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Trąbska-Kluch B, Braun M, Orzechowska M, Paszek S, Zuchowska A, Sołek J, Kluska A, Fijuth J, Jesionek-Kupnicka D, Zawlik I. Potential Prognostic Value of GATA4 Depends on the p53 Expression in Primary Glioblastoma Patients. Genes (Basel) 2023; 14:1146. [PMID: 37372326 DOI: 10.3390/genes14061146] [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: 03/31/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Primary glioblastoma is characterized by an extremely poor prognosis. The promoter methylation of GATA4 leads to the loss of its expression in many cancer types. The formation of high-grade astrocytomas can be promoted by the concurrent loss of TP53 and GATA4 in normal human astrocytes. Nevertheless, the impact of GATA4 alterations with linkage to TP53 changes in gliomagenesis is poorly understood. This study aimed to evaluate GATA4 protein expression, GATA4 promoter methylation, p53 expression, TP53 promoter methylation, and mutation status in patients with primary glioblastoma and to assess the possible prognostic impact of these alterations on overall survival. MATERIALS AND METHODS Thirty-one patients with primary glioblastoma were included. GATA4 and p53 expressions were determined immunohistochemically, and GATA4 and TP53 promoter methylations were analyzed via methylation-specific PCR. TP53 mutations were investigated via Sanger sequencing. RESULTS The prognostic value of GATA4 depends on p53 expression. Patients without GATA4 protein expression were more frequently negative for TP53 mutations and had better prognoses than the GATA4 positive patients. In patients positive for GATA4 protein expression, p53 expression was associated with the worst outcome. However, in patients positive for p53 expression, the loss of GATA4 protein expression seemed to be associated with improved prognosis. GATA4 promoter methylation was not associated with a lack of GATA4 protein expression. CONCLUSIONS Our data indicate that there is a possibility that GATA4 could function as a prognostic factor in glioblastoma patients, but in connection with p53 expression. A lack of GATA4 expression is not dependent on GATA4 promoter methylation. GATA4 alone has no influence on survival time in glioblastoma patients.
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Affiliation(s)
- Berenika Trąbska-Kluch
- Department of Teleradiotherapy, Copernicus Memorial Hospital, 93-513 Lodz, Poland
- Department of Radiotherapy, Chair of Oncology, Medical University of Lodz, 93-513 Lodz, Poland
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Lodz, 93-513 Lodz, Poland
| | - Magdalena Orzechowska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 93-513 Lodz, Poland
| | - Sylwia Paszek
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszow, 35-959 Rzeszow, Poland
- Department of General Genetics, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland
| | - Alina Zuchowska
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszow, 35-959 Rzeszow, Poland
- Department of General Genetics, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland
| | - Julia Sołek
- Department of Pathology, Chair of Oncology, Medical University of Lodz, 93-513 Lodz, Poland
| | - Adam Kluska
- Brachytherapy Department, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Jacek Fijuth
- Department of Teleradiotherapy, Copernicus Memorial Hospital, 93-513 Lodz, Poland
- Department of Radiotherapy, Chair of Oncology, Medical University of Lodz, 93-513 Lodz, Poland
| | | | - Izabela Zawlik
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszow, 35-959 Rzeszow, Poland
- Department of General Genetics, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland
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Munquad S, Si T, Mallik S, Li A, Das AB. Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine. Brief Funct Genomics 2022; 21:408-421. [PMID: 35923100 DOI: 10.1093/bfgp/elac025] [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: 03/31/2022] [Revised: 06/23/2022] [Accepted: 07/17/2022] [Indexed: 11/13/2022] Open
Abstract
Classifying lower-grade gliomas (LGGs) is a crucial step for accurate therapeutic intervention. The histopathological classification of various subtypes of LGG, including astrocytoma, oligodendroglioma and oligoastrocytoma, suffers from intraobserver and interobserver variability leading to inaccurate classification and greater risk to patient health. We designed an efficient machine learning-based classification framework to diagnose LGG subtypes and grades using transcriptome data. First, we developed an integrated feature selection method based on correlation and support vector machine (SVM) recursive feature elimination. Then, implementation of the SVM classifier achieved superior accuracy compared with other machine learning frameworks. Most importantly, we found that the accuracy of subtype classification is always high (>90%) in a specific grade rather than in mixed grade (~80%) cancer. Differential co-expression analysis revealed higher heterogeneity in mixed grade cancer, resulting in reduced prediction accuracy. Our findings suggest that it is necessary to identify cancer grades and subtypes to attain a higher classification accuracy. Our six-class classification model efficiently predicts the grades and subtypes with an average accuracy of 91% (±0.02). Furthermore, we identify several predictive biomarkers using co-expression, gene set enrichment and survival analysis, indicating our framework is biologically interpretable and can potentially support the clinician.
