1
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Rajabi A, Safaralizadeh R, Saber A, Pourmahdi M, Teimourian S, Montazeri V, Fakhrjou A, Hosseinpourfeizi M. Apoptotic effect of melatonin on ER-positive breast cancer cell lines: ADGRL4 gene expression and promoter methylation. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03383-2. [PMID: 39177783 DOI: 10.1007/s00210-024-03383-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
Breast cancer (BC) is the second most common malignancy worldwide. ADGRL4, as a modulator of angiogenesis, undergoes various epigenetic modifications affecting its biological functions. In this study, we aimed to assess ADGRL4 promoter methylation status and its expression levels in primary breast tumors and to evaluate its potency as a plausible prognostic biomarker in BC. Furthermore, we evaluated the effect of melatonin on ADGRL4 expression and viability of BC cells in vitro. One hundred breast tumor tissue samples and adjacent non-tumor tissues were collected, followed by DNA isolation, bisulfite conversion, qRT-PCR, qMSP assay, and immunoblotting. In addition, four BC cell lines were treated with melatonin and subjected to ADGRL4 expression analysis and apoptosis assay. We found a significant correlation between ADGRL4 expression levels and HER2 status and stage of disease (P < 0.05). We observed a substantial attenuation in ADGRL4 promoter methylation in tumor samples compared to marginal non-tumor samples. A significantly lower expression of ADGRL4 was detected in two BC cell lines in the presence of melatonin. MCF-7 and BT474 melatonin-treated cell lines showed a significantly higher number of apoptotic cells than non-treated cells (P < 0.0001). Based on the receiver operating characteristic (ROC) curve analysis, ADGRL4 expression and ADGRL4 promoter methylation status showed moderate prognostic value. We found that melatonin has anti-cancer effects on BC cells. In addition, ADGRL4 expression can potentially be used as a prognostic biomarker in BC.
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Affiliation(s)
- Ali Rajabi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Ali Saber
- Dr. Saber Medical Genetics Laboratory, Almas Complex, Namaz Blvd, Rasht, Gilan, Iran
| | - Mahsa Pourmahdi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Shahram Teimourian
- Department of Medical Genetics, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Vahid Montazeri
- Department of Thoracic Surgery, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ashraf Fakhrjou
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Stone TC, Ward V, Hogan A, Alexander Ho KM, Wilson A, McBain H, Duku M, Wolfson P, Cheung S, Rosenfeld A, Lovat LB. Using saliva epigenetic data to develop and validate a multivariable predictor of esophageal cancer status. Epigenomics 2024; 16:109-125. [PMID: 38226541 PMCID: PMC10825730 DOI: 10.2217/epi-2023-0248] [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: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Background: Salivary epigenetic biomarkers may detect esophageal cancer. Methods: A total of 256 saliva samples from esophageal adenocarcinoma patients and matched volunteers were analyzed with Illumina EPIC methylation arrays. Three datasets were created, using 64% for discovery, 16% for testing and 20% for validation. Modules of gene-based methylation probes were created using weighted gene coexpression network analysis. Module significance to disease and gene importance to module were determined and a random forest classifier generated using best-scoring gene-related epigenetic probes. A cost-sensitive wrapper algorithm maximized cancer diagnosis. Results: Using age, sex and seven probes, esophageal adenocarcinoma was detected with area under the curve of 0.72 in discovery, 0.73 in testing and 0.75 in validation datasets. Cancer sensitivity was 88% with specificity of 31%. Conclusion: We have demonstrated a potentially clinically viable classifier of esophageal cancer based on saliva methylation.
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Affiliation(s)
- Timothy C Stone
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Vanessa Ward
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Aine Hogan
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Kai Man Alexander Ho
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Ash Wilson
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Hazel McBain
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Margaret Duku
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Paul Wolfson
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Sharon Cheung
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Avi Rosenfeld
- Department of Computer Science, Jerusalem College of Technology, Havaad Haleumi 21, Givat Mordechai, 91160, Jerusalem, Israel
| | - Laurence B Lovat
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Department of Gastrointestinal Services, University College London Hospital, 235 Euston Road, London, NW1 2BU, UK
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3
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Sun Y, Jin D, Zhang Z, Ji H, An X, Zhang Y, Yang C, Sun W, Zhang Y, Duan Y, Kang X, Jiang L, Zhao X, Lian F. N6-methyladenosine (m6A) methylation in kidney diseases: Mechanisms and therapeutic potential. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194967. [PMID: 37553065 DOI: 10.1016/j.bbagrm.2023.194967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The N6-methyladenosine (m6A) modification is regulated by methylases, commonly referred to as "writers," and demethylases, known as "erasers," leading to a dynamic and reversible process. Changes in m6A levels have been implicated in a wide range of cellular processes, including nuclear RNA export, mRNA metabolism, protein translation, and RNA splicing, establishing a strong correlation with various diseases. Both physiologically and pathologically, m6A methylation plays a critical role in the initiation and progression of kidney disease. The methylation of m6A may also facilitate the early diagnosis and treatment of kidney diseases, according to accumulating research. This review aims to provide a comprehensive overview of the potential role and mechanism of m6A methylation in kidney diseases, as well as its potential application in the treatment of such diseases. There will be a thorough examination of m6A methylation mechanisms, paying particular attention to the interplay between m6A writers, m6A erasers, and m6A readers. Furthermore, this paper will elucidate the interplay between various kidney diseases and m6A methylation, summarize the expression patterns of m6A in pathological kidney tissues, and discuss the potential therapeutic benefits of targeting m6A in the context of kidney diseases.
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Affiliation(s)
- Yuting Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - De Jin
- Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Ziwei Zhang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Hangyu Ji
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuedong An
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuehong Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cunqing Yang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenjie Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Duan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaomin Kang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Jiang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuefei Zhao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengmei Lian
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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Lim NR, Chung WC. Helicobacter pylori-associated Chronic Atrophic Gastritis and Progression of Gastric Carcinogenesis. THE KOREAN JOURNAL OF GASTROENTEROLOGY = TAEHAN SOHWAGI HAKHOE CHI 2023; 82:171-179. [PMID: 37876256 DOI: 10.4166/kjg.2023.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
Chronic inflammation due to a Helicobacter pylori (H. pylori) infection is a representative cause of gastric cancer that can promote gastric carcinogenesis by abnormally activating immune cells and increasing the inflammatory cytokines levels. H. pylori infections directly cause DNA double-strand breaks in gastric epithelial cells and genetic damage by increasing the enzymatic activity of cytidine deaminase. Eventually, gastric cancer is induced through dysplasia. Hypermethylation of tumor suppressor genes is an important cause of gastric cancer because of a H. pylori infection. In addition, the changes in gastric microbiota and the mucosal inflammatory changes associated with a co-infection with the Epstein-Barr virus are associated with gastric cancer development. DNA damage induced by H. pylori and the subsequent responses of gastric stem cells have implications for gastric carcinogenesis. Although the pathogenesis of H. pylori has been established, many uncertainties remain, requiring more study.
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Affiliation(s)
- Na Rae Lim
- Department of Internal Medicine, St. Vincent Hospital, The Catholic University of Korea, Suwon, Korea
| | - Woo Chul Chung
- Department of Internal Medicine, St. Vincent Hospital, The Catholic University of Korea, Suwon, Korea
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5
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Biswas S, Shukla PK. A DFT study on the scavenging activity of curcumin toward methyl and ethyl radicals. MOLECULAR SIMULATION 2023. [DOI: 10.1080/08927022.2023.2178236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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6
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Ruzic D, Ellinger B, Djokovic N, Santibanez JF, Gul S, Beljkas M, Djuric A, Ganesan A, Pavic A, Srdic-Rajic T, Petkovic M, Nikolic K. Discovery of 1-Benzhydryl-Piperazine-Based HDAC Inhibitors with Anti-Breast Cancer Activity: Synthesis, Molecular Modeling, In Vitro and In Vivo Biological Evaluation. Pharmaceutics 2022; 14:pharmaceutics14122600. [PMID: 36559094 PMCID: PMC9785542 DOI: 10.3390/pharmaceutics14122600] [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: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Isoform-selective histone deacetylase (HDAC) inhibition is promoted as a rational strategy to develop safer anti-cancer drugs compared to non-selective HDAC inhibitors. Despite this presumed benefit, considerably more non-selective HDAC inhibitors have undergone clinical trials. In this report, we detail the design and discovery of potent HDAC inhibitors, with 1-benzhydryl piperazine as a surface recognition group, that differ in hydrocarbon linker. In vitro HDAC screening identified two selective HDAC6 inhibitors with nanomolar IC50 values, as well as two non-selective nanomolar HDAC inhibitors. Structure-based molecular modeling was employed to study the influence of linker chemistry of synthesized inhibitors on HDAC6 potency. The breast cancer cell lines (MDA-MB-231 and MCF-7) were used to evaluate compound-mediated in vitro anti-cancer, anti-migratory, and anti-invasive activities. Experiments on the zebrafish MDA-MB-231 xenograft model revealed that a novel non-selective HDAC inhibitor with a seven-carbon-atom linker exhibits potent anti-tumor, anti-metastatic, and anti-angiogenic effects when tested at low micromolar concentrations.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), 22525 Hamburg, Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, University of Belgrade, Dr. Subotića 4, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), 22525 Hamburg, Germany
| | - Milan Beljkas
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Ana Djuric
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Arasu Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Aleksandar Pavic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Milos Petkovic
- Department of Organic Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
- Correspondence: (M.P.); (K.N.)
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
- Correspondence: (M.P.); (K.N.)
