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Wang X, Jiang Y, Sun Y. Revealing genomic heterogeneity and commonality: A penalized integrative analysis approach accounting for the adjacency structure of measurements. Genet Epidemiol 2024; 48:114-140. [PMID: 38317326 DOI: 10.1002/gepi.22549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Advancements in high-throughput genomic technologies have revolutionized the field of disease biomarker identification by providing large-scale genomic data. There is an increasing focus on understanding the relationships among diverse patient groups with distinct disease subtypes and characteristics. Complex diseases exhibit both heterogeneity and shared genomic factors, making it essential to investigate these patterns to accurately detect markers and comprehensively understand the diseases. Integrative analysis has emerged as a promising approach to address this challenge. However, existing studies have been limited by ignoring the adjacency structure of genomic measurements, such as single nucleotide polymorphisms (SNPs) and DNA methylations. In this study, we propose a structured integrative analysis method that incorporates a spline type penalty to accommodate this adjacency structure. We utilize a fused lasso type penalty to identify both heterogeneity and commonality across the groups. Extensive simulations demonstrate its superiority compared to several direct competing methods. The analysis of The Cancer Genome Atlas melanoma data with DNA methylation measurements and GENEVA diabetes data with SNP measurements exhibit that the proposed analysis lead to meaningful findings with better prediction performance and higher selection stability.
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Affiliation(s)
- Xindi Wang
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Yu Jiang
- School of Public Health, The University of Memphis, Memphis, Tennessee, USA
| | - Yifan Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
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2
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Fang Q. The Versatile Attributes of MGMT: Its Repair Mechanism, Crosstalk with Other DNA Repair Pathways, and Its Role in Cancer. Cancers (Basel) 2024; 16:331. [PMID: 38254819 PMCID: PMC10814553 DOI: 10.3390/cancers16020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT or AGT) is a DNA repair protein with the capability to remove alkyl groups from O6-AlkylG adducts. Moreover, MGMT plays a crucial role in repairing DNA damage induced by methylating agents like temozolomide and chloroethylating agents such as carmustine, and thereby contributes to chemotherapeutic resistance when these agents are used. This review delves into the structural roles and repair mechanisms of MGMT, with emphasis on the potential structural and functional roles of the N-terminal domain of MGMT. It also explores the development of cancer therapeutic strategies that target MGMT. Finally, it discusses the intriguing crosstalk between MGMT and other DNA repair pathways.
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Affiliation(s)
- Qingming Fang
- Department of Biochemistry and Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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3
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Todeschi J, Dannhoff G, Chibbaro S, Segbedji F, Spatola G, Mallereau CH, Noel G, Schott R, Lhermitte B, Cebula H, Ganau M. Second Cancer Affecting the Central Nervous System: Systematic Literature Review Exploring the Link Between Malignant Melanoma and Glioblastoma. World Neurosurg 2023; 179:178-184. [PMID: 37625631 DOI: 10.1016/j.wneu.2023.08.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is a malignant primary brain cancer, among the most devastating and lethal diseases of the central nervous system. Similarly, malignant melanoma (MM) is responsible for most skin cancer-related deaths. A link between those 2 aggressive cancers has not yet been established. We present here a systematic review of the literature and an exemplificative case. METHODS A systematic review of the literature was conducted to assess possible commonalities between MM and GBM. An exemplificative surgical vignette of a 73-year-old patient with the occurrence of a frontobasal GBM after surgical removal of a metastasis of MM in the same location was then detailed. RESULTS Fifteen studies published in the English international literature support a link between MM and GBM, both based on epidemiologic and pathophysiologic/genetic aspects. This theory is reinforced by our surgical vignette of a collision tumor with the occurrence of both tumors in the same location several years apart. CONCLUSIONS The evidence reported in the literature, as well as our surgical vignette, support a likely link between the pathogenesis of GBM and MM.