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Affiliation(s)
- Sana Munquad
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Tapas Si
- Department of Computer Science and Engineering, Bankura Unnayani Institute of Engineering, Bankura 722146, West Bengal, India
| | - Saurav Mallik
- Department of Environmental Epigenetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Asim Bikas Das
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
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Singh K, Rustagi Y, Abouhashem AS, Tabasum S, Verma P, Hernandez E, Pal D, Khona DK, Mohanty SK, Kumar M, Srivastava R, Guda PR, Verma SS, Mahajan S, Killian JA, Walker LA, Ghatak S, Mathew-Steiner SS, Wanczyk K, Liu S, Wan J, Yan P, Bundschuh R, Khanna S, Gordillo GM, Murphy MP, Roy S, Sen CK. Genome-wide DNA hypermethylation opposes healing in chronic wound patients by impairing epithelial-to-mesenchymal transition. J Clin Invest 2022; 132:157279. [PMID: 35819852 PMCID: PMC9433101 DOI: 10.1172/jci157279] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
An extreme chronic wound tissue microenvironment causes epigenetic gene silencing. An unbiased whole-genome methylome was studied in the wound-edge tissue of patients with chronic wounds. A total of 4,689 differentially methylated regions (DMRs) were identified in chronic wound-edge skin compared with unwounded human skin. Hypermethylation was more frequently observed (3,661 DMRs) in the chronic wound-edge tissue compared with hypomethylation (1,028 DMRs). Twenty-six hypermethylated DMRs were involved in epithelial-mesenchymal transition (EMT). Bisulfite sequencing validated hypermethylation of a predicted specific upstream regulator TP53. RNA-Seq analysis was performed to qualify findings from methylome analysis. Analysis of the downregulated genes identified the TP53 signaling pathway as being significantly silenced. Direct comparison of hypermethylation and downregulated genes identified 4 genes, ADAM17, NOTCH, TWIST1, and SMURF1, that functionally represent the EMT pathway. Single-cell RNA-Seq studies revealed that these effects on gene expression were limited to the keratinocyte cell compartment. Experimental murine studies established that tissue ischemia potently induces wound-edge gene methylation and that 5′-azacytidine, inhibitor of methylation, improved wound closure. To specifically address the significance of TP53 methylation, keratinocyte-specific editing of TP53 methylation at the wound edge was achieved by a tissue nanotransfection-based CRISPR/dCas9 approach. This work identified that reversal of methylation-dependent keratinocyte gene silencing represents a productive therapeutic strategy to improve wound closure.
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Affiliation(s)
- Kanhaiya Singh
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Yashika Rustagi
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Ahmed S Abouhashem
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Saba Tabasum
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Priyanka Verma
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Edward Hernandez
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Durba Pal
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Ropar, India
| | - Dolly K Khona
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Sujit K Mohanty
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Manishekhar Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Rajneesh Srivastava
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Poornachander R Guda
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Sumit S Verma
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Sanskruti Mahajan
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Jackson A Killian
- Department of Physics, Ohio State University, Columbus, United States of America
| | - Logan A Walker
- Department of Physics, Ohio State University, Columbus, United States of America
| | - Subhadip Ghatak
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Shomita S Mathew-Steiner
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Kristen Wanczyk
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Sheng Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, United States of America
| | - Jun Wan
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, United States of America
| | - Pearlly Yan
- Comprehensive Cancer Center, Ohio State University, Columbus, United States of America
| | - Ralf Bundschuh
- Department of Physics, Ohio State University, Columbus, United States of America
| | - Savita Khanna
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Gayle M Gordillo
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Michael P Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Sashwati Roy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
| | - Chandan K Sen
- Department of Surgery, Indiana University School of Medicine, Indianapolis, United States of America
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The relationship between P16 INK4A and TP53 promoter methylation and the risk and prognosis in patients with oesophageal cancer in Thailand. Sci Rep 2022; 12:10337. [PMID: 35725923 PMCID: PMC9209525 DOI: 10.1038/s41598-022-14658-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
DNA methylation can regulate the expression of tumour suppressor genes P16 and TP53, environmental factors, which are both important factors related to an increased risk and prognosis of oesophageal cancer (EC). However, the association between these two genes methylation status, as well as the effects of gene-environment interactions, EC risk remains unclear. A Hospital-based case-control study data were collected from 105 new EC cases and 108 controls. Promoter methylation status was investigated for P16 and TP53 genes using methylation-specific polymerase (MSP) chain reaction methods with SYBR green. Logistic and Cox regression models were used to analyse the association of P16 and TP53 promotor methylation status with EC risk and prognosis, respectively. Our results suggest P16, TP53 methylation significantly increased the risk of EC (OR = 5.24, 95% CI: 2.57-10.66, P < 0.001; OR = 3.38, 95% CI: 1.17-6.67, P < 0.001, respectively). In addition, P16 and TP53 promoter methylation status and the combined effects between environmental factors and its methylations in tissue were correlated with the EC risk and prognosis of EC patients. As a new biomarker, the methylation of P16 and TP53 can serve as a potential predictive biomarker of EC.
