1
|
Lei J, Huang Y, Zhao Y, Zhou Z, Mao L, Liu Y. Nanotechnology as a new strategy for the diagnosis and treatment of gliomas. J Cancer 2024; 15:4643-4655. [PMID: 39006067 PMCID: PMC11242339 DOI: 10.7150/jca.96859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
Glioma is the most common malignant tumor of the central nervous system (CNS), and is characterized by high aggressiveness and a high recurrence rate. Currently, the main treatments for gliomas include surgical resection, temozolomide chemotherapy and radiotherapy. However, the prognosis of glioma patients after active standardized treatment is still poor, especially for glioblastoma (GBM); the median survival is still only 14.6 months, and the 5-year survival rate is only 4-5%. The current challenges in glioma treatment include difficulty in complete surgical resection, poor blood‒brain barrier (BBB) drug permeability, therapeutic resistance, and difficulty in tumor-specific targeting. In recent years, the rapid development of nanotechnology has provided new directions for diagnosing and treating gliomas. Nanoparticles (NPs) are characterized by excellent surface tunability, precise targeting, excellent biocompatibility, and high safety. In addition, NPs can be used for gene therapy, photodynamic therapy, and antiangiogenic therapy and can be combined with biomaterials for thermotherapy. In recent decades, breakthroughs in diagnosing and treating gliomas have been made with various functional NPs, and NPs are expected to become a new strategy for glioma diagnosis and treatment. In this paper, we review the main obstacles in the treatment of glioma and discuss the potential and challenges of the latest nanotechnology in the diagnosis and treatment of glioma.
Collapse
Affiliation(s)
- Jun Lei
- Department of Neurosurgery, The First People's Hospital of Shuangliu District (West China Airport Hospital of Sichuan University), Chengdu 610200, China
- Department of Neurosurgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yiyang Huang
- Department of Neurosurgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yichuan Zhao
- Southwest Medical University, Luzhou 646000, China
| | - Zhi Zhou
- Department of Neurosurgery, The First People's Hospital of Shuangliu District (West China Airport Hospital of Sichuan University), Chengdu 610200, China
| | - Lei Mao
- Department of Neurosurgery, The First People's Hospital of Shuangliu District (West China Airport Hospital of Sichuan University), Chengdu 610200, China
| | - Yanhui Liu
- Department of Neurosurgery, West China Hospital of Sichuan University, Chengdu 610041, China
| |
Collapse
|
2
|
Zappe K, Cichna-Markl M. Temperature-Wise Calibration Increases the Accuracy of DNA Methylation Levels Determined by High-Resolution Melting (HRM). Int J Mol Sci 2024; 25:5082. [PMID: 38791122 PMCID: PMC11121480 DOI: 10.3390/ijms25105082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
High-resolution melting (HRM) is a cost-efficient tool for targeted DNA methylation analysis. HRM yields the average methylation status across all CpGs in PCR products. Moreover, it provides information on the methylation pattern, e.g., the occurrence of monoallelic methylation. HRM assays have to be calibrated by analyzing DNA methylation standards of known methylation status and mixtures thereof. In general, DNA methylation levels determined by the classical calibration approach, including the whole temperature range in between normalization intervals, are in good agreement with the mean of the DNA methylation status of individual CpGs determined by pyrosequencing (PSQ), the gold standard of targeted DNA methylation analysis. However, the classical calibration approach leads to highly inaccurate results for samples with heterogeneous DNA methylation since they result in more complex melt curves, differing in their shape compared to those of DNA standards and mixtures thereof. Here, we present a novel calibration approach, i.e., temperature-wise calibration. By temperature-wise calibration, methylation profiles over temperature are obtained, which help in finding the optimal calibration range and thus increase the accuracy of HRM data, particularly for heterogeneous DNA methylation. For explaining the principle and demonstrating the potential of the novel calibration approach, we selected the promoter and two enhancers of MGMT, a gene encoding the repair protein MGMT.