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7
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Pieroni S, Castelli M, Piobbico D, Ferracchiato S, Scopetti D, Di-Iacovo N, Della-Fazia MA, Servillo G. The Four Homeostasis Knights: In Balance upon Post-Translational Modifications. Int J Mol Sci 2022; 23:ijms232214480. [PMID: 36430960 PMCID: PMC9696182 DOI: 10.3390/ijms232214480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A cancer outcome is a multifactorial event that comes from both exogenous injuries and an endogenous predisposing background. The healthy state is guaranteed by the fine-tuning of genes controlling cell proliferation, differentiation, and development, whose alteration induces cellular behavioral changes finally leading to cancer. The function of proteins in cells and tissues is controlled at both the transcriptional and translational level, and the mechanism allowing them to carry out their functions is not only a matter of level. A major challenge to the cell is to guarantee that proteins are made, folded, assembled and delivered to function properly, like and even more than other proteins when referring to oncogenes and onco-suppressors products. Over genetic, epigenetic, transcriptional, and translational control, protein synthesis depends on additional steps of regulation. Post-translational modifications are reversible and dynamic processes that allow the cell to rapidly modulate protein amounts and function. Among them, ubiquitination and ubiquitin-like modifications modulate the stability and control the activity of most of the proteins that manage cell cycle, immune responses, apoptosis, and senescence. The crosstalk between ubiquitination and ubiquitin-like modifications and post-translational modifications is a keystone to quickly update the activation state of many proteins responsible for the orchestration of cell metabolism. In this light, the correct activity of post-translational machinery is essential to prevent the development of cancer. Here we summarize the main post-translational modifications engaged in controlling the activity of the principal oncogenes and tumor suppressors genes involved in the development of most human cancers.
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8
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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9
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Yamashita M, Adachi T, Ono S, Yoshino K, Imamura H, Matsushima H, Tanaka T, Kosaka T, Soyama A, Hidaka M, Kanetaka K, Eguchi S. Helicobacter bilis infection induces oxidative stress in and enhances the proliferation of human cholangiocytes. Helicobacter 2022; 27:e12908. [PMID: 35661483 DOI: 10.1111/hel.12908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/02/2022] [Accepted: 05/17/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND Helicobacter bilis, an enterohepatic Helicobacter species, represents a carcinogenic risk factor for cholangiocytes owing to the prevalence of infections in patients with biliary tract cancer, cholecystitis, and pancreaticobiliary maljunction. However, the effect of H. bilis infection on cholangiocytes and the process and mechanism of carcinogenesis are not known. We aimed to determine the effects of H. bilis on cholangiocytes, focusing on inflammation and oxidative stress. MATERIALS AND METHODS Helicobacter bilis and MMNK-1 cells were cocultured for 24 h and inflammatory cytokine secretion was evaluated. Furthermore, MMNK-1 cell proliferation, intracellular reactive oxidant species (ROS) production, and DNA damage caused by ROS were investigated. All factors were compared with and without H. bilis infection. RESULTS Interleukin (IL)-6 and IL-8 secretion were significantly increased in MMNK-1 cocultures with H. bilis (IL-6, 24.3 ± 12.2 vs. 271.1 ± 286.4 pg/ml; IL-8, 167.6 ± 78.7 vs. 1085.1 ± 1047.1 pg/ml, p < .05). MMNK-1 proliferation was also significantly higher in H. bilis cocultures (1.05 ± 0.02 vs. 1.00-fold, respectively; p < .05). Coculturing enhanced the production of ROS in MMNK-1 cells depending on the cell concentration of H. bilis (1.0 vs. 1.17 ± 0.06, p < .05); however, DNA injury was not observed in cocultures with H. bilis (5.35 ± 0.87 vs. 6.08 ± 0.55 pg/μl, p = .06). CONCLUSIONS Helicobacter bilis infection induced ROS production in and enhanced the proliferation of cholangiocytes.
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Affiliation(s)
- Mampei Yamashita
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomohiko Adachi
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinichiro Ono
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kyohei Yoshino
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hajime Imamura
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hajime Matsushima
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takayuki Tanaka
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Taichiro Kosaka
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akihiko Soyama
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaaki Hidaka
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kengo Kanetaka
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Susumu Eguchi
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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10
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Rysz J, Franczyk B, Rysz-Górzyńska M, Gluba-Brzózka A. Are Alterations in DNA Methylation Related to CKD Development? Int J Mol Sci 2022; 23:7108. [PMID: 35806113 PMCID: PMC9267048 DOI: 10.3390/ijms23137108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/29/2022] Open
Abstract
The modifications in genomic DNA methylation are involved in the regulation of normal and pathological cellular processes. The epigenetic regulation stimulates biological plasticity as an adaptive response to variations in environmental factors. The role of epigenetic changes is vital for the development of some diseases, including atherogenesis, cancers, and chronic kidney disease (CKD). The results of studies presented in this review have suggested that altered DNA methylation can modulate the expression of pro-inflammatory and pro-fibrotic genes, as well those essential for kidney development and function, thus stimulating renal disease progression. Abnormally increased homocysteine, hypoxia, and inflammation have been suggested to alter epigenetic regulation of gene expression in CKD. Studies of renal samples have demonstrated the relationship between variations in DNA methylation and fibrosis and variations in estimated glomerular filtration rate (eGFR) in human CKD. The unravelling of the genetic-epigenetic profile would enhance our understanding of processes underlying the development of CKD. The understanding of multifaceted relationship between DNA methylation, genes expression, and disease development and progression could improve the ability to identify individuals at risk of CKD and enable the choice of appropriate disease management.
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Affiliation(s)
- Jacek Rysz
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland; (J.R.); (B.F.)
| | - Beata Franczyk
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland; (J.R.); (B.F.)
| | - Magdalena Rysz-Górzyńska
- Department of Otolaryngology, Laryngological Oncology, Audiology and Phoniatrics, Medical Univesity of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland;
| | - Anna Gluba-Brzózka
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 113 Żeromskego Street, 90-549 Lodz, Poland; (J.R.); (B.F.)
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11
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Witasp A, Luttropp K, Qureshi AR, Barany P, Heimbürger O, Wennberg L, Ekström TJ, Shiels PG, Stenvinkel P, Nordfors L. Longitudinal genome-wide DNA methylation changes in response to kidney failure replacement therapy. Sci Rep 2022; 12:470. [PMID: 35013499 PMCID: PMC8748627 DOI: 10.1038/s41598-021-04321-5] [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: 06/08/2021] [Accepted: 12/13/2021] [Indexed: 01/01/2023] Open
Abstract
Chronic kidney disease (CKD) is an emerging public health priority associated with high mortality rates and demanding treatment regimens, including life-style changes, medications or even dialysis or renal transplantation. Unavoidably, the uremic milieu disturbs homeostatic processes such as DNA methylation and other vital gene regulatory mechanisms. Here, we aimed to investigate how dialysis or kidney transplantation modifies the epigenome-wide methylation signature over 12 months of treatment. We used the Infinium HumanMethylation450 BeadChip on whole blood samples from CKD-patients undergoing either dialysis (n = 11) or kidney transplantation (n = 12) and 24 age- and sex-matched population-based controls. At baseline, comparison between patients and controls identified several significant (PFDR < 0.01) CpG methylation differences in genes with functions relevant to inflammation, cellular ageing and vascular calcification. Following 12 months, the global DNA methylation pattern of patients approached that seen in the control group. Notably, 413 CpG sites remained differentially methylated at follow-up in both treatment groups compared to controls. Together, these data indicate that the uremic milieu drives genome-wide methylation changes that are partially reversed with kidney failure replacement therapy. Differentially methylated CpG sites unaffected by treatment may be of particular interest as they could highlight candidate genes for kidney disease per se.
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Affiliation(s)
- Anna Witasp
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Karin Luttropp
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Abdul Rashid Qureshi
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Peter Barany
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Olof Heimbürger
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Lars Wennberg
- Division of Transplantation Surgery, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas J Ekström
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Shiels
- College of Medical, Veterinary and Life Sciences Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden
| | - Louise Nordfors
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, M99, 141 86, Stockholm, Sweden.
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12
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Choi JM, Kim SG. Effect of Helicobacter pylori Eradication on Epigenetic Changes in Gastric Cancer-related Genes. THE KOREAN JOURNAL OF HELICOBACTER AND UPPER GASTROINTESTINAL RESEARCH 2021. [DOI: 10.7704/kjhugr.2021.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is known that gastric carcinogenesis results from the progressive changes from chronic gastritis to gastric atrophy, intestinal metaplasia, dysplasia, and invasive carcinoma. Several genetic and epigenetic alterations are involved in this process, and Helicobacter pylori (H. pylori) infection is believed to induce the initiation and progression of these steps. From an epigenetic point of view, H. pylori induces hypermethylation of genes involved in the development of gastric cancer and regulates the expression of various microRNAs (miRNAs). These H. pylori-related epigenetic changes are accumulated not only at the site of neoplasm but also in the adjacent non-cancerous gastric mucosa. Thereby, a state vulnerable to gastric cancer known as an epigenetic field defect is formed. H. pylori eradication can have an effective chemopreventive effect in gastric carcinogenesis. However, the molecular biological changes that occur in the stomach environment during H. pylori eradication have not yet been established. Several studies have reported that H. pylori eradication can restore infection-related changes, especially epigenetic alterations in gastric cancer-related genes, but some studies have shown otherwise. Simply put, it appears that the recovery of methylated gastric cancer-related genes and miRNAs during H. pylori eradication may vary among genes and may also differ depending on the histological subtype of the gastric mucosa. In this review, we will discuss the potential mechanism of gastric cancer prevention by H. pylori eradication, mainly from an epigenetic perspective.
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13
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Liu YX, Li QZ, Cao YN. The effect of key DNA methylation in different regions on gene expression in hepatocellular carcinoma. Mol Omics 2021; 18:57-70. [PMID: 34782907 DOI: 10.1039/d1mo00282a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common cancer with high morbidity and mortality. As we all know, the alteration of DNA methylation has a crucial impact on the occurrence of HCC. However, the mechanism of the effect of DNA methylation in different regions on gene expression is still unclear. Here, by computing and analyzing the distribution of differential methylation in 12 different regions in HCC tissues and adjacent normal tissues, not only the hypermethylation of CpG islands and global hypomethylation were found, but also a stable distribution pattern of differential methylation in HCC was found. Then the correlations between DNA methylations in different regions and gene expressions were calculated, and the diversity of correlations in different regions was determined. The key genes of differential methylation and differential expression related to the survival of HCC patients were obtained by using Cox regression analysis, a four-gene prognostic risk scoring model was constructed, and the prognostic performance was well verified. The regions of the differentially methylated CpG sites corresponding to the four key genes were located and their influences on the expression were analyzed. The results indicate that the promoter, first exon, 5'UTR, sixth exon, N_Shore, and S_Shore hypomethylation promotes the expression of key oncogenes, which together lead to the occurrence of HCC. These results might help to study the role of DNA methylation in HCC and provide potential biomarkers for the diagnosis of HCC.