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5
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Gousias K, Theocharous T, Simon M. Mechanisms of Cell Cycle Arrest and Apoptosis in Glioblastoma. Biomedicines 2022; 10:biomedicines10030564. [PMID: 35327366 PMCID: PMC8945784 DOI: 10.3390/biomedicines10030564] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Accepted: 02/26/2022] [Indexed: 12/13/2022] Open
Abstract
Cells of glioblastoma, the most frequent primary malignant brain tumor, are characterized by their rapid growth and infiltration of adjacent healthy brain parenchyma, which reflects their aggressive biological behavior. In order to maintain their excessive proliferation and invasion, glioblastomas exploit the innate biological capacities of the patients suffering from this tumor. The pathways involved in cell cycle regulation and apoptosis are the mechanisms most commonly affected. The following work reviews the regulatory pathways of cell growth in general as well as the dysregulated cell cycle and apoptosis relevant mechanisms observed in glioblastomas. We then describe the molecular targeting of the current established adjuvant therapy and present ongoing trials or completed studies on specific promising therapeutic agents that induce cell cycle arrest and apoptosis of glioblastoma cells.
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Affiliation(s)
- Konstantinos Gousias
- Department of Neurosurgery, St. Marien Academic Hospital Lünen, KLW St. Paulus Corporation, 44534 Luenen, Germany;
- Medical School, Westfälische Wilhelms University of Muenster, 48149 Muenster, Germany
- Medical School, University of Nicosia, Nicosia 2414, Cyprus
- Correspondence: ; Tel.: +49-2306-773151
| | - Theocharis Theocharous
- Department of Neurosurgery, St. Marien Academic Hospital Lünen, KLW St. Paulus Corporation, 44534 Luenen, Germany;
| | - Matthias Simon
- Department of Neurosurgery, Bethel Clinic, University of Bielefeld Medical School, 33617 Bielefeld, Germany;
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Hernández A, Domènech M, Muñoz-Mármol AM, Carrato C, Balana C. Glioblastoma: Relationship between Metabolism and Immunosuppressive Microenvironment. Cells 2021; 10:cells10123529. [PMID: 34944036 PMCID: PMC8700075 DOI: 10.3390/cells10123529] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive brain tumor in adults and is characterized by an immunosuppressive microenvironment. Different factors shaping this tumor microenvironment (TME) regulate tumor initiation, progression, and treatment response. Genetic alterations and metabolism pathways are two main elements that influence tumor immune cells and TME. In this manuscript, we review how both factors can contribute to an immunosuppressive state and overview the strategies being tested.
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Affiliation(s)
- Ainhoa Hernández
- B·ARGO (Badalona Applied Research Group of Oncology) Medical Oncology Department, Catalan Institute of Oncology Badalona, 08916 Badalona, Spain; (A.H.); (M.D.)
| | - Marta Domènech
- B·ARGO (Badalona Applied Research Group of Oncology) Medical Oncology Department, Catalan Institute of Oncology Badalona, 08916 Badalona, Spain; (A.H.); (M.D.)
| | - Ana M. Muñoz-Mármol
- Pathology Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (A.M.M.-M.); (C.C.)
| | - Cristina Carrato
- Pathology Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (A.M.M.-M.); (C.C.)
| | - Carmen Balana
- B·ARGO (Badalona Applied Research Group of Oncology) Medical Oncology Department, Catalan Institute of Oncology Badalona, 08916 Badalona, Spain; (A.H.); (M.D.)