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Affiliation(s)
- Julien Todeschi
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Guillaume Dannhoff
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France.
| | - Salvatore Chibbaro
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Felix Segbedji
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Giorgio Spatola
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | | | - Georges Noel
- Department of Radiotherapy, Strasbourg University Hospital, Strasbourg, France
| | - Roland Schott
- Department of Neuro-oncology, Strasbourg University Hospital, Strasbourg, France
| | - Benoit Lhermitte
- Histopathology Unit, Strasbourg University Hospital, Strasbourg, France
| | - Hélène Cebula
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Mario Ganau
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
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Association between MGMT status and response to alkylating agents in patients with neuroendocrine neoplasms: a systematic review and meta-analysis. Biosci Rep 2021; 40:222307. [PMID: 32141507 PMCID: PMC7098124 DOI: 10.1042/bsr20194127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 12/28/2022] Open
Abstract
Background: O6-methylguanine-DNA methyltransferase (MGMT) is a specific DNA damage reversal repair protein. The influence of MGMT status on alkylating agent sensitivity in patients with neuroendocrine neoplasms (NENs) is controversial. We conducted a meta-analysis to assess the influence of MGMT status on the therapeutic sensitivity of alkylating agents in patients with NENs. Methods: We searched PubMed, EmBase, and Cochrane library public databases through 3 July 2019. The objective response rate (ORR) was the outcome data of interest. Subgroup analysis was performed according based on MGMT methylation and expression of MGMT protein. Results: Eleven studies were included in the meta-analysis. The proportion of patients with NENs that achieved an ORR after alkylating agent treatment was higher in the MGMT-deficient group than the non-deficient group (OR: 5.00; 95% CI: 3.04–8.22; P < 0.001; I2: 3%). Similar results were noted in the MGMT methylation and MGMT protein expression subgroups. Conclusion: Patients with NENs and MGMT methylation or low protein expression had a higher ORR proportion than patients without MGMT methylation or high protein expression. The MGMT status can be used as a biological indicator of the response to alkylating agent treatment in patients with NENs.
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Yang K, Stein TD, Huber BR, Sartor EA, Rachlin JR, Mahalingam M. Glioblastoma and malignant melanoma: Serendipitous or anticipated association? Neuropathology 2020; 41:65-71. [PMID: 33103282 DOI: 10.1111/neup.12702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022]
Abstract
We describe a patient who had primary glioblastoma (GB) and malignant melanoma (MM). A 78-year-old man presented with several weeks to months of history of gait disturbance, confusion, memory disturbance, and worsening speech. Imaging studies performed on admission revealed a large frontotemporal lobe mass associated with the surrounding zone of vasogenic edema. Given the patient's medical history of incomplete biopsy of a midback tumor performed three weeks before, the presumptive clinical diagnosis was metastatic MM. Pathological examination of frozen sections of fragmented specimens obtained at stereotactic biopsy performed on admission revealed a high-grade malignant neoplasm characterized by discohesive cells in a blue myxoid background and abundant foci of tumor necrosis. Given these features, in conjunction with the abovementioned pathological report, the frozen section diagnosis by the neuropathologist was "neoplasm identified, favor melanoma." Due to the paucity of lesional tissue, a limited immunohistochemistry performed on the permanent sections revealed positive staining of lesional cells for Sox10 alone using a multiplex MART1/Sox10 immunostain and S-100 protein, an immunohistochemical profile supporting the presumptive frozen section diagnosis. A tumor debulk procedure, performed two weeks later, revealed histopathologic features most compatible with GB, IDH wild-type. Thus, additional immunohistochemistry on the permanent sections revealed positive staining of glial fibrillary acidic protein (GFAP), Sox10, and S-100 protein as well as negative staining of gp100, a complex carbohydrate matrix protein in embryonic melanosomes, using a specific antibody HMB45. The concomitant occurrence of MM and GB in our patient underscores the association between these two entities. Our literature review suggests that the sporadic co-occurrence of these two conditions is likely not serendipitous.
