective of this study is to explore the potential variations in metabolic activity across gliomas originating from distinct cortical regions, as assessed by O-(2-18F-fluoroethyl)-L-tyrosine positron emission tomography (18F-FET PET). Also, this study seeks to elucidate whether [...] Read more.
Objectives: The objective of this study is to explore the potential variations in metabolic activity across gliomas originating from distinct cortical regions, as assessed by O-(2-18F-fluoroethyl)-L-tyrosine positron emission tomography (18F-FET PET). Also, this study seeks to elucidate whether these metabolic disparities correlate with the molecular characteristics and clinical prognoses of the tumors. Specifically, this research aims to determine whether variations in 18F-FET PET uptake are indicative of underlying genetic or biochemical differences that could influence patients’ outcomes. Methods: The researchers retrospectively included 107 patients diagnosed with gliomas from neocortex and mesocortex, all of whom underwent hybrid PET/MR examinations, including 18F-FET PET and diffusion weighted imaging (DWI), prior to surgery. The mean and maximum tumor-to-background ratio (TBR) and apparent diffusion coefficient (ADC) values were calculated based on whole tumor volume segmentations. Comparisons of TBR, ADC values, and survival outcomes were performed to determine statistical differences between groups. Results: Among glioblastomas (GBMs, WHO grade 4) originating from the two cortical regions, there was a significant difference in the human Telomerase Reverse Transcriptase (TERT) promoter mutation rate, while no difference was observed in O6-Methylguanine-DNA Methyltransferase (MGMT) promoter methylation status. For WHO grade 3 gliomas, significant differences were found in the TERT promoter mutation rate and the proportion of 1p/19q co-deletion between the two cortical regions, whereas no difference was noted in MGMT methylation status. For WHO grade 2 gliomas, no molecular phenotypic differences were observed between the two cortical regions. In terms of survival, only GBMs originating from the mesocortex demonstrated significantly longer survival compared to those from the neocortex, while no statistically significant differences were found in survival for the other two groups. Conclusions: Gliomas originating from different cortical regions exhibit variations in metabolic activity, molecular phenotypes, and clinical outcomes. Full article
(This article belongs to the Special Issue Diagnosis, Pathogenesis and Treatment of CNS Tumors)
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13 pages, 1127 KiB  
Article
Analysis of Patients with Glioblastoma Treated with Standard 6-Week Chemoradiation Followed by Temozolomide: Treatment Outcomes and Prognostic Factors
by Sojung Lee and Myungsoo Kim
Medicina 2025, 61(3), 376; https://doi.org/10.3390/medicina61030376 - 21 Feb 2025
Viewed by 949
Abstract
Background and Objectives: We aimed to investigate the treatment outcomes and prognostic factors of survival among patients with glioblastoma who underwent 6-week concurrent chemoradiation therapy (CCRT) followed by temozolomide (TMZ) with Stupp’s regimen in a single tertiary institution. Materials and Methods: [...] Read more.