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Affiliation(s)
- Yu-Xian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China. .,The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
| | - Yan-Ni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
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14
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Xiao W, Zhou Q, Wen X, Wang R, Liu R, Wang T, Shi J, Hu Y, Hou J. Small-Molecule Inhibitors Overcome Epigenetic Reprogramming for Cancer Therapy. Front Pharmacol 2021; 12:702360. [PMID: 34603017 PMCID: PMC8484527 DOI: 10.3389/fphar.2021.702360] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer treatment is a significant challenge for the global health system, although various pharmacological and therapeutic discoveries have been made. It has been widely established that cancer is associated with epigenetic modification, which is reversible and becomes an attractive target for drug development. Adding chemical groups to the DNA backbone and modifying histone proteins impart distinct characteristics on chromatin architecture. This process is mediated by various enzymes modifying chromatin structures to achieve the diversity of epigenetic space and the intricacy in gene expression files. After decades of effort, epigenetic modification has represented the hallmarks of different cancer types, and the enzymes involved in this process have provided novel targets for antitumor therapy development. Epigenetic drugs show significant effects on both preclinical and clinical studies in which the target development and research offer a promising direction for cancer therapy. Here, we summarize the different types of epigenetic enzymes which target corresponding protein domains, emphasize DNA methylation, histone modifications, and microRNA-mediated cooperation with epigenetic modification, and highlight recent achievements in developing targets for epigenetic inhibitor therapy. This article reviews current anticancer small-molecule inhibitors targeting epigenetic modified enzymes and displays their performances in different stages of clinical trials. Future studies are further needed to address their off-target effects and cytotoxicity to improve their clinical translation.
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Affiliation(s)
- Wenjing Xiao
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Qiaodan Zhou
- Department of Ultrasonic, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xudong Wen
- Department of Gastroenterology and Hepatology, Chengdu First People's Hospital, Chengdu, China
| | - Rui Wang
- Information Department of Medical Security Center, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Ruijie Liu
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Tingting Wang
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jianyou Shi
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yonghe Hu
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Jun Hou
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
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15
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Zhang H, Xu C, Shi C, Zhang J, Qian T, Wang Z, Ma R, Wu J, Jiang F, Feng J. Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis. J Transl Med 2021; 19:98. [PMID: 33663522 PMCID: PMC7934273 DOI: 10.1186/s12967-021-02770-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The epigenetic abnormality of tumor-associated genes contributes to the pathogenesis of colorectal carcinoma (CRC). However, methylation in colorectal cancer is still poorly characterized. METHOD By integration of DNA methylation data from the GEO database and gene expression data from The Cancer Genome Atlas database, the aberrantly methylated genes involved in CRC tumorigenesis were identified. Subsequent in vitro experiments further validated their role in CRC. RESULTS We performed integrative genomic analysis and identified HPSE2, a novel tumor suppressor gene that is frequently inactivated through promoter methylation in CRC. K-M survival analysis showed that hypermethylation-low expression of heparanase 2 (HPSE2) was related to poor patient prognosis. Overexpression of HPSE2 reduced cell proliferation in vivo and in vitro. HPSE2 could regulate the p53 signaling pathway to block the cell cycle in G1 phase. CONCLUSION HPSE2, a novel tumor suppressor gene that is frequently inactivated through promoter methylation in CRC. HPSE2 performs a tumor suppressive function by activating the p53/ p21 signaling cascade. The promoter hypermethylation of HPSE2 is a potential therapeutic target in patients with CRC, especially those with late-stage CRC.
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Affiliation(s)
- Hui Zhang
- Department of General Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Chenxin Xu
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Chen Shi
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Junying Zhang
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Ting Qian
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Zhuo Wang
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Rong Ma
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Jianzhong Wu
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Feng Jiang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China.
| | - Jifeng Feng
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210000, Jiangsu, People's Republic of China.
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16
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Tawe L, Grover S, Zetola N, Robertson ES, Gaseitsiwe S, Moyo S, Kasvosve I, Paganotti GM, Narasimhamurthy M. Promoter Hypermethylation Analysis of Host Genes in Cervical Cancer Patients With and Without Human Immunodeficiency Virus in Botswana. Front Oncol 2021; 11:560296. [PMID: 33718129 PMCID: PMC7952881 DOI: 10.3389/fonc.2021.560296] [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: 05/11/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Epidemics of human immunodeficiency virus (HIV) and cervical cancer are interconnected. DNA hypermethylation of host genes' promoter in cervical lesions has also been recognized as a contributor to cervical cancer progression. Methods: For this purpose we analyzed promoter methylation of four tumor suppressor genes (RARB, CADM1, DAPK1 and PAX1) and explored their possible association with cervical cancer in Botswana among women of known HIV status. Overall, 228 cervical specimens (128 cervical cancers and 100 non-cancer subjects) were used. Yates-corrected chi-square test and Fisher's exact test were used to explore the association of promoter methylation for each host gene and cancer status. Subsequently, a logistic regression analysis was performed to find which factors, HIV status, high risk-HPV genotypes, patient's age and promoter methylation, were associated with the following dependent variables: cancer status, cervical cancer stage and promoter methylation rate. Results: In patients with cervical cancer the rate of promoter methylation observed was greater than 64% in all the genes studied. Analysis also showed a higher risk of cervical cancer according to the increased number of methylated promoter genes (OR = 6.20; 95% CI: 3.66–10.51; P < 0.001). RARB methylation showed the strongest association with cervical cancer compared to other genes (OR = 15.25; 95% CI: 6.06–40.0; P < 0.001). Cervical cancer and promoter methylation of RARB and DAPK1 genes were associated with increasing age (OR = 1.12; 95% CI: 1.01-1.26; P = 0.037 and OR = 1.05; 95% CI: 1.00-1.10; P = 0.040). The presence of epigenetic changes at those genes appeared to be independent of HIV status among subjects with cervical cancer. Moreover, we found that cervical cancer stage was influenced by RARB (χ2= 7.32; P = 0.002) and CADM1 (χ2=12.68; P = 0.013) hypermethylation, and HIV status (χ2= 19.93; P = 0.001). Conclusion: This study confirms the association between invasive cervical cancer and promoter gene methylation of tumor suppressing genes at the site of cancer. HIV infection did not show any association to methylation changes in this group of cervical cancer patients from Botswana. Further studies are needed to better understand the role of HIV in methylation of host genes among cancer subjects leading to cervical cancer progression.
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Affiliation(s)
- Leabaneng Tawe
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Surbhi Grover
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicola Zetola
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Erle S Robertson
- Department of Otorhinolaryngology-Head and Neck Surgery, and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Giacomo M Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Mohan Narasimhamurthy
- Department of Pathology, Faculty of Medicine, University of Botswana, Gaborone, Botswana
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17
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Wang Y, Huang XX, Leng D, Li JF, Liang Y, Jiang T. Effect of EZH2 on pulmonary artery smooth muscle cell migration in pulmonary hypertension. Mol Med Rep 2020; 23:129. [PMID: 33313943 PMCID: PMC7751464 DOI: 10.3892/mmr.2020.11768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
Pulmonary hypertension (PH) is a life‑threatening disease that often involves vascular remodeling. Although pulmonary arterial smooth muscle cells (PASMCs) are the primary participants in vascular remodeling, their biological role is not entirely clear. The present study analyzed the role of enhancer of zeste homolog 2 (EZH2) in vascular remodeling of PH by investigating the behavior of PASMCs. The expression levels of EZH2 in PASMCs in chronic thromboembolic pulmonary hypertension (CTEPH), a type of PH, were detected. The role of EZH2 in PASMC migration was investigated by wound‑healing assay following overexpression and knockdown. Functional enrichment analysis of the whole‑genome expression profiles of PASMCs with EZH2 overexpression was performed using an mRNA Human Gene Expression Microarray. Quantitative (q)PCR was performed to confirm the results of the microarray. EZH2 expression levels increased in CTEPH cell models. The overexpression of EZH2 enhanced PASMC migration compared with control conditions. Functional enrichment analysis of the differentially expressed genes following EZH2 overexpression indicated a strong link between EZH2 and the immune inflammatory response and oxidoreductase activity in PASMCs. mRNA expression levels of superoxide dismutase 3 were verified by qPCR. The results suggested that EZH2 was involved in the migration of PASMCs in PH, and may serve as a potential target for the treatment of PH.
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Affiliation(s)
- Ying Wang
- Department of Clinical Laboratory, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xiao-Xi Huang
- Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing 100020, P.R. China
| | - Dong Leng
- Department of Clinical Laboratory, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Ji-Feng Li
- Key Laboratory of Respiratory and Pulmonary Circulation Disorders, Institute of Respiratory Medicine, Beijing 100020, P.R. China
| | - Yan Liang
- Department of Clinical Laboratory, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China
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18
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Gu Y, Niu S, Wang Y, Duan L, Pan Y, Tong Z, Zhang X, Yang Z, Peng B, Wang X, Han X, Li Y, Cheng T, Liu Y, Shang L, Liu T, Yang X, Sun M, Jiang S, Zhang C, Zhang N, Ye Q, Gao S. DMDRMR-Mediated Regulation of m 6A-Modified CDK4 by m 6A Reader IGF2BP3 Drives ccRCC Progression. Cancer Res 2020; 81:923-934. [PMID: 33293428 DOI: 10.1158/0008-5472.can-20-1619] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022]
Abstract
Aberrant N 6-methyladenosine (m6A) modification has emerged as a driver of tumor initiation and progression, yet how long noncoding RNAs (lncRNA) are involved in the regulation of m6A remains unknown. Here we utilize data from 12 cancer types from The Cancer Genome Atlas to comprehensively map lncRNAs that are potentially deregulated by DNA methylation. A novel DNA methylation-deregulated and RNA m6A reader-cooperating lncRNA (DMDRMR) facilitated tumor growth and metastasis in clear cell renal cell carcinoma (ccRCC). Mechanistically, DMDRMR bound insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) to stabilize target genes, including the cell-cycle kinase CDK4 and three extracellular matrix components (COL6A1, LAMA5, and FN1), by specifically enhancing IGF2BP3 activity on them in an m6A-dependent manner. Consequently, DMDRMR and IGF2BP3 enhanced the G1-S transition, thus promoting cell proliferation in ccRCC. In patients with ccRCC, high coexpression of DMDRMR and IGF2BP3 was associated with poor outcomes. Our findings reveal that DMDRMR cooperates with IGF2BP3 to regulate target genes in an m6A-dependent manner and may represent a potential diagnostic, prognostic, and therapeutic target in ccRCC. SIGNIFICANCE: This study demonstrates that the lncRNA DMDRMR acts as a cofactor for IGF2BP3 to stabilize target genes in an m6A-dependent manner, thus exerting essential oncogenic roles in ccRCC.