- Correspondence: ; Tel.: +34-4978925
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7
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Sfifou F, Ouzir M, Hakkou EM, Obtel M, Errihani H, Bouzidi AA, Abouqal R, El Ouahabi A, Cherradi N. Immunohistochemical expression of HIF-1α, IDH1 and TP53: Prognostic profile of Moroccan patients with diffuse glioma. J Chem Neuroanat 2021; 119:102056. [PMID: 34871733 DOI: 10.1016/j.jchemneu.2021.102056] [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: 06/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022]
Abstract
Diffuse gliomas are growing brain tumors that occur in adult life. This study was designed to determine whether the immunohistochemical analysis of IDH1, HIF-1alpha, or TP53 can provide useful biomarkers of clinical severity and progression of diffuse gliomas. Also, it is hypothesized that the expression of IDH1 mutant induces HIF-1alpha. Immunohistochemical staining for HIF-1alpha, IDH1, and TP 53 was performed in biopsy or resection (sub-total or gross-total) tissue from diffuse gliomas in a clinical series of 32 patients. Associations of the HIF-1alpha, IDH1, and TP53 with clinical characteristics were evaluated and the co-expression of two biomarkers (HIF-1alpha and IDH1) was tested. Our data revealed that each biomarker is expressed in a subset of gliomas (IDH1 was positive in 56% cases, HIF-1alpha was positive in 50% cases and TP53 was positive in 44% cases). While no associations were found between clinical characteristics and the expression of HIF-1alpha, and TP53, IDH1 expression was associated with less severe clinical presentation (Karnofsky Performance Status) and disease progression and was more often expressed in females than males. In addition, there was no clear association between IDH1 and HIF-1alpha expression (21.9% of patients co-expressed IDH1 and HIF-1alpha). The current series provides clinical and immunohistochemical findings that can be useful for the clinical management of patients with diffused gliomas.
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Affiliation(s)
- Fatima Sfifou
- Research's Pedagogic Unit of Pathological Anatomy, Laboratory of Pathological Anatomy, Research Team in Tumour Pathology, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco; Pathological Anatomy Department, Hospital of Specialities in Rabat, Morocco.
| | - Mounir Ouzir
- Group of Research in Physiology and Physiopathology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, BP 1014 Rabat, Morocco
| | - El Mehdi Hakkou
- Neurosurgery Department, Hospital of Specialities in Rabat, Morocco
| | - Majdouline Obtel
- Laboratory of Biostatistics, Clinical Research and Epidemiology, Rabat Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Hassan Errihani
- National Oncology Centre Sidi Mohamed Ben Abdallah in Rabat, Morocco
| | - Abderrahmane Al Bouzidi
- Research's Pedagogic Unit of Pathological Anatomy, Laboratory of Pathological Anatomy, Research Team in Tumour Pathology, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Redouane Abouqal
- Laboratory of Biostatistics, Clinical Research and Epidemiology, Rabat Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | | | - Nadia Cherradi
- Research's Pedagogic Unit of Pathological Anatomy, Laboratory of Pathological Anatomy, Research Team in Tumour Pathology, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco; Pathological Anatomy Department, Hospital of Specialities in Rabat, Morocco
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8
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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9
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Aftab A, Afzal S, Idrees M, Shahid AA. p53 and rb promoter methylation in hepatitis C virus-related chronic hepatitis and hepatocellular carcinoma. Future Virol 2021. [DOI: 10.2217/fvl-2020-0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To identify methylation in p53 and rb during hepatitis C virus (HCV) infection in individuals in Pakistan. Materials & methods: Methylation-specific PCR was used on liver biopsies from hepatocellular carcinoma and chronic hepatitis C patients and on blood samples from healthy individuals. Real-time PCR was used to assess changes in the expression of p53 and rb in Huh-7 cells transfected with HCV-3a. Results: The p53 and rb promoters were methylated in hepatocellular carcinoma patients. The presence of HCV-3a- Core (p = 0.03), HCV-3a- NS-3 (p = 0.01) and HCV-3a- NS-5a (p = 0.02) downregulated p53 expression. Exposure to HCV-3a- Core (p = 0.04) downregulated rb expression. Conclusion: It can be hypothesized that HCV-induced epigenetic modifications may lead to the development of hepatic cancer that in turn inactivates p53 and rb.