Background and Objectives: We aimed to investigate the treatment outcomes and prognostic factors of survival among patients with glioblastoma who underwent 6-week concurrent chemoradiation therapy (CCRT) followed by temozolomide (TMZ) with Stupp’s regimen in a single tertiary institution. Materials and Methods: Eighty patients with glioblastoma who underwent 6-week CCRT followed by TMZ between June 2010 and January 2024 were retrospectively investigated. A survival analysis was performed of factors such as age, O (6)-methylguanine-DNA methyltransferase promoter (MGMT) methylation, extent of resection, pre- and post-operative Karnofsky Performance Status, and inflammatory markers such as neutrophil-to-lymphocyte ratio, lymphocyte-to-monocyte ratio (LMR), and platelet-to-lymphocyte ratio. Post-operative inflammatory markers were assessed at 2–3 weeks post-operative before the initiation of CCRT. A subgroup analysis was performed of patients who underwent non-gross total resection (GTR). Results: The median progression-free survival (PFS) and overall survival (OS) of the entire cohort were 8.97 months and 19.0 months, respectively. Older age (≥65 years) and non-GTR status were adverse prognostic factors of PFS and OS. MGMT methylation is a favorable prognostic factor for PFS and OS. In the subgroup of patients who underwent non-GTR, MGMT methylation and post-operative LMR (<3.2/>3.2) were independent prognostic factors for PFS and OS. Conclusions: As with previous studies, older age, MGMT methylation, and extent of resection were independent prognostic factors for the survival of patients with glioblastoma who underwent standard treatment with Stupp’s regimen. MGMT methylation and post-operative LMR were significant prognostic factors for PFS and OS among patients who underwent non-GTR. The prognostic significance of post-operative inflammatory markers for treatment response and survival should be further validated in glioblastoma patients treated with Stupp’s regimen. Full article
(This article belongs to the Special Issue Early Diagnosis and Management of Glioma)
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19 pages, 2372 KiB  
Article
Single-Molecule Nanopore Sequencing of the CpG Island from the Promoter of O6-Methylguanine-DNA Methyltransferase Provides Insights into the Mechanism of De Novo Methylation of G/C-Rich Regions
by Alexander V. Sergeev, Daniil P. Malyshev, Adelya I. Genatullina, Galina V. Pavlova, Elizaveta S. Gromova and Maria I. Zvereva
Epigenomes 2025, 9(1), 4; https://doi.org/10.3390/epigenomes9010004 - 26 Jan 2025
Cited by 1 | Viewed by 1918
Abstract
Background: The methylation of cytosine residues at CpG sites within the O6-methylguanine-DNA methyltransferase (MGMT) promoter is a key biomarker in glioblastoma therapy. The MGMT promoter (MGMTp) contains multiple guanine-rich sequences capable of folding into G-quadruplexes (G4s), but their relevance for MGMTp [...] Read more.
Background: The methylation of cytosine residues at CpG sites within the O6-methylguanine-DNA methyltransferase (MGMT) promoter is a key biomarker in glioblastoma therapy. The MGMT promoter (MGMTp) contains multiple guanine-rich sequences capable of folding into G-quadruplexes (G4s), but their relevance for MGMTp methylation is poorly understood. Objectives: Our study explores the impact of potential G-quadruplex-forming sequences (PQS) in the MGMT promoter CpG island on the activity of de novo DNA methyltransferase Dnmt3a. Additionally, we investigate their influence on the accuracy of methylation pattern detection using nanopore sequencing. Methods: Nanopore sequencing was employed to analyze the methylation of 94 clinically significant CpG sites in the human MGMTp using an in vitro de novo methylation system. Circular dichroism spectroscopy was used to identify G4 structures within the MGMTp CpG island. Interactions between the catalytic domain of Dnmt3a and the PQS from the MGMTp were examined by biolayer interferometry. Results: Guanine-rich DNA strands of the PQSs in the MGMTp were hypomethylated, while the complementary cytosine-rich strands were methylated by DNA methyltransferase Dnmt3a with higher efficiency. The accuracy of detecting modified bases in the PQS was significantly lower compared to surrounding sequences. Single-stranded guanine-rich DNA sequences from the MGMTp exhibited strong binding to Dnmt3a-CD, with an affinity approximately 10 times higher than their cytosine-rich complements (Kd = 3 × 10−8 M and 3 × 10−7 M, respectively). By binding to Dnmt3a, G4-forming oligonucleotides from MGMTp effectively inhibited the methylation reaction (IC50 6 × 10−7 M). Conclusions: The obtained data indicate the role of PQSs in establishing de novo methylation of the MGMT promoter. They also highlight the challenges of sequencing guanine-rich regions and the impact of specific de novo methylation patterns on clinical data interpretation. Full article
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30 pages, 15119 KiB  
Article
Novel Pathways of Oxidative and Nitrosative Inactivation of the Human MGMT Protein in Colon Cancer and Glioblastoma Cells: Increased Efficacy of Alkylating Agents In Vitro and In Vivo
by Debasish Basak, Agm Mostofa, Hanumantha Rao Madala and Kalkunte S. Srivenugopal
Diseases 2025, 13(2), 32; https://doi.org/10.3390/diseases13020032 - 25 Jan 2025
Viewed by 1028
Abstract
Background: O6-Methylguanine-DNA methyltransferase (MGMT) is a unique antimutagenic DNA repair protein that plays a crucial role in conferring resistance to various alkylating agents in brain tumor therapy. In this study, we exploited the susceptibility of the active site Cys145 of MGMT [...] Read more.