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Affiliation(s)
- Yinmin Gu
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shaoxi Niu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yang Wang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Liqiang Duan
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Yongbo Pan
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Zhou Tong
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xu Zhang
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhenyu Yang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Bo Peng
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaodong Wang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoqi Han
- Medical College, Guizhou University, Guiyang, China
| | - Yuxin Li
- Pharmaceutical Analysis, College of Pharmacy, Beihua University, Jilin, China
| | - Tianyou Cheng
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Yajuan Liu
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Lina Shang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Tongfeng Liu
- Medical College, Guizhou University, Guiyang, China
| | - Xiwang Yang
- Medical College, Guizhou University, Guiyang, China
| | - Minxuan Sun
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Siyuan Jiang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Chang Zhang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Ning Zhang
- College of Life Science, Northwest A&F University, Yangling, China
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Collaborative Innovation Center for Cancer Medicine, Beijing, China
| | - Shan Gao
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China. .,Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
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19
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Niaz K, Shah SZA, Khan F, Bule M. Ochratoxin A-induced genotoxic and epigenetic mechanisms lead to Alzheimer disease: its modulation with strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44673-44700. [PMID: 32424756 DOI: 10.1007/s11356-020-08991-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Ochratoxin A (OTA) is a naturally occurring mycotoxin mostly found in food items including grains and coffee beans. It induces DNA single-strand breaks and has been considered to be carcinogenic. It is recognized as a serious threat to reproductive health both in males and females. OTA is highly nephrotoxic and carcinogenic, and its potency changes evidently between species and sexes. There is a close association between OTA, mutagenicity, carcinogenicity, and genotoxicity, but the underlying mechanisms are not clear. Reports regarding genotoxic effects in relation to OTA which leads to the induction of DNA adduct formation, protein synthesis inhibition, perturbation of cellular energy production, initiation of oxidative stress, induction of apoptosis, influences on mitosis, induction of cell cycle arrest, and interference with cytokine pathways. All these mechanisms are associated with nephrotoxicity, hepatotoxicity, teratotoxicity, immunological toxicity, and neurotoxicity. OTA administration activates various mechanisms such as p38 MAPK, JNKs, and ERKs dysfunctions, BDNF disruption, TH overexpression, caspase-3 and 9 activation, and ERK-1/2 phosphorylation which ultimately lead to Alzheimer disease (AD) progression. The current review will focus on OTA in terms of recent discoveries in the field of molecular biology. The main aim is to investigate the underlying mechanisms of OTA in regard to genotoxicity and epigenetic modulations that lead to AD. Also, we will highlight the strategies for the purpose of attenuating the hazards posed by OTA exposure.
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Affiliation(s)
- Kamal Niaz
- Department of Pharmacology and Toxicology, Faculty of Bio-Sciences, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
| | - Syed Zahid Ali Shah
- Department of Pathology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Fazlullah Khan
- The Institute of Pharmaceutical Sciences (TIPS), School of Pharmacy, International Campus, Tehran University of Medical Sciences (IC-TUMS), Tehran, 1417614411, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, 1417614411, Iran
| | - Mohammed Bule
- Department of Pharmacy, College of Medicine and Health Sciences, Ambo University, Ambo, Oromia, Ethiopia
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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21
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Wang L, Wang B, Quan Z. Identification of aberrantly methylated‑differentially expressed genes and gene ontology in prostate cancer. Mol Med Rep 2019; 21:744-758. [PMID: 31974616 PMCID: PMC6947816 DOI: 10.3892/mmr.2019.10876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is the most frequent urological malignancy in men worldwide. DNA methylation has an essential role in the etiology and pathogenesis of PCa. The purpose of the present study was to identify the aberrantly methylated-differentially expressed genes and to determine their potential roles in PCa. The important node genes identified were screened by integrated analysis. Gene expression microarrays and gene methylation microarrays were downloaded and aberrantly methylated-differentially expressed genes were obtained. Enrichment analysis and protein-protein interactions (PPI) were obtained, their interactive and visual networks were created, and the node genes in the PPI network were validated. A total of 105 hypomethylation-high expression genes and 561 hypermethylation-low expression genes along with their biological processes were identified. The top 10 node genes obtained from the PPI network were identified for each of the two gene groups. The methylation and gene expression status of node genes in TCGA database, GEPIA tool, and the HPA database were generally consistent with those of our results. In conclusion, the present study identified 20 aberrantly methylated-differentially expressed genes in PCa by combining bioinformatics analyses of gene expression and gene methylation microarrays, and concurrently, the survival of these genes was analyzed. Notably, methylation is a reversible biological process, which makes it of great biological significance for the diagnosis and treatment of prostate cancer using bioinformatics technology to determine abnormal methylation gene markers. The present study provided novel therapeutic targets for the treatment of PCa.
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Affiliation(s)
- Linbang Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bing Wang
- Laboratory of Environmental Monitoring, Shaanxi Province Health Inspection Institution, Xi'an, Shaanxi 710077, P.R. China
| | - Zhengxue Quan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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22
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Singh N, Kazim SN, Sultana R, Tiwari D, Borkotoky R, Kakati S, Nath Das N, Kumar Saikia A, Bose S. Oxidative stress and deregulations in base excision repair pathway as contributors to gallbladder anomalies and carcinoma - a study involving North-East Indian population. Free Radic Res 2019; 53:473-485. [PMID: 31117842 DOI: 10.1080/10715762.2019.1606423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Gallbladder cancer (GBC) is a fatal condition with dismal prognosis and aggressive local invasiveness; and with uncharacterised molecular pathology relating to non-specific therapeutic modalities. Given the importance of oxidative stress in chronic diseases and carcinogenesis, and the lacunae in literature regarding its role in gallbladder diseases, this study aimed to study the involvement of oxidative stress and deregulation in the base excision repair (BER) pathway in the pathogenesis of gallbladder diseases including GBC. This study involved patients from the North-East Indian population, where the numbers of reported cases are increasing rapidly and alarmingly. Oxidative stress, based on 8-OH-dG levels, was found to be significantly higher in gallbladder anomalies (cholelithiasis [CL] and cholecystitis [CS]) and GBC at the plasma and DNA level, and was associated with GBC severity. The expressions of key BER pathway genes were downregulated in gallbladder anomalies and GBC compared to controls, and in GBC compared to both non-neoplastic controls and gallbladder anomalies. Expression of XRCC1 and hOGG1 was significantly associated with both susceptibility and severity of GBC. The XRCC1 codon280 polymorphism was associated with disease susceptibility; and significantly higher oxidative stress was observed in hOGG1 genotypic variants. The genomes of GBC patients were found to be more hypermethylated compared to controls, with the promoters of XRCC1 and hOGG1 being hypermethylated and, therefore, being silenced. This study underlined the prognostic significance of the oxidative stress marker 8-OH-dG and BER pathway genes, especially hOGG1 and XRCC1, in gallbladder anomalies and GBC, as well as stated their potential for therapeutic targeting.
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Affiliation(s)
- Nidhi Singh
- a Department of Biotechnology , Gauhati University , Guwahati , India
| | - Syed Naqui Kazim
- b Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Rizwana Sultana
- c Bioengineering and Technology , Gauhati University , Guwahati , India
| | - Diptika Tiwari
- c Bioengineering and Technology , Gauhati University , Guwahati , India
| | - Raktim Borkotoky
- a Department of Biotechnology , Gauhati University , Guwahati , India
| | | | | | - Anjan Kumar Saikia
- e Central Railway Hospital , Guwahati , India.,f GNRC Hospital , Guwahati , India
| | - Sujoy Bose
- a Department of Biotechnology , Gauhati University , Guwahati , India
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23
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Zhang H, Dong S, Feng J. Epigenetic profiling and mRNA expression reveal candidate genes as biomarkers for colorectal cancer. J Cell Biochem 2019; 120:10767-10776. [PMID: 30672027 DOI: 10.1002/jcb.28368] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hui Zhang
- Department of Medical Oncology The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research Nanjing Jiangsu People's Republic of China
| | - Shuchen Dong
- Department of Medical Oncology The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research Nanjing Jiangsu People's Republic of China
| | - Jifeng Feng
- Department of Medical Oncology The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research Nanjing Jiangsu People's Republic of China
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24
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Zhou C, Ye M, Ni S, Li Q, Ye D, Li J, Shen Z, Deng H. DNA methylation biomarkers for head and neck squamous cell carcinoma. Epigenetics 2018; 13:398-409. [PMID: 29927694 DOI: 10.1080/15592294.2018.1465790] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA methylation plays an important role in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (FAM135B and ZNF610) and 2 hypomethylated-high-expression genes (HOXA9 and DCC) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that FAM135B methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.
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Affiliation(s)
- Chongchang Zhou
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Meng Ye
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Shumin Ni
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Qun Li
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Dong Ye
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Jinyun Li
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhisen Shen
- a Department of Otorhinolaryngology Head and Neck Surgery , Lihuili Hospital of Ningbo University , Ningbo , Zhejiang , China
| | - Hongxia Deng
- b Department of Oncology and Hematology , Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
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Liu Y, Luo M, Li Q, Lu J, Zhao M, Qu H. CIGene: a literature-based online resource for cancer initiation genes. BMC Genomics 2018; 19:552. [PMID: 30045691 PMCID: PMC6060465 DOI: 10.1186/s12864-018-4944-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 07/16/2018] [Indexed: 11/17/2022] Open
Abstract
Background Cancer initiation genes (CIGs) are genes that can directly promote cell proliferation or induce cancer. There are thousands of published studies identifying various CIGs; however, no systematic collection or description is available. Results To construct a CIG reference for genetic screening, we have collected 177 human genes curated from 1507 PubMed abstracts. To facilitate data queries and browsing, the identified CIGs along with extensive bioinformatic annotations were stored in an online database called CIGene. Initial functional analysis revealed an overlooked role for cell motility in cancer initiation. Subsequent cross-referencing of known tumor suppressor genes and oncogenes against the 177 CIGs identified 96 and 81 CIGs with and without known oncogenic roles, respectively. Successive network analyses of all 177 CIGs determined that the two groups of genes were more likely to link within their group. The distinct molecular functions for these groups were also confirmed with functional studies. While the 96 known oncogenic genes had fundamental roles in gene regulation and signaling, the remaining 81 genes possessed more ancillary functions, such enhancer binding. Further network and mutational analysis of the 96 known oncogenic genes revealed that mutations in these genes were highly prevalent in multiple cancers. By focusing on breast cancer, we found that 32 of the 96 genes with mutations in breast cancers were significantly associated with patient survival. Conclusions As the first literature-based online resource for CIGs, CIGene will serve as a useful gateway for the systematic analysis of cancer initiation. CIGene is freely available to all academic users at http://soft.bioinfo-minzhao.org/cigene/. Electronic supplementary material The online version of this article (10.1186/s12864-018-4944-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yining Liu
- School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou, 510182, China
| | - Mingyu Luo
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Qijun Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Jiachun Lu
- School of Public Health, The First affiliated Hospital, Guangzhou Medical University, Guangzhou, 510120, China
| | - Min Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, People's Republic of China.