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Affiliation(s)
- Ayma Aftab
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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10
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Xiong Y, Zhang Y, Xiong S, Williams-Villalobo AE. A Glance of p53 Functions in Brain Development, Neural Stem Cells, and Brain Cancer. BIOLOGY 2020; 9:biology9090285. [PMID: 32932978 PMCID: PMC7564678 DOI: 10.3390/biology9090285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/01/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022]
Abstract
p53 is one of the most intensively studied tumor suppressors. It transcriptionally regulates a broad range of genes to modulate a series of cellular events, including DNA damage repair, cell cycle arrest, senescence, apoptosis, ferroptosis, autophagy, and metabolic remodeling, which are fundamental for both development and cancer. This review discusses the role of p53 in brain development, neural stem cell regulation and the mechanisms of inactivating p53 in gliomas. p53 null or p53 mutant mice show female biased exencephaly, potentially due to X chromosome inactivation failure and/or hormone-related gene expression. Oxidative cellular status, increased PI3K/Akt signaling, elevated ID1, and metabolism are all implicated in p53-loss induced neurogenesis. However, p53 has also been shown to promote neuronal differentiation. In addition, p53 mutations are frequently identified in brain tumors, especially glioblastomas. Mechanisms underlying p53 inactivation in brain tumor cells include disruption of p53 protein stability, gene expression and transactivation potential as well as p53 gene loss or mutation. Loss of p53 function and gain-of-function of mutant p53 are both implicated in brain development and tumor genesis. Further understanding of the role of p53 in the brain may provide therapeutic insights for brain developmental syndromes and cancer.
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Affiliation(s)
- Yuqing Xiong
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA;
| | - Yun Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA;
- Correspondence: ; Tel.: +1-713-313-7557
| | - Shunbin Xiong
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Abie E. Williams-Villalobo
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA;
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11
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Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, Reimand J, Stuart JM, Raphael BJ. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun 2020; 11:729. [PMID: 32024854 PMCID: PMC7002574 DOI: 10.1038/s41467-020-14367-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/18/2019] [Indexed: 12/14/2022] Open
Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
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Affiliation(s)
- Matthew A Reyna
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA
- Department of Biomedical Informatics, Emory University, Atlanta, GA, 30322, USA
| | - David Haan
- Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Marta Paczkowska
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lieven P C Verbeke
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, the Netherlands
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, the Netherlands
| | - Miguel Vazquez
- Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Abdullah Kahraman
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, CH-8057, Zurich, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, CH-8091, Zurich, Switzerland
| | - Sergio Pulido-Tamayo
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, the Netherlands
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, the Netherlands
| | - Jonathan Barenboim
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lina Wadi
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Raunak Shrestha
- Vancouver Prostate Centre, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA, 02129, USA
- Harvard Medical School, 250 Longwood Avenue, Boston, MA, 02115, USA
- Massachusetts General Hospital, Department of Pathology, Boston, MA, 02114, USA
| | - Michael S Lawrence
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA, 02129, USA
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Mark A Rubin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Søren Brunak
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jose M G Izarzugaza
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ekta Khurana
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, the Netherlands
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, the Netherlands
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, CH-8057, Zurich, Switzerland
| | - S Cenk Sahinalp
- Vancouver Prostate Centre, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
- ICREA, Barcelona, 08010, Spain
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
| | - Joshua M Stuart
- Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95060, USA.
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA.
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12
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Epigenetic Control of a Local Chromatin Landscape. Int J Mol Sci 2020; 21:ijms21030943. [PMID: 32023873 PMCID: PMC7038174 DOI: 10.3390/ijms21030943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Proper regulation of the chromatin landscape is essential for maintaining eukaryotic cell identity and diverse cellular processes. The importance of the epigenome comes, in part, from the ability to influence gene expression through patterns in DNA methylation, histone tail modification, and chromatin architecture. Decades of research have associated this process of chromatin regulation and gene expression with human diseased states. With the goal of understanding how chromatin dysregulation contributes to disease, as well as preventing or reversing this type of dysregulation, a multidisciplinary effort has been launched to control the epigenome. Chemicals that alter the epigenome have been used in labs and in clinics since the 1970s, but more recently there has been a shift in this effort towards manipulating the chromatin landscape in a locus-specific manner. This review will provide an overview of chromatin biology to set the stage for the type of control being discussed, evaluate the recent technological advances made in controlling specific regions of chromatin, and consider the translational applications of these works.