Background: O6-Methylguanine-DNA methyltransferase (MGMT) is a unique antimutagenic DNA repair protein that plays a crucial role in conferring resistance to various alkylating agents in brain tumor therapy. In this study, we exploited the susceptibility of the active site Cys145 of MGMT for thiolation and nitrosylation, both of which inactivate the enzyme. Methods: We designed a redox perturbing glutathione mimetic, a platinated homoglutathione disulfide (hGTX) by adding small amounts of cisplatin (1000:10) and used a nitric oxide-donor spermine NONOate. N6022, a potent inhibitor of S-nitrosoglutathione reductase was used to extend the retention of nitrosylated MGMT in tumor cell culture and subcutaneous xenografts. Results: Both hGTX and spermine NONOate inhibited MGMT activity in HT29, SF188, T98G, and other brain tumor cells. There was a robust increase in the alkylation-induced DNA interstrand cross-linking, G2/M cell cycle arrest, cytotoxicity, and the levels of apoptotic markers when either of the agents was used with alkylating agents. In the nude mice bearing T98G and HT29-luc2 xenografts, combinations of hGTX and spermine NONOate with alkylating agents produced a marked reduction in MGMT protein and tumor growth delay and regressions. N6022 treatment increased the presence of nitrosylated MGMT for a longer time, thereby extending the DNA-repair deficient state both in cell culture and preclinical settings. Conclusions: Our findings highlight the options for redox-driven therapeutic strategies for MGMT and suggest that oxidative and/or nitrosative inactivation of DNA repair in combination with alkylating agents could be exploited. Full article
(This article belongs to the Section Oncology)
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29 pages, 1598 KiB  
Review
Virtual Biopsy for the Prediction of MGMT Promoter Methylation in Gliomas: A Comprehensive Review of Radiomics and Deep Learning Approaches Applied to MRI
by Augusto Leone, Veronica Di Napoli, Nicola Pio Fochi, Giuseppe Di Perna, Uwe Spetzger, Elena Filimonova, Flavio Angileri, Francesco Carbone and Antonio Colamaria
Diagnostics 2025, 15(3), 251; https://doi.org/10.3390/diagnostics15030251 - 22 Jan 2025
Viewed by 1794
Abstract
Background/Objectives: The methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) promoter in gliomas has emerged as a critical biomarker for prognosis and treatment response. Conventional methods for assessing MGMT promoter methylation, such as methylation-specific PCR, are invasive and require tissue sampling. Methods: [...] Read more.
Background/Objectives: The methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) promoter in gliomas has emerged as a critical biomarker for prognosis and treatment response. Conventional methods for assessing MGMT promoter methylation, such as methylation-specific PCR, are invasive and require tissue sampling. Methods: A comprehensive literature search was performed in compliance with the updated PRISMA 2020 guidelines within electronic databases MEDLINE/PubMed, Scopus, and IEEE Xplore. Search terms, including “MGMT”, “methylation”, “glioma”, “glioblastoma”, “machine learning”, “deep learning”, and “radiomics”, were adopted in various MeSH combinations. Original studies in the English, Italian, German, and French languages were considered for inclusion. Results: This review analyzed 34 studies conducted in the last six years, focusing on assessing MGMT methylation status using radiomics (RD), deep learning (DL), or combined approaches. These studies utilized radiological data from the public (e.g., BraTS, TCGA) and private institutional datasets. Sixteen studies focused exclusively on glioblastoma (GBM), while others included low- and high-grade gliomas. Twenty-seven studies reported diagnostic accuracy, with fourteen achieving values above 80%. The combined use of DL and RD generally resulted in higher accuracy, sensitivity, and specificity, although some studies reported lower minimum accuracy compared to studies using a single model. Conclusions: The integration of RD and DL offers a powerful, non-invasive tool for precisely recognizing MGMT promoter methylation status in gliomas, paving the way for enhanced personalized medicine in neuro-oncology. The heterogeneity of study populations, data sources, and methodologies reflected the complexity of the pipeline and machine learning algorithms, which may require general standardization to be implemented in clinical practice. Full article
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15 pages, 744 KiB  
Systematic Review
[18F]FDG PET-Based Radiomics and Machine Learning for the Assessment of Gliomas and Glioblastomas: A Systematic Review
by Francesco Dondi, Roberto Gatta, Maria Gazzilli, Pietro Bellini, Gian Luca Viganò, Cristina Ferrari, Antonio Rosario Pisani, Giuseppe Rubini and Francesco Bertagna
Information 2025, 16(1), 58; https://doi.org/10.3390/info16010058 - 16 Jan 2025
Cited by 1 | Viewed by 1096
Abstract
Background: Some evidence of the value of 18F-fluorodesoxyglucose ([18F]FDG) positron emission tomography (PET) imaging for the assessment of gliomas and glioblastomas (GBMs) is emerging. The aim of this systematic review was to assess the role of [18F]FDG PET-based radiomics and machine learning (ML) [...] Read more.