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26
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Gu Y, Zhang CWH, Wang L, Zhao Y, Wang H, Ye Q, Gao S. Association Analysis between Body Mass Index and Genomic DNA Methylation across 15 Major Cancer Types. J Cancer 2018; 9:2532-2542. [PMID: 30026852 PMCID: PMC6036895 DOI: 10.7150/jca.23535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 05/01/2018] [Indexed: 12/17/2022] Open
Abstract
Cancer incidence and mortality increase with increasing body mass index (BMI), but BMI-associated epigenetic alterations in cancer remain elusive. We hypothesized that BMI would be associated with DNA methylation alterations in cancers. To test this hypothesis, here, we estimated the associations between DNA methylation and BMI through two different methods across 15 cancer types, at approximately 485,000 CpG sites and 2415 samples using data from The Cancer Genome Atlas. After comparing the DNA methylation levels in control BMI and high BMI individuals, we found differentially methylated CpG sites (DMSs) in cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), and uterine corpus endometrial carcinoma (UCEC) (False Discovery Rate < 0.05). The DMSs of COAD or UCEC were enriched in several obesity-induced and cancer-related pathways. Next, when BMI was used as a continuous variable, we identified BMI-associated methylated CpG sites (BMS) (P (Bonferroni) < 0.05) in CHOL (BMS = 1), COAD (BMS = 1), and UCEC (BMS = 4) using multivariable linear regression. In UCEC, three of the BMSs can predict the clinical outcomes and survival of patients with the tumors. Overall, we observed associations between DNA methylation and high BMI in CHOL, COAD, and UCEC. Furthermore, three BMI-associated CpGs were identified as potential biomarkers for UCEC prognosis.
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Affiliation(s)
- Yinmin Gu
- University of Science and Technology of China, Hefei 230026, China.,CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | | | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuhui Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Wang
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
| | - Shan Gao
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.,Medical College, Guizhou University, Guiyang 550025, China
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27
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Abstract
Since every cell of a multicellular organism contains the same genome, it is intriguing to understand why genetically homogenous cells are different from each other and what controls this. Several observations indicate that DNA methylation has an essential regulatory function in mammalian development, which is to establish the correct pattern of gene expression, and that DNA methylation pattern is tightly correlated with chromatin structure. Various physiological processes are controlled by specific DNA methylation patterns including genomic imprinting, inactivation of the X chromosome, regulation of tissue-specific gene expression and repression of transposons. Moreover, aberrant methylation could confer a selective advantage to cells, leading to cancerous growth. In this review we focus on the epigenetic molecular mechanisms during normal development and discuss how DNA methylation could affect the expression of genes leading to cancer transformation.
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Affiliation(s)
- Marcella Macaluso
- Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA, USA
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28
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Taylor KM, Wheeler R, Singh N, Vosloo D, Ray DW, Sommer P. The tobacco carcinogen NNK drives accumulation of DNMT1 at the GR promoter thereby reducing GR expression in untransformed lung fibroblasts. Sci Rep 2018; 8:4903. [PMID: 29559689 PMCID: PMC5861118 DOI: 10.1038/s41598-018-23309-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/01/2018] [Indexed: 12/19/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive, predominantly cigarette smoke-induced tumour with poor prognosis. The glucocorticoid receptor (GR), a SCLC tumour suppressor gene, is typically reduced in SCLC. We now show that SCLC cells express high levels of DNA methyltransferase 1 (DNMT1) which accumulates at the GR promoter. DNMT1 expression is further increased by exposure to the tobacco carcinogen NNK. In the untransformed human lung fibroblast cell line, MRC-5, short term NNK treatment decreases GRα mRNA and protein expression due to accumulation of DNMT1 at the GR promoter. Long term NNK treatment results in persistently augmented DNMT1 levels with lowered GR levels. Long term exposure to NNK slows cell proliferation and induces DNA damage, while the GR antagonist RU486 stimulates proliferation and protects against DNA damage. Although both NNK and RU486 treatment increases methylation at the GR promoter, neither are sufficient to prevent senescence in this context. NNK exposure results in accumulation of DNMT1 at the GR promoter in untransformed lung cells mimicking SCLC cells, directly linking tobacco smoke exposure to silencing of the GR, an important step in SCLC carcinogenesis.
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Affiliation(s)
- Kerryn M Taylor
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Roxanne Wheeler
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nimisha Singh
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Dalene Vosloo
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - David W Ray
- Division of Endocrinology, Diabetes and Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Paula Sommer
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa.
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29
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Association between MGMT Promoter Methylation and Risk of Breast and Gynecologic Cancers: A Systematic Review and Meta-Analysis. Sci Rep 2017; 7:12783. [PMID: 28986566 PMCID: PMC5630583 DOI: 10.1038/s41598-017-13208-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/21/2017] [Indexed: 12/27/2022] Open
Abstract
The role of the promoter methylation of O6-methylguanine-DNA methyltransferase (MGMT) remains controversial for breast and gynecologic cancers. We conducted a meta-analysis to assess the association between hypermethylation of MGMT promoter and the risk of breast and gynecologic cancers. A comprehensive search was conducted in PubMed and Embase electronic databases up to 19th August 2017 for studies about the association between MGMT promoter hypermethylation and breast and gynecologic cancers. A total of 28 articles including 2,171 tumor tissues and 1,191 controls were involved in the meta-analysis. The pooled results showed that MGMT promoter methylation status was significantly associated with an increased risk of breast and gynecologic cancers (OR = 4.37, 95% CI: 2.68–7.13, P < 0.05). The associations were robust in subgroup analysis based on ethnicity, cancer type, methylation detection method, and control source. This meta-analysis indicated that MGMT hypermethylation was significantly associated with the risk of breast and gynecological cancers, and it may be utilized as a valuable biomarker in early diagnostics and prognostication of these cancers. Further efforts are needed to identify and validate this finding in prospective studies, especially in situation with new methylation testing methods and samples from plasma circulating DNA.
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30
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Wu D, Yang X, Peng H, Guo D, Zhao W, Zhao C, Zhou X. OCIAD2 suppressed tumor growth and invasion via AKT pathway in Hepatocelluar carcinoma. Carcinogenesis 2017; 38:910-919. [PMID: 28911005 DOI: 10.1093/carcin/bgx073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive tumor and the third leading cause of cancer-related death worldwide. Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) has been found frequently methylated in various cancers, including HCC. The aim of the present study was to investigate the role of OCIAD2 in HCC progression. We analyzed liver hepatocellular carcinoma patients' data from the Cancer Genome Atlas (TCGA), including data extracted from 371 HCC tissues and 50 adjacent normal liver tissues. The RNA sequencing and DNA methylation data revealed that OCIAD2 were significantly hypermethylated and its expression level in the tumor tissues was much lower than that in the corresponding adjacent normal tissues. The methylation level in the promoter was negatively correlated with the expression level of OCAID2. Treatment of HCC cell lines with the DNA methylation inhibitor 5-aza-2'-deoxycitydine (5-Aza) induced a significant increase in the OCIAD2 mRNA and protein. Knocking-down OCIAD2 led to an increased colony formation, migration and invasion dramatically, accompanying with an enhanced expression of MMP9 and activation of AKT and FAK. Inhibition of AKT signaling restored OCIAD2-mediated changes in HCC cell clonogenic growth, migration and invasion. Survival analysis of HCC patient's data indicated patients with a higher expression ratio of OCIAD2/MMP9 had a shorter overall survival than those with a lower expression ratio of OCIAD2/MMP9. Overall, our data indicate that reduced expression of OCIAD2 by DNA hypermethylation plays an important role in HCC tumor growth and invasion. Hypermethylation of OCIAD2 may contribute to HCC treatment development.
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Affiliation(s)
- Dan Wu
- Department of Radiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Xufang Yang
- Department of Pathophysiology, MuDanJiang Medical College, Heilongjiang, 150000, P.R.China
| | - Huiming Peng
- Department of Radiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Dongmin Guo
- Department of Radiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Weiling Zhao
- Department of Radiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Chen Zhao
- Department of Radiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Xiaobo Zhou
- Department of Radiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.,College of Computer Science and Software Engineering, Shenzhen University, ShenZhen, China
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31
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Current epigenetic aspects the clinical kidney researcher should embrace. Clin Sci (Lond) 2017; 131:1649-1667. [DOI: 10.1042/cs20160596] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 02/06/2023]
Abstract
Chronic kidney disease (CKD), affecting 10–12% of the world’s adult population, is associated with a considerably elevated risk of serious comorbidities, in particular, premature vascular disease and death. Although a wide spectrum of causative factors has been identified and/or suggested, there is still a large gap of knowledge regarding the underlying mechanisms and the complexity of the CKD phenotype. Epigenetic factors, which calibrate the genetic code, are emerging as important players in the CKD-associated pathophysiology. In this article, we review some of the current knowledge on epigenetic modifications and aspects on their role in the perturbed uraemic milieu, as well as the prospect of applying epigenotype-based diagnostics and preventive and therapeutic tools of clinical relevance to CKD patients. The practical realization of such a paradigm will require that researchers apply a holistic approach, including the full spectrum of the epigenetic landscape as well as the variability between and within tissues in the uraemic milieu.