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Zeng F, Heng J, Guo X, Wang Y, Wu W, Tang L, Chen M, Wang S, Deng H, Wang J. The novel TP53 3'-end methylation pattern associated with its expression would be a potential biomarker for breast cancer detection. Breast Cancer Res Treat 2020; 180:237-245. [PMID: 31983017 DOI: 10.1007/s10549-020-05536-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Deficiency or silence of TP53 is an early event in breast tumorigenesis. Aberrant methylation and mutation in regulatory regions were considered as crucial regulators of gene expression. METHODS Using multiplex-PCR and next-generation sequencing technology, we analyzed TP53 mutation spectrum in its promoter region. Using PCR target sequence enrichment and next-generation bisulfite sequencing technology, we analyzed the methylation profile of the promoter and 3'-end regions of TP53 gene in paired breast tumor and normal tissues from 120 breast cancer patients. The expression of TP53 and the flanking gene ATP1B2 was explored with qPCR method in the same cohort. RESULTS No promoter mutation of TP53 gene was found in the cohort of the 120 breast cancer patients. The 3'-end of TP53 gene was hyper-methylated (average 78.71%) compared with the promoter region (average less than 1%) in breast tumor tissues. TP53 was significantly lower expressed (P = 1.68E-15) and hyper-methylated in 3'-end (P = 1.82E-18) in tumor. Negative cis correlation was found between the TP53 expression and its 3'-end methylation (P = 9.02E-8, R = 0.337). TP53 expression was significantly associated with PR status (P = 0.0128), Ki67 level (P = 0.0091), and breast cancer subtypes (P = 0.0109). TP53 3'-end methylation and expression showed a good performance in discriminating breast cancer and normal tissues with an AUC of 0.930. CONCLUSIONS The 3'-end methylation of TP53 might be a crucial regulator for its expression in breast cancer, suggesting that TP53 3'-end hyper-methylation associated with its lower expression could be a potential biomarker for breast cancer diagnosis.
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Affiliation(s)
- Feng Zeng
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jianfu Heng
- Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, 410013, China
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Xinwu Guo
- Sansure Biotech Inc., Changsha, 410205, Hunan, China
| | - Yue Wang
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Wenhan Wu
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Lili Tang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Min Chen
- Sansure Biotech Inc., Changsha, 410205, Hunan, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Hongyu Deng
- Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, 410013, China
| | - Jun Wang
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China.
- Sansure Biotech Inc., Changsha, 410205, Hunan, China.
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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14
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Detection and Correlation of Single and Concomitant TP53, PTEN, and CDKN2A Alterations in Gliomas. Int J Mol Sci 2019; 20:ijms20112658. [PMID: 31151164 PMCID: PMC6600458 DOI: 10.3390/ijms20112658] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/16/2022] Open
Abstract
Gliomas are the most frequent primary tumors of central nervous system and represent a heterogeneous group of tumors that originates from the glial cells. TP53, PTEN, and CDKN2A are important tumor suppressor genes that encode proteins involved in sustaining cellular homeostasis by different signaling pathways. Though genetic alterations in these genes play a significant role in tumorigenesis, few studies are available regarding the incidence and relation of concomitant TP53, PTEN, and CDKN2A alterations in gliomas. The purpose of this study was to evaluate the occurrence of mutation and deletion in these genes, through single-strand conformational polymorphism, array-comparative genomic hybridization, and fluorescence in situ hybridization techniques, in 69 gliomas samples. Molecular results demonstrated a significant higher prevalence of TP53, PTEN, and CDKN2A alterations in astrocytoma than other tumor subtypes, and heterozygous deletion was the most frequent event. In addition, a significant association was observed between TP53 and CDKN2A alterations (p = 0.0424), which tend to coexist in low grade astrocytomas (5/46 cases (10.9%)), suggesting that they are early events in development of these tumors, and PTEN and CDKN2A deletions (p = 0.0022), which occurred concomitantly in 9/50 (18%) patients, with CDKN2A changes preceding PTEN deletions, present preferably in high-grade gliomas.