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Affiliation(s)
- Kevin Yang
- Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Thor D Stein
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA.,VA Boston Healthcare System, Jamaica Plain, Massachusetts, USA
| | - Bertrand R Huber
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA.,VA Boston Healthcare System, Jamaica Plain, Massachusetts, USA
| | - Emmett A Sartor
- VA Boston Healthcare System, Jamaica Plain, Massachusetts, USA
| | - Jacob R Rachlin
- VA Boston Healthcare System, Jamaica Plain, Massachusetts, USA
| | - Meera Mahalingam
- Tufts University School of Medicine, Boston, Massachusetts, USA.,Dermatopathology Section, Department of Pathology and Laboratory Medicine, VA Consolidated Laboratories, West Roxbury, Massachusetts, USA
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Yu W, Zhang L, Wei Q, Shao A. O 6-Methylguanine-DNA Methyltransferase (MGMT): Challenges and New Opportunities in Glioma Chemotherapy. Front Oncol 2020; 9:1547. [PMID: 32010632 PMCID: PMC6979006 DOI: 10.3389/fonc.2019.01547] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/20/2019] [Indexed: 12/18/2022] Open
Abstract
Chemoresistance has been a significant problem affecting the efficacy of drugs targeting tumors for decades. MGMT, known as O6-methylguanine-DNA methyltransferase, is a DNA repair enzyme that plays an important role in chemoresistance to alkylating agents. Hence, MGMT is considered a promising target for tumor treatment. Several methods are employed to detect MGMT, each with its own advantages and disadvantages. Some of the detection methods are; immunohistochemistry, methylation-specific PCR (MSP), pyrophosphate sequencing, MGMT activity test, and real-time quantitative PCR. Methylation of MGMT promoter is a key predictor of whether alkylating agents can effectively control glioma cells. The prognostic value of MGMT in glioma is currently being explored. The expression of MGMT gene mainly depends on epigenetic modification–methylation of CpG island of MGMT promoter. CpG island covers a length of 762 bp, with 98 CpG sites located at the 5' end of the gene, ranging from 480 to 1,480 nucleotides. The methylation sites and frequencies of CpG islands vary in MGMT-deficient tumor cell lines, xenografts of glioblastoma and in situ glioblastoma. Methylation in some regions of promoter CpG islands is particularly associated with gene expression. The change in the methylation status of the MGMT promoter after chemotherapy, radiotherapy or both is not completely understood, and results from previous studies have been controversial. Several studies have revealed that chemotherapy may enhance MGMT expression in gliomas. This could be through gene induction or selection of high MGMT-expressing cells during chemotherapy. Selective survival of glioma cells with high MGMT expression during alkylating agent therapy may change MGMT status in case of recurrence. Several strategies have been pursued to improve the anti-tumor effects of temozolomide. These include the synthesis of analogs of O6-meG such as O6-benzylguanine (O6-BG) and O6-(4-bromothenyl) guanine (O6-BTG), RNAi, and viral proteins. This review describes the regulation of MGMT expression and its role in chemotherapy, especially in glioma. Targeting MGMT seems to be a promising approach to overcome chemoresistance. Further studies exploring new agents targeting MGMT with better curative effect and less toxicity are advocated. We anticipate that these developments will improve the current poor prognosis of glioma patients.
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Affiliation(s)
- Wei Yu
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute (Ministry of Education Key Laboratory of Cancer Prevention and Intervention), Zhejiang University Cancer Institute, Hangzhou, China
| | - Lili Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute (Ministry of Education Key Laboratory of Cancer Prevention and Intervention), Zhejiang University Cancer Institute, Hangzhou, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute (Ministry of Education Key Laboratory of Cancer Prevention and Intervention), Zhejiang University Cancer Institute, Hangzhou, China
| | - Anwen Shao
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Guo Y, Long J, Lei S. Promoter methylation as biomarkers for diagnosis of melanoma: A systematic review and meta-analysis. J Cell Physiol 2018; 234:7356-7367. [PMID: 30370527 DOI: 10.1002/jcp.27495] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 09/06/2018] [Indexed: 01/19/2023]
Abstract