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32
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Meta-analysis demonstrates no association between p16 ink4a promoter methylation and epithelial ovarian cancer. Arch Gynecol Obstet 2016; 295:697-704. [PMID: 28000027 DOI: 10.1007/s00404-016-4264-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/02/2016] [Indexed: 01/13/2023]
Abstract
BACKGROUND p16 INK4A (p16) functions as a tumor suppressor gene in various malignancies. Aberrant p16 methylation has been proposed to be essential in ovarian carcinogenesis. However, it is unclear whether p16 can be used as a diagnostic marker owing to the small sample sizes in previous studies. METHODS To determine whether p16 promoter methylation is associated with epithelial ovarian cancer and can thus be used as a diagnostic marker, we performed a meta-analysis of published studies. The following databases were searched using a systematic search method: PubMed, Web of Science, EMBASE, and Chinese National Knowledge Infrastructure. We used a random-effects model to analyze the relative risk (RR); we also evaluated between-study heterogeneity, subgroup heterogeneity, and publication bias. RESULTS Our meta-analysis included eight eligible studies, with 428 ovarian cancers and 278 normal tissue samples and benign neoplasms. p16 promoter methylation was identified in 5.4 to 43.2% (median 27.86%) of ovarian cancers and 0 to 37.5% (median 15.8%) of normal tissue and benign neoplasms indicating that no significant association exists between p16 promoter methylation and epithelial ovarian cancer. However, the pooled results also showed that the RR was 1.52 (95% CI 0.80-2.87) in the ovarian cancer cases versus the corresponding normal and benign cases under the random-effects model. Between-study heterogeneity was determined through a sensitivity analysis; the I 2 value did not change when one study was excluded. CONCLUSIONS Our study showed that p16 promoter methylation cannot be used to differentiate benign from malignant epithelial ovarian tumors. Therefore, p16 promoter methylation cannot be used as a marker for diagnosing the early stage of ovarian cancer.
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33
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Babaian A, Mager DL. Endogenous retroviral promoter exaptation in human cancer. Mob DNA 2016; 7:24. [PMID: 27980689 PMCID: PMC5134097 DOI: 10.1186/s13100-016-0080-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression. Dispersed across the human genome, endogenous retroviruses (ERVs) provide an enormous reservoir of autonomous gene regulatory modules, some of which have been co-opted by the host during evolution to play important roles in normal regulation of genes and gene networks. This review focuses on the “dark side” of such ERV regulatory capacity. Specifically, we discuss a growing number of examples of normally dormant or epigenetically repressed ERVs that have been harnessed to drive oncogenes in human cancer, a process we term onco-exaptation, and we propose potential mechanisms that may underlie this phenomenon.
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Affiliation(s)
- Artem Babaian
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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Li Y, Buckhaults P, Cui X, Tollefsbol TO. Combinatorial epigenetic mechanisms and efficacy of early breast cancer inhibition by nutritive botanicals. Epigenomics 2016; 8:1019-37. [PMID: 27478970 PMCID: PMC5066124 DOI: 10.2217/epi-2016-0024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aim: Aberrant epigenetic events are important contributors to the pathogenesis of different types of cancers and dietary botanicals with epigenetic properties can influence early cancer development leading to cancer prevention effects. We sought to investigate potential combinatorial effects of bioactive dietary components including green tea polyphenols (GTPs) and broccoli sprouts (BSp) on neutralizing epigenetic aberrations during breast tumorigenesis. Materials & methods: The combinatorial effects were evaluated in a breast cancer transformation cellular system and breast cancer mouse xenografts. Results & conclusion: Combined treatment with epigallocatechin-3-gallate in GTPs and sulforaphane in BSp resulted in a synergistic inhibition of breast cancer cellular growth. Further studies revealed this combination led to genome-wide epigenetic alterations. Combinatorial diets significantly inhibited tumor growth in breast cancer mouse xenografts. Collectively, these studies indicate that combined GTPs and BSp are highly effective in inhibiting early breast cancer development by, at least in part, regulating epigenetic mechanisms.
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Affiliation(s)
- Yuanyuan Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Phillip Buckhaults
- Department of Drug Discovery & Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Xiangqin Cui
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Kasai H. What causes human cancer? Approaches from the chemistry of DNA damage. Genes Environ 2016; 38:19. [PMID: 27375797 PMCID: PMC4929788 DOI: 10.1186/s41021-016-0046-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/11/2016] [Indexed: 11/23/2022] Open
Abstract
To prevent human cancers, environmental mutagens must be identified. A common mechanism of carcinogenesis is DNA damage, and thus it is quite possible that environmental mutagens can be trapped as adducts by DNA components. It is also important to identify new types of DNA damaging reactions and clarify their mechanisms. In this paper, I will provide typical examples of our efforts to identify DNA damage by environmental agents, from chemistry-based studies. 1) Oxidative DNA damage: 8-Hydroxydeoxyguanosine (8-OHdG, 8-oxodG) was discovered during a structural study of DNA modifications caused in vitro by heating glucose, which was used as a model of cooked foods. We found that various oxygen radical-forming agents induced the formation of 8-OHdG in DNA, in vitro and in vivo. Analyses of the urinary 8-OHdG levels are useful to assess the extent of oxidative DNA damage in a human population. 2) Lipid peroxide-derived DNA adducts: We searched for mutagens that react with deoxynucleosides, in model systems of lipid peroxidation. The reaction mixtures were analyzed by high performance liquid chromatography (HPLC), and we discovered various lipid peroxide-derived mutagens, including new mutagens. Some of these adducts were detected in human DNA. These mutagens may be involved in lipid peroxide-related cancers. 3) Methylation of cytosine by free radicals: Methylation of the cytosine C-5 position is an important mechanism of carcinogenesis, in addition to gene mutations. However, the actual mechanisms of de novo methylation in relation to environmental agents are not clear. We found that cytosine C-5 methylation occurred by a free radical mechanism. The possible role of this radical-induced DNA methylation in carcinogenesis will be discussed, in relation to the presently accepted concept of cancer epigenetics. In these studies, chemical analyses of the adducts formed in model reactions led to the discoveries of new mutagens and important types of DNA modifications, which seem to be involved in human carcinogenesis.
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Affiliation(s)
- Hiroshi Kasai
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1, Iseigaoka, Kitakyushu, Yahatanishi-ku 807-8555 Japan
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36
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Epigenetic mechanisms regulating the development of hepatocellular carcinoma and their promise for therapeutics. Hepatol Int 2016; 11:45-53. [PMID: 27271356 DOI: 10.1007/s12072-016-9743-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers around the globe and third most fatal malignancy. Chronic liver disorders such as chronic hepatitis and liver cirrhosis often lead to the development of HCC. Accumulation of genetic and epigenetic alterations are involved in the development of HCC. Genetic research sparked by recent developments in next generation sequencing has identified the frequency of genetic alterations that occur in HCC and has led to the identification of genetic hotspots. Emerging evidence suggests that epigenetic aberrations are strongly associated with the initiation and development of HCC. Various important genes encoding tumor suppressors including P16, RASSF1A, DLC-1, RUNX3 and SOCS-1 are targets of epigenetic dysregulation during the development of HCC. The present review discusses the importance of epigenetic regulations including DNA methylation, histone modification and microRNA mediated regulation of gene expression during tumorigenesis and their use as disease biomarkers. Furthermore, these epigenetic alterations have been discussed in relationship with promising therapeutic perspectives for HCC and related cancers.
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Zhang C, Peng Y, Yang F, Qin R, Liu W, Zhang C. PCDH8 is Frequently Inactivated by Promoter Hypermethylation in Liver Cancer: Diagnostic and Clinical Significance. J Cancer 2016; 7:446-52. [PMID: 26918058 PMCID: PMC4749365 DOI: 10.7150/jca.13065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 12/08/2015] [Indexed: 12/16/2022] Open
Abstract
AIM: Protocadherin-8 (PCDH8) plays an important role in signaling pathways of cell adhesin, proliferation, and migration. It has been reported that PCDH8 is mutated or methylated in several human cancers. However, little is known about PCDH8 in liver cancer. The aim of this study was to investigate the protein expression and promoter methylation status of PCDH8 in liver cancer and evaluate the association between PCDH8 methylation and the clinicopathological features. METHODS: The methylation status of PCDH8 in 42 hepatocellular carcinoma (HCC), 8 Cholangiocarcinoma (CC) and 50 normal liver tissues were examined using methylation-specific PCR (MSP) and the protein expression of PCDH8 was detected by immunohistochemistry. The relationships between PCDH8 methylation and clinicopathological features as well as overall survival of patients were evaluated. RESULTS: The PCDH8 methylation was more frequent in liver cancer tissues than that in the normal liver tissues (88% vs. 32%, P < 0.001), and is significantly associated with loss of its protein expression (P = 0.004). Moreover, there is a significant correlation between PCDH8 methylation and the alpha-fetoprotein (AFP) level (P = 0.008). Kaplan-Meier survival analysis revealed that patients with PCDH8 methylation have shorter OS and PFS than those without PCDH8 methylation (P = 0.041 and P = 0.028, respectively). CONCLUSION: PCDH8 is often inactivated by promoter methylation in liver cancer. PCDH8 methylation can serve as a valuable diagnostic biomarker for early detection of liver cancer and might be useful to predict an unfavorable clinical feature.
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Affiliation(s)
- Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, P. R. China
| | - Yunfei Peng
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, P. R. China
| | - Fan Yang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, P. R. China
| | - Ruixi Qin
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, P. R. China
| | - Wenjun Liu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, P. R. China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, P. R. China
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Kim TW, Lee SJ, Oh BM, Lee H, Uhm TG, Min JK, Park YJ, Yoon SR, Kim BY, Kim JW, Choe YK, Lee HG. Epigenetic modification of TLR4 promotes activation of NF-κB by regulating methyl-CpG-binding domain protein 2 and Sp1 in gastric cancer. Oncotarget 2016; 7:4195-209. [PMID: 26675260 PMCID: PMC4826199 DOI: 10.18632/oncotarget.6549] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/23/2015] [Indexed: 12/17/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is important in promoting the immune response in various cancers. Recently, TLR4 is highly expressed in a stage-dependent manner in gastric cancer, but the regulatory mechanism of TLR4 expression has been not elucidated it. Here, we investigated the mechanism underlying regulation of TLR4 expression through promoter methylation and histone modification between transcriptional regulation and silencing of the TLR4 gene in gastric cancer cells. Chromatin immunoprecipitation was carried out to screen for factors related to TLR4 methylation such as MeCP2, HDAC1, and Sp1 on the TLR4 promoter. Moreover, DNA methyltransferase inhibitor 5-aza-deoxycytidine (5-aza-dC) induced demethylation of the TLR4 promoter and increased H3K4 trimethylation and Sp1 binding to reactivate silenced TLR4. In contrast, although the silence of TLR4 activated H3K9 trimethylation and MeCP2 complex, combined treatment with TLR4 agonist and 5-aza-dC upregulated H3K4 trimethylation and activated with transcription factors as Sp1 and NF-κB. This study demonstrates that recruitment of the MeCP2/HDAC1 repressor complex increases the low levels of TLR4 expression through epigenetic modification of DNA and histones on the TLR4 promoter, but Sp1 activates TLR4 high expression by hypomethylation and NF-κB signaling in gastric cancer cells.