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15
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Mansourian M, Mahnam K, Rajabi HR, Roushani M, Doustimotlagh AH. Exploring the binding mechanism of saccharin and sodium saccharin to promoter of human p53 gene by theoretical and experimental methods. J Biomol Struct Dyn 2019; 38:548-564. [PMID: 30856053 DOI: 10.1080/07391102.2019.1582438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the past few decades, extensive discussions have been on the impact of artificial sweeteners on the risk of cancer. The present study aimed to evaluate the interaction of saccharin (SA) and sodium saccharin (SSA) with the promoter of the human p53 gene. The binding ability was assessed using the spectroscopic technique, molecular docking and molecular dynamics (MD) simulation methods. Free energy of binding has been calculated using Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Fluorescence spectra of mentioned gene with concentration profiles of SA and SSA were obtained in a physiological condition. A gradual increase without any significant spectral shift in the fluorescence intensity of around 350 nm was evident, indicating the presence of an interaction between both compounds and gene. The docking results showed that both compounds were susceptible to bind to 5'-DG56DG57-3' nucleotide sequence of gene. Furthermore, the MD simulation demonstrated that the binding positions for SA and SSA were 5'-A1T3T4-3' and 5'-G44T45-3' sequences of gene, respectively. The binding of these sweeteners to gene made significant conformational changes to the DNA structure. Hydrogen and hydrophobic interactions are the major forces in complexes stability. Through the groove binding mode, the non-interactive DNA-binding nature of SSA and SA has been demonstrated by the results of spectrofluorometric and molecular modeling. This study could provide valuable insight into the binding mechanism of SA and its salt with p53 gene promoter as macromolecule at the molecular level in atomistic details. This work can contribute to the possibility of the potential hazard of carcinogenicity of this sweetener and to design and apply new and safer artificial sweeteners. AbbreviationsSASaccharinSSASodium SaccharinPp53gpromoter of human p53 geneMDMolecular dynamicsRMSDRoot-mean-square deviationRMSFRoot-mean-square fluctuationRgRadius of GyrationSASASolvent-Accessible Surface AreaADIAcceptable daily intakeMM/PBSAMolecular Mechanics/Poisson-Boltzmann Surface AreaCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahboubeh Mansourian
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Department of Pharmacology, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, I.R. Iran
| | - Karim Mahnam
- Faculty of Science, Department of Biology, Shahrekord University, Shahrekord, Iran.,Nanotechnology Research Center, Shahrekord University, Shahrekord, Iran
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16
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Jesionek-Kupnicka D, Braun M, Trąbska-Kluch B, Czech J, Szybka M, Szymańska B, Kulczycka-Wojdala D, Bieńkowski M, Kordek R, Zawlik I. MiR-21, miR-34a, miR-125b, miR-181d and miR-648 levels inversely correlate with MGMT and TP53 expression in primary glioblastoma patients. Arch Med Sci 2019; 15:504-512. [PMID: 30899304 PMCID: PMC6425218 DOI: 10.5114/aoms.2017.69374] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/25/2017] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION TP53 and MGMT alterations play a crucial role in glioblastoma (GB) pathogenesis. TP53 and MGMT function is affected by several pathologic mechanisms, such as point mutations or promoter methylation, which are well characterized. Expression of both genes can be regulated by other mechanisms as well, e.g., microRNAs (miRNAs). Moreover, cross-talk among various pathologic processes may occur, further affecting MGMT and TP53 functionality. MATERIAL AND METHODS In 49 GB patients, we analyzed the possible associations between TP53 and its miRNA regulators miR-125b, miR-21, and miR-34a, as well as MGMT and its miRNA regulators miR-181d and miR-648. We evaluated the possible influence of mutational and methylation status on the pre-identified associations. RESULTS In patients with immunohistochemistry-detected TP53 overexpression, expression levels of miR-34a and TP53 were negatively correlated (r = -0.56, p = 0.0195), and in patients with TP53 mutations, expression levels of TP53 and miR-21 were negatively correlated (r = -0.67, p = 0.0330). In patients with MGMT methylation, expression levels of MGMT were negatively correlated with miR-648 and miR-125b expression levels (r = -0.61, p = 0.0269 and r = -0.34, p = 0.0727, respectively). CONCLUSIONS Our findings demonstrate that selected miRNAs are significantly correlated with MGMT and TP53 levels, but the extent of this correlation differs regarding the TP53 and MGMT mutational and promoter methylation status.