Collapse
Affiliation(s)
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
| |
Collapse
|
3
|
Gibson D, Vo AH, Lambing H, Bhattacharya P, Tahir P, Chehab FF, Butowski N. A systematic review of high impact CpG sites and regions for MGMT methylation in glioblastoma [A systematic review of MGMT methylation in GBM]. BMC Neurol 2024; 24:103. [PMID: 38521933 PMCID: PMC10960428 DOI: 10.1186/s12883-024-03605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/17/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND MGMT (O 6 -methylguanine-DNA methyltransferase) promoter methylation is a commonly assessed prognostic marker in glioblastoma (GBM). Epigenetic silencing of the MGMT gene by promoter methylation is associated with greater overall and progression free survival with alkylating agent regimens. To date, there is marked heterogeneity in how MGMT promoter methylation is tested and which CpG sites are interrogated. METHODS To further elucidate which MGMT promoter CpG sites are of greatest interest, we performed comprehensive searches in PubMed, Web of Science, and Embase and reviewed 2,925 article abstracts. We followed the GRADE scoring system to assess risk of bias and the quality of the studies we included. RESULTS We included articles on adult glioblastoma that examined significant sites or regions within MGMT promoter for the outcomes: overall survival, progression free survival, and/or MGMT expression. We excluded systemic reviews and articles on lower grade glioma. fifteen articles met inclusion criteria with variable overlap in laboratory and statistical methods employed, as well as CpG sites interrogated. Pyrosequencing or BeadChip arrays were the most popular methods utilized, and CpG sites between CpG's 70-90 were most frequently investigated. Overall, there was moderate concordance between the CpG sites that the studies reported to be highly predictive of prognosis. Combinations or means of sites between CpG's 73-89 were associated with improved OS and PFS. Six studies identified CpG sites associated with prognosis that were closer to the transcription start site: CpG's 8, 19, 22, 25, 27, 32,38, and CpG sites 21-37, as well as low methylation level of the enhancer regions. CONCLUSION The following systematic review details a comprehensive investigation of the current literature and highlights several potential key CpG sites that demonstrate significant association with OS, PFS, and MGMT expression. However, the relationship between extent of MGMT promoter methylation and survival may be non-linear and could be influenced by potential CpG hotspots, the extent of methylation at each CpG site, and MGMT enhancer methylation status. There were several limitations within the studies such as smaller sample sizes, variance between methylation testing methods, and differences in the various statistical methods to test for association to outcome. Further studies of high impact CpG sites in MGMT methylation is warranted.
Collapse
Affiliation(s)
- David Gibson
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
- Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anh Huan Vo
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA.
| | - Hannah Lambing
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Prithanjan Bhattacharya
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
| | - Peggy Tahir
- University of California, San Francisco Library, San Francisco, CA, USA
| | - Farid F Chehab
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas Butowski
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
| |
Collapse
|
4
|
Weber R, Weller M, Reifenberger G, Vasella F. Epigenetic modification and characterization of the MGMT promoter region using CRISPRoff in glioblastoma cells. Front Oncol 2024; 14:1342114. [PMID: 38357209 PMCID: PMC10864556 DOI: 10.3389/fonc.2024.1342114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024] Open
Abstract
The methylation status of the O6-methylguanine DNA methyltransferase (MGMT) promoter region is a critical predictor of response to alkylating agents in glioblastoma. However, current approaches to study the MGMT status focus on analyzing models with non-identical backgrounds. Here, we present an epigenetic editing approach using CRISPRoff to introduce site-specific CpG methylation in the MGMT promoter region of glioma cell lines. Sanger sequencing revealed successful introduction of methylation, effectively generating differently methylated glioma cell lines with an isogenic background. The introduced methylation resulted in reduced MGMT mRNA and protein levels. Furthermore, the cell lines with MGMT promoter region methylation exhibited increased sensitivity to temozolomide, consistent with the impact of methylation on treatment outcomes in patients with glioblastoma. This precise epigenome-editing approach provides valuable insights into the functional relevance of MGMT promoter regional methylation and its potential for prognostic and predictive assessments, as well as epigenetic-targeted therapies.