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Affiliation(s)
- Tae Woo Kim
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
| | - Seon-Jin Lee
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
| | - Byung Moo Oh
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
| | - Heesoo Lee
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
| | - Tae Gi Uhm
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Jeong-Ki Min
- Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Young-Jun Park
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Suk Ran Yoon
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Bo-Yeon Kim
- World Class Institute, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Republic of Korea
| | - Jong Wan Kim
- Department of Laboratory Medicine, College of Medicine, Dankook University, Cheonan, Chungnam, Republic of Korea
| | - Yong-Kyung Choe
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Hee Gu Lee
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Department of Biomolecular Science, University of Science and Technology (UST), Yuseong-gu, Daejeon, Republic of Korea
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Kishino T, Niwa T, Yamashita S, Takahashi T, Nakazato H, Nakajima T, Igaki H, Tachimori Y, Suzuki Y, Ushijima T. Integrated analysis of DNA methylation and mutations in esophageal squamous cell carcinoma. Mol Carcinog 2016; 55:2077-2088. [PMID: 26756304 DOI: 10.1002/mc.22452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]
Abstract
The recent development of next-generation sequencing technology for extensive mutation analysis, and beadarray technology for genome-wide DNA methylation analysis has made it possible to obtain integrated pictures of genetic and epigenetic alterations, using the same cancer samples. In this study, we aimed to characterize such a picture in esophageal squamous cell carcinomas (ESCCs). Base substitutions of 55 cancer-related genes and copy number alterations (CNAs) of 28 cancer-related genes were analyzed by targeted sequencing. Forty-four of 57 ESCCs (77%) had 64 non-synonymous somatic mutations, and 24 ESCCs (42%) had 35 CNAs. A genome-wide DNA methylation analysis using an Infinium HumanMethylation450 BeadChip array showed that the CpG island methylator phenotype was unlikely to be present in ESCCs, a different situation from gastric and colon cancers. Regarding individual pathways affected in ESCCs, the WNT pathway was activated potentially by aberrant methylation of its negative regulators, such as SFRP1, SFRP2, SFRP4, SFRP5, SOX17, and WIF1 (33%). The p53 pathway was inactivated by TP53 mutations (70%), and potentially by aberrant methylation of its downstream genes. The cell cycle was deregulated by mutations of CDKN2A (9%), deletions of CDKN2A and RB1 (32%), and by aberrant methylation of CDKN2A and CHFR (9%). In conclusion, ESCCs had unique methylation profiles different from gastric and colon cancers. The genes involved in the WNT pathway were affected mainly by epigenetic alterations, and those involved in the p53 pathway and cell cycle regulation were affected mainly by genetic alterations. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan.,Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takamasa Takahashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hidetsugu Nakazato
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Takeshi Nakajima
- Division of Endoscopy, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyasu Igaki
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Tachimori
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuyuki Suzuki
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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40
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Pisanic TR, Athamanolap P, Poh W, Chen C, Hulbert A, Brock MV, Herman JG, Wang TH. DREAMing: a simple and ultrasensitive method for assessing intratumor epigenetic heterogeneity directly from liquid biopsies. Nucleic Acids Res 2015; 43:e154. [PMID: 26304549 PMCID: PMC4678844 DOI: 10.1093/nar/gkv795] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/25/2015] [Indexed: 01/15/2023] Open
Abstract
Many cancers comprise heterogeneous populations of cells at primary and metastatic sites throughout the body. The presence or emergence of distinct subclones with drug-resistant genetic and epigenetic phenotypes within these populations can greatly complicate therapeutic intervention. Liquid biopsies of peripheral blood from cancer patients have been suggested as an ideal means of sampling intratumor genetic and epigenetic heterogeneity for diagnostics, monitoring and therapeutic guidance. However, current molecular diagnostic and sequencing methods are not well suited to the routine assessment of epigenetic heterogeneity in difficult samples such as liquid biopsies that contain intrinsically low fractional concentrations of circulating tumor DNA (ctDNA) and rare epigenetic subclonal populations. Here we report an alternative approach, deemed DREAMing (Discrimination of Rare EpiAlleles by Melt), which uses semi-limiting dilution and precise melt curve analysis to distinguish and enumerate individual copies of epiallelic species at single-CpG-site resolution in fractions as low as 0.005%, providing facile and inexpensive ultrasensitive assessment of locus-specific epigenetic heterogeneity directly from liquid biopsies. The technique is demonstrated here for the evaluation of epigenetic heterogeneity at p14ARF and BRCA1 gene-promoter loci in liquid biopsies obtained from patients in association with non-small cell lung cancer (NSCLC) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN), respectively.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD 21218, USA
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Weijie Poh
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Chen Chen
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Alicia Hulbert
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Malcolm V Brock
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - James G Herman
- Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Baltimore, MD 21218, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA Cancer Biology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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DAPK1 Promoter Methylation and Cervical Cancer Risk: A Systematic Review and a Meta-Analysis. PLoS One 2015; 10:e0135078. [PMID: 26267895 PMCID: PMC4534406 DOI: 10.1371/journal.pone.0135078] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/17/2015] [Indexed: 12/16/2022] Open
Abstract
Objective The Death-Associated Protein Kinase 1 (DAPK1) gene has been frequently investigated in cervical cancer (CC). The aim of the present study was to carry out a systematic review and a meta-analysis in order to evaluate DAPK1 promoter methylation as an epigenetic marker for CC risk. Methods A systematic literature search was carried out. The Cochrane software package Review Manager 5.2 was used. The fixed-effects or random-effects models, according to heterogeneity across studies, were used to calculate odds ratios (ORs) and 95% Confidence Intervals (CIs). Furthermore, subgroup analyses were conducted by histological type, assays used to evaluate DAPK1 promoter methylation, and control sample source. Results A total of 20 papers, published between 2001 and 2014, on 1929 samples, were included in the meta-analysis. DAPK1 promoter methylation was associated with an increased CC risk based on the random effects model (OR: 21.20; 95%CI = 11.14–40.35). Omitting the most heterogeneous study, the between study heterogeneity decreased and the association increased (OR: 24.13; 95% CI = 15.83–36.78). The association was also confirmed in all the subgroups analyses. Conclusions A significant strong association between DAPK1 promoter methylation and CC was shown and confirmed independently by histological tumor type, method used to evaluate methylation and source of control samples. Methylation markers may have value in early detection of CC precursor lesions, provide added reassurances of safety for women who are candidates for less frequent screens, and predict outcomes of women infected with human papilloma virus.
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Wang G, Li X, Tian W, Wang Y, Wu D, Sun Z, Zhao E. Promoter DNA methylation is associated withKLF11expression in epithelial ovarian cancer. Genes Chromosomes Cancer 2015; 54:453-62. [PMID: 25931269 DOI: 10.1002/gcc.22257] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/09/2015] [Indexed: 01/19/2023] Open
Affiliation(s)
- Guan Wang
- Department of Obstetrics and Gynecology; Tianjin Central Hospital of Obstetrics and Gynecology; Tianjin 300100 China
| | - Xianfeng Li
- State Key Laboratory of Medical Genetics; Central South University; Changsha Hunan 410078 China
| | - Weiping Tian
- Tianjin Research Center of Basic Medical Science; Tianjin Medical University; Tianjin 300070 China
| | - Yan Wang
- Institute of Psychology, Chinese Academy of Sciences; Beijing 100101 China
| | - Dandan Wu
- Department of Obstetrics and Gynecology; Tianjin Central Hospital of Obstetrics and Gynecology; Tianjin 300100 China
| | - Zhongsheng Sun
- Beijing Institute of Life Science, Chinese Academy of Science; Beijing 100101 China
| | - Enfeng Zhao
- Department of Obstetrics and Gynecology; Chinese PLA General Hospital; Beijing 100853 China
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Abstract
Increasingly, the gut microbiome is implicated in the etiology of cancer, not only as an infectious agent but also by altering exposure to dietary compounds that influence disease risk. Whereas the composition and metabolism of the gut microbiome is influenced by diet, the gut microbiome can also modify dietary exposures in ways that are beneficial or detrimental to the human host. The colonic bacteria metabolize macronutrients, either as specialists or in consortia of bacteria, in a variety of diverse metabolic pathways. Microbial metabolites of diet can also be epigenetic activators of gene expression that may influence cancer risk in humans. Epigenetics involves heritable changes in gene expression via post-translational and post-transcriptional modifications. Microbial metabolites can influence epigenetics by altering the pool of compounds used for modification or by directly inhibiting enzymes involved in epigenetic pathways. Colonic epithelium is immediately exposed to these metabolites, although some metabolites are also found in systemic circulation. In this review, we discuss the role of the gut microbiome in dietary metabolism and how microbial metabolites may influence gene expression linked to colon cancer risk.
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Ouadid-Ahidouch H, Rodat-Despoix L, Matifat F, Morin G, Ahidouch A. DNA methylation of channel-related genes in cancers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2621-8. [PMID: 25703813 DOI: 10.1016/j.bbamem.2015.02.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 02/04/2015] [Accepted: 02/12/2015] [Indexed: 12/31/2022]
Abstract
DNA methylation at CpG sites is an epigenetic mechanism that regulates cellular gene expression. In cancer cells, aberrant methylation is correlated with the abnormalities in expression of genes that are known to be involved in the particular characteristics of cancer cells such as proliferation, apoptosis, migration or invasion. During the past 30 years, accumulating data have definitely convinced the scientific community that ion channels are involved in cancerogenesis and cancer properties. As they are situated at the cell surface, they might be prime targets in the development of new therapeutic strategies besides their potential use as prognostic factors. Despite the progress in our understanding of the remodeling of ion channels in cancer cells, the molecular mechanisms underlying their over- or down-expression remained enigmatic. In this review, we aimed to summarize the available data on gene promoter methylation of ion channels and to investigate their clinical significance as novel biomarkers in cancer. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers.