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Affiliation(s)
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Joanna Czech
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Małgorzata Szybka
- Department of Microbiology and Laboratory Medical Immunology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Bożena Szymańska
- Central Scientific Laboratory, Medical University of Lodz, Lodz, Poland
| | | | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Radzisław Kordek
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
| | - Izabela Zawlik
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Laboratory of Molecular Biology, Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszow, Rzeszow, Poland
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17
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Huo X, Li Z, Zhang S, Li C, Guo M, Lu J, Lv J, Du X, Chen Z. Analysis of the expression level and methylation of tumor protein p53, phosphatase and tensin homolog and mutS homolog 2 in N-methyl-N-nitrosourea-induced thymic lymphoma in C57BL/6 mice. Oncol Lett 2017; 14:4339-4348. [PMID: 28943948 DOI: 10.3892/ol.2017.6721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/23/2017] [Indexed: 12/29/2022] Open
Abstract
Tumorigenesis is often caused by somatic mutation or epigenetic changes in genes that regulate aspects of cell death, proliferation and survival. Although the functions of multiple tumor suppressor genes have been well studied in isolation, how these genes cooperate during the progression of a single tumor remains unclear in numerous cases. The present study used N-methyl-N-nitrosourea (MNU), one of the most potent mutagenic nitrosourea compounds, to induce thymic lymphoma in C57BL/6J mice. Subsequently, the protein expression levels of phosphatase and tensin homolog (PTEN), transformation protein 53 and mutS homolog 2 (MSH2) were evaluated concomitantly in the thymus, liver, kidney and spleen of MNU-treated mice by western blotting. To determine whether changes in expression level were due to aberrant epigenetic regulation, the present study further examined the methylation status of each gene by MassARRAY analysis. During the tumorigenesis process of an MNU-induced single thymic lymphoma, the expression level of PTEN was revealed to be reduced in thymic lymphoma samples but not in normal or non-tumor thymus tissue samples. Furthermore, a marked reduction of P53 expression levels were demonstrated in thymic lymphomas and spleens with a metastatic tumor. Conversely, MSH2 upregulation was identified only in liver, kidney, and spleen samples that were infiltrated by thymic lymphoma cells. Furthermore, the present study revealed that a number of 5'-C-phosphate-G-3' sites located in the promoter of aberrantly expressed genes had significantly altered methylation statuses. These results improve the understanding of the course of mutagen-induced cancer, and highlight that epigenetic regulation may serve an important function in cancer.
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Affiliation(s)
- Xueyun Huo
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Zhenkun Li
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Shuangyue Zhang
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Changlong Li
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Meng Guo
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Jing Lu
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Jianyi Lv
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Xiaoyan Du
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Zhenwen Chen
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
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18
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Molecular Mechanisms of p53 Deregulation in Cancer: An Overview in Multiple Myeloma. Int J Mol Sci 2016; 17:ijms17122003. [PMID: 27916892 PMCID: PMC5187803 DOI: 10.3390/ijms17122003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/14/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022] Open
Abstract
The p53 pathway is inactivated in the majority of human cancers. Although this perturbation frequently occurs through the mutation or deletion of p53 itself, there are other mechanisms that can attenuate the pathway and contribute to tumorigenesis. For example, overexpression of important p53 negative regulators, such as murine double minute 2 (MDM2) or murine double minute 4 (MDM4), epigenetic deregulation, or even alterations in TP53 mRNA splicing. In this work, we will review the different mechanisms of p53 pathway inhibition in cancer with special focus on multiple myeloma (MM), the second most common hematological malignancy, with low incidence of p53 mutations/deletions but growing evidence of indirect p53 pathway deregulation. Translational implications for MM and cancer prognosis and treatment are also reviewed.
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The expression of microRNA-34a is inversely correlated with c-MET and CDK6 and has a prognostic significance in lung adenocarcinoma patients. Tumour Biol 2015; 36:9327-37. [PMID: 26104764 DOI: 10.1007/s13277-015-3428-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/06/2015] [Indexed: 02/06/2023] Open
Abstract
We aimed to establish whether the expression of microRNA-34a (miR-34a) is correlated with that of c-MET and G1 phase regulators such as cyclin dependent kinase (CDK) 4, CDK6, and cyclin D (CCND) 1 in non-small cell lung cancer (NSCLC), and whether a relationship exists between miR-34a expression and both clinicopathologic factors and recurrence-free survival (RFS). For 58 samples archived from NSCLC patients, we measured the expression of miR-34a and c-MET, CDK4/6, and CCND1 by quantitative RT-PCR and assessed the relationship between miR-34a expression, clinicopathological factors, and RFS. The expression of miR-34a was significantly lower in squamous cell tumors (P < 0.001) and in tumors associated with lymphatic invasion (P = 0.001). We found significant inverse correlations between miR-34a and c-MET (R = -0.316, P = 0.028) and CDK6 expression (R = -0.4582, P = 0.004). RFS were longer in adenocarcinoma patients with high miR-34a expression than in those with low miR-34a expression (55.6 vs. 21.6 months; P = 0.020). With univariate analysis, statistically significant prognostic factors for RFS in adenocarcinoma patients were miR-34a expression (Relative risk (RR), 8.14; P = 0.049), TNM stage (RR, 13.55; P = 0.001), LN metastasis (RR, 4.19; P = 0.043), and the presence of lymphatic invasion (RR, 7.05; P = 0.015). In multivariate analysis, only miR-34a was prognostic for RFS (RR, 11.5; P = 0.027). miR-34a expression was inversely correlated with that of c-MET and CDK6 in NSCLC, and had prognostic significance for RFS, especially in adenocarcinoma patients.
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