Collapse
Affiliation(s)
- Remi Weber
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University of Zurich, Zurich, Switzerland
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Flavio Vasella
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| |
Collapse
|
5
|
Zappe K, Pühringer K, Pflug S, Berger D, Weis S, Spiegl-Kreinecker S, Cichna-Markl M. Association of MGMT Promoter and Enhancer Methylation with Genetic Variants, Clinical Parameters, and Demographic Characteristics in Glioblastoma. Cancers (Basel) 2023; 15:5777. [PMID: 38136323 PMCID: PMC10742072 DOI: 10.3390/cancers15245777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The response of glioblastoma (GBM) patients to the alkylating agent temozolomide (TMZ) vitally depends on the expression level of the repair protein O6-methylguanine-DNA methyltransferase (MGMT). Since MGMT is strongly regulated by promoter methylation, the methylation status of the MGMT promoter has emerged as a prognostic and predictive biomarker for GBM patients. By determining the methylation levels of the four enhancers located within or close to the MGMT gene, we recently found that enhancer methylation contributes to MGMT regulation. In this study, we investigated if methylation of the four enhancers is associated with SNP rs16906252, TERT promoter mutations C228T and C250T, TERT SNP rs2853669, proliferation index Ki-67, overall survival (OS), age, and sex of the patients. In general, associations with genetic variants, clinical parameters, and demographic characteristics were caused by a complex interplay of multiple CpGs in the MGMT promoter and of multiple CpGs in enhancer regions. The observed associations for intragenic enhancer 4, located in intron 2 of MGMT, differed from associations observed for the three intergenic enhancers. Some findings were restricted to subgroups of samples with either methylated or unmethylated MGMT promoters, underpinning the relevance of the MGMT promoter status in GBMs.
Collapse
Affiliation(s)
- Katja Zappe
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (K.Z.); (K.P.); (S.P.); (D.B.)
| | - Katharina Pühringer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (K.Z.); (K.P.); (S.P.); (D.B.)
| | - Simon Pflug
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (K.Z.); (K.P.); (S.P.); (D.B.)
| | - Daniel Berger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (K.Z.); (K.P.); (S.P.); (D.B.)
| | - Serge Weis
- Division of Neuropathology, Department of Pathology and Molecular Pathology, Kepler University Hospital GmbH, Johannes Kepler University, 4040 Linz, Austria;
| | - Sabine Spiegl-Kreinecker
- Department of Neurosurgery, Kepler University Hospital GmbH, Johannes Kepler University, 4040 Linz, Austria;
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (K.Z.); (K.P.); (S.P.); (D.B.)
| |
Collapse
|
6
|
Petrova EI, Galstyan SA, Telysheva EN, Ryzhova MV. [Total DNA methylation profile in assessing the MGMT gene promoter status in malignant gliomas]. ZHURNAL VOPROSY NEIROKHIRURGII IMENI N. N. BURDENKO 2023; 87:52-58. [PMID: 38054227 DOI: 10.17116/neiro20238706152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Methylation of the O-6-methylguanine-DNA methyltransferase (MGMT) gene promoter is currently the most important prognostic biomarker in therapy of IDH-wild-type glioblastoma. One can obtain information about this methylation from total DNA methylation profile. OBJECTIVE To analyze the DNA methylation signal intensity in the MGMT gene in samples of malignant gliomas and identify the most significant genomic positions for calculating the MGMT gene promoter status for further improvement of diagnostics and prediction of therapeutic options in patients with malignant gliomas. MATERIAL AND METHODS The study is based on 43 samples (frozen tissue or paraffin blocks) from patients with malignant gliomas. Tumor DNA samples were prepared using the Illumina Infinium MethylationEPIC BeadChip Kit and the Illumina Next-Seq 550 Sequencing System platform. DNA methylation profiles were analyzed using computational algorithms in the R language, specialized libraries minfi and mgmtstp27, as well as basic statistical functions in the Rstudio environment. RESULTS We established the MGMT gene promoter status in 43 samples of malignant gliomas considering total DNA methylation profile. In 24 samples (55%), the MGMT gene promoter was methylated. We compared methylation signal in certain CpG islands in groups with methylated and unmethylated MGMT gene promoters and identified the most significant positions for further improvement of data analysis algorithm. CONCLUSION These data demonstrate the possibilities and prospects for further improvement of algorithm for analysis of the MGMT gene promoter status based on total DNA methylation profile in patients with malignant gliomas as an alternative to methyl-specific PCR. Our results are consistent with data of other neuro-oncology researchers. Indeed, computational methods like MGMT-STP27 are quite powerful and can be used in scientific and clinical practice to assess prognosis and make decisions about chemotherapy with alkylating agents.
Collapse
Affiliation(s)
- E I Petrova
- Burdenko Neurosurgical Center, Moscow, Russia
| | | | | | - M V Ryzhova
- Burdenko Neurosurgical Center, Moscow, Russia
| |
Collapse
|