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Affiliation(s)
- Halima Ouadid-Ahidouch
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France.
| | - Lise Rodat-Despoix
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France
| | - Fabrice Matifat
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France
| | - Gilles Morin
- EA 4666 and Department of Molecular and Clinical Genetics, Amiens University Hospital, University of Picardie Jules Verne, Amiens, France
| | - Ahmed Ahidouch
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France; Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir Morocco
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Boyanapalli SSS, Kong ANT. "Curcumin, the King of Spices": Epigenetic Regulatory Mechanisms in the Prevention of Cancer, Neurological, and Inflammatory Diseases. ACTA ACUST UNITED AC 2015; 1:129-139. [PMID: 26457241 DOI: 10.1007/s40495-015-0018-x] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Curcumin (diferuloylmethane), a polyphenolic compound, is a component of Curcuma longa, commonly known as turmeric. It is a well-known anti-inflammatory, anti-oxidative, and anti-lipidemic agent and has recently been shown to modulate several diseases via epigenetic regulation. Many recent studies have demonstrated the role of epigenetic inactivation of pivotal genes that regulate human pathologies, such as neurocognitive disorders, inflammation, obesity, and cancers. Epigenetic changes involve changes in DNA methylation, histone modifications, or altered microRNA expression patterns which are known to be interconnected and play a key role in tumor progression and failure of conventional chemotherapy. The majority of epigenetic changes are influenced by lifestyle and diets. In this regard, dietary phytochemicals as dietary supplements have emerged as a promising source that are able to reverse these epigenetic alterations, to actively regulate gene expression and molecular targets that are known to promote tumorigenesis, and also to prevent age-related diseases through epigenetic modifications. There have been several studies which reported the role of curcumin as an epigenetic regulator in neurological disorders, inflammation, and in diabetes apart from cancers. The epigenetic regulatory roles of curcumin include (1) inhibition of DNA methyltransferases (DNMTs), which has been well defined from the recent studies on its function as a DNA hypomethylating agent; (2) regulation of histone modifications via regulation of histone acetyltransferases (HATs) and histone deacetylases (HDACs); and (3) regulation of micro RNAs (miRNA). This review summarizes the current knowledge on the effect of curcumin in the treatment and/or prevention of inflammation, neurodegenerative diseases, and cancers by regulating histone deacetylases, histone acetyltransferases, and DNA methyltransferases.
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Affiliation(s)
- Sarandeep S S Boyanapalli
- Center for Cancer Prevention Research, Department of Pharmaceutics, Ernest-Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Ah-Ng. Tony Kong
- Center for Cancer Prevention Research, Department of Pharmaceutics, Ernest-Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA
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Anestopoulos I, Voulgaridou GP, Georgakilas AG, Franco R, Pappa A, Panayiotidis MI. Epigenetic therapy as a novel approach in hepatocellular carcinoma. Pharmacol Ther 2014; 145:103-19. [PMID: 25205159 DOI: 10.1016/j.pharmthera.2014.09.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/02/2014] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver malignancy and one with high fatality. Its 5-year survival rate remains low and thus, there is a need for improvement of current treatment strategies as well as development of novel targeted methodologies in order to optimize existing therapeutic protocols. To this end, only recently, it was discovered that its pathophysiology also involves epigenetic alterations in DNA methylation, histone modifications and/or non-coding microRNA patterns. Unlike genetic events, epigenetic alterations are reversible and thus potentially considered to be an alternative option in cancer treatment protocols. In this review, we describe the general characteristics and resulted major alterations of the epigenetic machinery as well as current state of progress of epigenetic therapy (via different single or combinatorial experimental approaches) in HCC.
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Affiliation(s)
- Ioannis Anestopoulos
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Alexandros G Georgakilas
- School of Applied Mathematical & Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Rodrigo Franco
- Redox Biology Center, School of Veterinary Medicine & Biomedical Sciences, Redox Biology Center, University of Nebraska-Lincoln, USA
| | - Aglaia Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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47
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Methylation-associated gene silencing of RARB in areca carcinogens induced mouse oral squamous cell carcinoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:378358. [PMID: 25197641 PMCID: PMC4150525 DOI: 10.1155/2014/378358] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/08/2014] [Accepted: 06/10/2014] [Indexed: 12/17/2022]
Abstract
Regarding oral squamous cell carcinoma (OSCC) development, chewing areca is known to be a strong risk factor in many Asian cultures. Therefore, we established an OSCC induced mouse model by 4-nitroquinoline-1-oxide (4-NQO), or arecoline, or both treatments, respectively. These are the main two components of the areca nut that could increase the occurrence of OSCC. We examined the effects with the noncommercial MCGI (mouse CpG islands) microarray for genome-wide screening the DNA methylation aberrant in induced OSCC mice. The microarray results showed 34 hypermethylated genes in 4-NQO plus arecoline induced OSCC mice tongue tissues. The examinations also used methylation-specific polymerase chain reaction (MS-PCR) and bisulfite sequencing to realize the methylation pattern in collected mouse tongue tissues and human OSCC cell lines of different grades, respectively. These results showed that retinoic acid receptor β (RARB) was indicated in hypermethylation at the promoter region and the loss of expression during cancer development. According to the results of real-time PCR, it was shown that de novo DNA methyltransferases were involved in gene epigenetic alternations of OSCC. Collectively, our results showed that RARB hypermethylation was involved in the areca-associated oral carcinogenesis.
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48
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Yu G, Bing Y, Li W, Xia L, Liu Z. Hepatitis B virus inhibits the expression of CD82 through hypermethylation of its promoter in hepatoma cells. Mol Med Rep 2014; 10:2580-6. [PMID: 25119390 DOI: 10.3892/mmr.2014.2495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/23/2014] [Indexed: 12/20/2022] Open
Abstract
The tumor suppressor gene CD82, also known as KAI1, may act as a general suppressor of metastasis in numerous types of cancer. It is hypothesized that downregulation of CD82 gene expression may be an important factor in the induction of hepatocellular carcinoma (HCC), however the mechanism for this requires further study. In the present study, the relative mRNA and protein expression levels of the CD82 gene were determined in HCC and adjacent non‑tumor tissues. The association between the CD82 gene and the hepatitis B virus (HBV) was also investigated, by quantitative polymerase chain reaction, western blotting, luciferase reporter assays and mass spectrometry with matrix‑assisted laser desorption/ionization time‑of‑flight mass array. CD82 expression was shown to be suppressed in response to HCC promoter methylation. Relative CD82 mRNA and protein expression levels were downregulated in HCC tissues (P<0.05). HBx protein inhibited CD82 promoter activity and subsequently the mRNA and protein expression levels. Furthermore, it was demonstrated that HBV could inhibit the expression of CD82 at the transcriptional level, and repress the activity of the CD82 promoter through hypermethylation. In addition, the methyl enzyme inhibitor 5‑aza‑CdR could induce the CD82 promoter activity and the relative expression level of CD82 mRNA, as observed by an increase in luciferase activity driven by the CD82 promoter. The observations of the present study suggest that hypermethylation of the CD82 promoter may be an event leading to the development of HCC. Low expression of CD82 is likely to be involved in tumor progression. HBV may inhibit the expression of CD82 through hypermethylation of the promoter in hepatoma cells.
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Affiliation(s)
- Guozheng Yu
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yuntao Bing
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Wei Li
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Wuhan, Hubei 430079, P.R. China
| | - Lin Xia
- Department of Internal Medicine Oncology, Huangshi Central Hospital, Huangshi, Hubei 435005, P.R. China
| | - Zhisu Liu
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Wang SC, Lee TH, Hsu CH, Chang YJ, Chang MS, Wang YC, Ho YS, Wen WC, Lin RK. Antroquinonol D, isolated from Antrodia camphorata, with DNA demethylation and anticancer potential. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5625-35. [PMID: 24784321 DOI: 10.1021/jf4056924] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA methyltransferase 1 (DNMT1) catalyzes DNA methylation and is overexpressed in various human diseases, including cancer. A rational approach to preventing tumorigenesis involves the use of pharmacologic inhibitors of DNA methylation; these inhibitors should reactivate tumor suppressor genes (TSGs) in tumor cells and restore tumor suppressor pathways. Antroquinonol D (3-demethoxyl antroquinonol), a new DNMT1 inhibitor, was isolated from Antrodia camphorata and identified using nuclear magnetic resonance. Antroquinonol D inhibited the growth of MCF7, T47D, and MDA-MB-231 breast cancer cells without harming normal MCF10A and IMR-90 cells. The SRB assay showed that the 50% growth inhibition (GI50) in MCF7, T47D, and MDA-MB-231 breast cancer cells following treatment with antroquinonol D was 8.01, 3.57, and 25.08 μM, respectively. d-Antroquinonol also inhibited the migratory ability of MDA-MB-231 breast cancer cells in wound healing and Transwell assays. In addition, antroquinonol D inhibited DNMT1 activity, as assessed by the DNMT1 methyltransferase activity assay. As the cofactor SAM level increased, the inhibitory effects of d-antroquinonol on DNMT1 gradually decreased. An enzyme activity assay and molecular modeling revealed that antroquinonol D is bound to the catalytic domain of DNMT1 and competes for the same binding pocket in the DNMT1 enzyme as the cofactor SAM, but does not compete for the binding pocket in the DNMT3B enzyme. An Illumina Methylation 450 K array-based assay and real-time PCR assay revealed that antroquinonol D decreased the methylation status and reactivated the expression of multiple TSGs in MDA-MB-231 breast cancer cells. In conclusion, we showed that antroquinonol D induces DNA demethylation and the recovery of multiple tumor suppressor genes, while inhibiting breast cancer growth and migration potential.
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Affiliation(s)
- Sheng-Chao Wang
- Graduate Institute of Pharmacognosy, Taipei Medical University , 250 Wu-Hsing Street Taipei, TW 110, Taiwan, R. O. C
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Genetic Susceptibility to Head and Neck Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2014; 89:38-48. [DOI: 10.1016/j.ijrobp.2013.09.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 01/28/2023]
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