Background: Some evidence of the value of 18F-fluorodesoxyglucose ([18F]FDG) positron emission tomography (PET) imaging for the assessment of gliomas and glioblastomas (GBMs) is emerging. The aim of this systematic review was to assess the role of [18F]FDG PET-based radiomics and machine learning (ML) in the evaluation of these neoplasms. Methods: A wide literature search of the PubMed/MEDLINE, Scopus, and Cochrane Library databases was made to find relevant published articles on the role of [18F]FDG PET-based radiomics and ML for the assessment of gliomas and GBMs. Results: Eight studies were included in the systematic review. Signatures, including radiomics analysis and ML, generally demonstrated a possible diagnostic value to assess different characteristics of gliomas and GBMs, such as the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) promoter, the isocitrate dehydrogenase (IDH) genotype, alpha thalassemia/mental retardation X-linked (ATRX) mutation status, proliferative activity, differential diagnosis with solitary brain metastases or primary central nervous system lymphoma, and prognosis of these patients. Conclusion: Despite some intrinsic limitations of radiomics and ML affecting the studies included in the review, some initial insights on the promising role of these technologies for the assessment of gliomas and GBMs are emerging. Validation of these preliminary findings in multicentric studies is needed to translate radiomics and ML approaches in the clinical setting. Full article
(This article belongs to the Special Issue Computer Vision, Pattern Recognition and Machine Learning in Italy)
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17 pages, 12603 KiB  
Article
Targeting Metabolic and Epigenetic Vulnerabilities in Glioblastoma with SN-38 and Rabusertib Combination Therapy
by Jennifer Chiou, Valeria Impedovo, Yen Bao Huynh, Ruggiero Gorgoglione, Luiz O. F. Penalva, Alessia Lodi, Andrew J. Brenner and Stefano Tiziani
Int. J. Mol. Sci. 2025, 26(2), 474; https://doi.org/10.3390/ijms26020474 - 8 Jan 2025
Viewed by 1535
Abstract
Glioblastoma (GBM), the most prevalent primary malignant brain tumor, remains challenging to treat due to extensive inter- and intra-tumor heterogeneity. This variability demands combination treatments to improve therapeutic outcomes. A significant obstacle in treating GBM is the expression of O6-methylguanine-DNA methyltransferase, [...] Read more.