Melanoma is one of the most common skin cancer that is characterized by rapid growth, early metastasis, high malignant, and mortality. Accumulating evidence demonstrated that promoter methylation of tumor-suppressor genes is implicated in the pathogenesis of melanoma. In the current study, we performed a meta-analysis to identify promising methylation biomarkers in the diagnosis of melanoma. We carried out a systematic literature search using Pubmed, Embase, and ISI web knowledge database and found that gene promoter methylation of 50 genes was reported to be associated with the risk of melanoma. Meta-analysis revealed that hypermethylation of claudin 11 (CLDN11; odds ratio [OR], 16.82; 95% confidence interval [CI], 1.97-143.29; p = 0.010), O-6-methylguanine-DNA methyltransferase (MGMT; OR, 5.59; 95% CI, 2.51-12.47; p < 0.0001), cyclin-dependent kinase inhibitor 2A (p16; OR, 6.57; 95% CI, 2.19-19.75; p = 0.0008), retinoic acid receptor β (RAR-β2; OR, 24.31; 95% CI, 4.58-129.01; p = 0.0002), and Ras association domain family member (RASSF1A; OR, 9.35; 95% CI, 4.73-18.45; p < 0.00001) was significantly higher in melanoma patients compared with controls. CLDN11 (OR, 14.52; 95% CI, 1.84-114.55; p = 0.01), MGMT (OR, 8.08; 95% CI, 1.84-35.46; p = 0.006), p16 (OR, 9.44; 95% CI, 2.68-33.29; p = 0.0005), and RASSF1A (OR, 7.72; 95% CI, 1.05-56.50; p = 0.04) hypermethylation was significantly increased in primary melanoma compared with controls. Methylation frequency of CLDN11 (OR, 25.56; 95% CI, 2.32-281.66; p = 0.008), MGMT (OR, 4.64; 95% CI, 1.98-10.90; p = 0.0004), p16 (OR, 4.31; 95% CI, 1.33-13.96; p = 0.01), and RASSF1A (OR, 10.10; 95% CI, 2.87-35.54; p = 0.0003) was significantly higher in metastasis melanoma compared with controls. These findings indicated that CLDN11, MGMT, p16, RAR-β2, and RASSF1A hypermethylation is a risk factor and a potential biomarker for melanoma. CLDN11, MGMT, p16, and RASSF1A promoter methylation may take part in the development of melanoma and become useful biomarkers in the early diagnosis of the disease.
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Affiliation(s)
- Yu Guo
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jianhong Long
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Shaorong Lei
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
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Rare Stochastic Expression of O6-Methylguanine- DNA Methyltransferase (MGMT) in MGMT-Negative Melanoma Cells Determines Immediate Emergence of Drug-Resistant Populations upon Treatment with Temozolomide In Vitro and In Vivo. Cancers (Basel) 2018; 10:cancers10100362. [PMID: 30274152 PMCID: PMC6209933 DOI: 10.3390/cancers10100362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/01/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022] Open
Abstract
The chemotherapeutic agent temozolomide (TMZ) kills tumor cells preferentially via alkylation of the O6-position of guanine. However, cells that express the DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT), or harbor deficient DNA mismatch repair (MMR) function, are profoundly resistant to this drug. TMZ is in clinical use for melanoma, but objective response rates are low, even when TMZ is combined with O6-benzylguanine (O6BG), a potent MGMT inhibitor. We used in vitro and in vivo models of melanoma to characterize the early events leading to cellular TMZ resistance. Melanoma cell lines were exposed to a single treatment with TMZ, at physiologically relevant concentrations, in the absence or presence of O6BG. Surviving clones and mass cultures were analyzed by Western blot, colony formation assays, and DNA methylation studies. Mice with melanoma xenografts received TMZ treatment, and tumor tissue was analyzed by immunohistochemistry. We found that MGMT-negative melanoma cell cultures, before any drug treatment, already harbored a small fraction of MGMT-positive cells, which survived TMZ treatment and promptly became the dominant cell type within the surviving population. The MGMT-negative status in individual cells was not stable, as clonal selection of MGMT-negative cells again resulted in a mixed population harboring MGMT-positive, TMZ-resistant cells. Blocking the survival advantage of MGMT via the addition of O6BG still resulted in surviving clones, although at much lower frequency and independent of MGMT, and the resistance mechanism of these clones was based on a common lack of expression of MSH6, a key MMR enzyme. TMZ treatment of mice implanted with MGMT-negative melanoma cells resulted in effective tumor growth delay, but eventually tumor growth resumed, with tumor tissue having become MGMT positive. Altogether, these data reveal stochastic expression of MGMT as a pre-existing, key determinant of TMZ resistance in melanoma cell lines. Although MGMT activity can effectively be eliminated by pharmacologic intervention with O6BG, additional layers of TMZ resistance, although considerably rarer, are present as well and minimize the cytotoxic impact of TMZ/O6BG combination treatment. Our results provide rational explanations regarding clinical observations, where the TMZ/O6BG regimen has yielded mostly disappointing outcomes in melanoma patients.
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