Glioblastoma (GBM), the most prevalent primary malignant brain tumor, remains challenging to treat due to extensive inter- and intra-tumor heterogeneity. This variability demands combination treatments to improve therapeutic outcomes. A significant obstacle in treating GBM is the expression of O6-methylguanine-DNA methyltransferase, a DNA repair enzyme that reduces the efficacy of the standard alkylating agent, temozolomide, in about 50% of patients. This underscores the need for novel, more targeted therapies. Our study investigates the metabolic–epigenetic impact of combining SN-38, a novel topoisomerase inhibitor inducing DNA double-strand breaks, with rabusertib, a checkpoint kinase 1 inhibitor. We identified this synergistic combination through high-throughput drug screening across a panel of GBM cell lines using a cancer drug library combined with SN-38. A secondary metabolic screening with the PEDS algorithm demonstrated a synergistic modulation of purine, one-carbon, and redox metabolism. Furthermore, the combined treatment led to the significant depletion of epigenetically relevant metabolites such as 5-methyl-cytosine, acetyl-lysine, and trimethyl-lysine. Reduced intermediates of the glutathione cycle indicated increased cellular stress following combinatorial treatment. Overall, the combination of SN-38 and rabusertib synergistically disrupts metabolites associated with epigenetic adaptations, leading to cytotoxicity independent of O6-methylguanine-DNA methyltransferase status, thereby underpinning this combination as a promising candidate for combinatorial therapy in GBM. Full article
(This article belongs to the Special Issue Current Developments in Glioblastoma Research and Therapy)
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24 pages, 3412 KiB  
Article
Mutations in the PIK3C2B, ERBB3, KIT, and MLH1 Genes and Their Relationship with Resistance to Temozolomide in Patients with High-Grade Gliomas
by León Darío Ortiz Gómez, Heidy Johanna Contreras Martínez, David Andrés Galvis Pareja, Sara Vélez Gómez, Jorge Emilio Salazar Flórez, Fernando P. Monroy and Ronald Guillermo Peláez Sánchez
Biomedicines 2024, 12(12), 2777; https://doi.org/10.3390/biomedicines12122777 - 6 Dec 2024
Viewed by 1468
Abstract
Introduction. The treatment for patients with high-grade gliomas includes surgical resection of tumor, radiotherapy, and temozolomide chemotherapy. However, some patients do not respond to temozolomide due to a methylation reversal mechanism by the enzyme O6-methylguanine-DNA-methyltransferase (MGMT). In patients receiving treatment with [...] Read more.
Introduction. The treatment for patients with high-grade gliomas includes surgical resection of tumor, radiotherapy, and temozolomide chemotherapy. However, some patients do not respond to temozolomide due to a methylation reversal mechanism by the enzyme O6-methylguanine-DNA-methyltransferase (MGMT). In patients receiving treatment with temozolomide, this biomarker has been used as a prognostic factor. However, not all patients respond in the same way, which suggests the existence of other proteins involved in resistance to temozolomide chemotherapy. Methods. A group of thirty-one patients was recruited who were clinically and pathologically diagnosed with high-grade gliomas. The sequencing of 324 genes related to different types of cancer was performed to detect mutations. Subsequently, a statistical analysis was conducted to determine the mutated genes that were most related to resistance to treatment. Results. According to the Stupp protocol and metronomic dose of the temozolomide treatment, the mutated genes related to the second relapse of patients with high-grade glioma were PIK3C2B, KIT, ERBB3, and MLH1. Conclusions. Considering the results obtained, we suggest that mutations in the four genes and methylation of the gene promoter that codes for the MGMT protein could be related to response to treatment with temozolomide. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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20 pages, 3927 KiB  
Review
Impact of Sex Hormones on Glioblastoma: Sex-Related Differences and Neuroradiological Insights
by Jessica Rossi, Marialuisa Zedde, Manuela Napoli, Rosario Pascarella, Anna Pisanello, Giuseppe Biagini and Franco Valzania
Life 2024, 14(12), 1523; https://doi.org/10.3390/life14121523 - 21 Nov 2024
Viewed by 2054
Abstract
Glioblastoma (GBM) displays significant gender disparities, being 1.6 times more prevalent in men, with a median survival time of 15.0 months for males compared to 25.5 months for females. These differences may be linked to gonadal steroid hormones, particularly testosterone, which interacts with [...] Read more.
Glioblastoma (GBM) displays significant gender disparities, being 1.6 times more prevalent in men, with a median survival time of 15.0 months for males compared to 25.5 months for females. These differences may be linked to gonadal steroid hormones, particularly testosterone, which interacts with the androgen receptor (AR) to promote tumor proliferation. Conversely, estrogen (E2), progesterone (P4), and P4 metabolites exert more complex effects on GBM. Despite these insights, the identification of reliable hormonal tumor markers remains challenging, and studies investigating hormone therapies yield inconclusive results due to small sample sizes and heterogeneous tumor histology. Additionally, genetic, epigenetic, and immunological factors play critical roles in sex disparities, with female patients demonstrating increased O6-Methylguanine-DNA methyltransferase promoter methylation and greater genomic instability. These complexities highlight the need for personalized therapeutic strategies that integrate hormonal influences alongside other sex-specific biological characteristics in the management of GBM. In this review, we present the current understanding of the potential role of sex hormones in the natural history of GBM. Full article
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16 pages, 5276 KiB  
Article
Multimodal MRI and 1H-MRS for Preoperative Stratification of High-Risk Molecular Subtype in Adult-Type Diffuse Gliomas
by Xin Han, Kai Xiao, Jie Bai, Fengqi Li, Bixiao Cui, Ye Cheng, Huawei Liu and Jie Lu
Diagnostics 2024, 14(22), 2569; https://doi.org/10.3390/diagnostics14222569 - 15 Nov 2024
Viewed by 1309
Abstract
Isocitrate dehydrogenase (IDH) and O6-methylguanine-DNA methyltransferase (MGMT) genes are critical molecular markers in determining treatment options and predicting the prognosis of adult-type diffuse gliomas. Objectives: this study aimed to investigate whether multimodal MRI enables the differentiation of genotypes in adult-type [...] Read more.
Isocitrate dehydrogenase (IDH) and O6-methylguanine-DNA methyltransferase (MGMT) genes are critical molecular markers in determining treatment options and predicting the prognosis of adult-type diffuse gliomas. Objectives: this study aimed to investigate whether multimodal MRI enables the differentiation of genotypes in adult-type diffuse gliomas. Methods: a total of 116 adult-type diffuse glioma patients (61 males, 51.5 (37, 62) years old) who underwent multimodal MRI before surgery were retrospectively analysed. Multimodal MRI included conventional MRI, proton magnetic resonance spectroscopy (1H-MRS), and diffusion tensor imaging (DTI). Conventional visual features, N-acetyl-aspartate (NAA)/Creatine (Cr), Choline (Cho)/Cr, Cho/NAA, fractional anisotropy (FA), mean diffusivity (MD), and diffusion histogram parameters were extracted on the whole tumour. Multimodal MRI parameters of IDH-mutant and IDH-wildtype gliomas were compared using the Mann–Whitney U test, Student’s t-test, or Pearson chi-square tests. Logistic regression was used to select the MRI parameters to predict IDH-mutant gliomas. Furthermore, multimodal MRI parameters were selected to establish models for predicting MGMT methylation in the IDH-wildtype gliomas. The performance of models was evaluated by the receiver operating characteristics curve. Results: a total of 56 patients with IDH-mutant gliomas and 60 patients with IDH-wildtype glioblastomas (GBM) (37 with methylated MGMT and 17 with unmethylated MGMT) were diagnosed by 2021 WHO classification criteria. The enhancement degree (OR = 4.298, p < 0.001), necrosis/cyst (OR = 5.381, p = 0.011), NAA/Cr (OR = 0.497, p = 0.037), FA-Skewness (OR = 0.497, p = 0.033), MD-Skewness (OR = 1.849, p = 0.035), FAmean (OR = 1.924, p = 0.049) were independent factors for the multimodal combined prediction model in predicting IDH-mutant gliomas. The combined modal based on conventional MRI, 1H-MRS, DTI parameters, and histogram performed best in predicting IDH-wildtype status (AUC = 0.890). However, only NAA/Cr (OR = 0.17, p = 0.043) and FA (OR = 0.38, p = 0.015) were associated with MGMT methylated in IDH-wildtype GBM. The combination of NAA/Cr and FA-Median is more accurate for predicting MGMT methylation levels than using these elements alone (AUC, 0.847 vs. 0.695/0.684). Conclusions: multimodal MRI based on conventional MRI, 1H-MRS, and DTI can provide compound imaging markers for stratified individual diagnosis of IDH mutant and MGMT promoter methylation in adult-type diffuse gliomas. Full article
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