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Terrazzan A, Vanini R, Ancona P, Bianchi N, Taccioli C, Aguiari G. State-of-the-art in transposable element modulation affected by drugs in malignant prostatic cancer cells. J Cell Biochem 2024; 125:e30557. [PMID: 38501160 DOI: 10.1002/jcb.30557] [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: 08/30/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Over recent years, the investigation of transposable elements (TEs) has granted researchers a deeper comprehension of their characteristics and functions, particularly regarding their significance in the mechanisms contributing to cancer development. This manuscript focuses on prostate carcinoma cell lines and offers a comprehensive review intended to scrutinize the associations and interactions between TEs and genes, as well as their response to treatment using various chemical drugs, emphasizing their involvement in cancer progression. We assembled a compendium of articles retrieved from the PubMed database to construct networks demonstrating correlations with genes and pharmaceuticals. In doing so, we linked the transposition of certain TE types to the expression of specific transcripts directly implicated in carcinogenesis. Additionally, we underline that treatment employing different drugs revealed unique patterns of TE reactivation. Our hypothesis gathers the current understanding and guides research toward evidence-based investigations, emphasizing the association between antiviral drugs, chemotherapy, and the reduced expression of TEs in patients affected by prostate cancer.
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Affiliation(s)
- Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, Ferrara, Italy
| | - Riccardo Vanini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Gianluca Aguiari
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
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Cancel M, Crottes D, Bellanger D, Bruyère F, Mousset C, Pinault M, Mahéo K, Fromont G. Variable effects of periprostatic adipose tissue on prostate cancer cells: Role of adipose tissue lipid composition and cancer cells related factors. Prostate 2024; 84:358-367. [PMID: 38112233 DOI: 10.1002/pros.24655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Periprostatic adipose tissue (PPAT) is likely to modulate prostate cancer (PCa) progression. We analyzed the variations in the effect of PPAT on cancer cells, according to its fatty acid (FA) composition and tumor characteristics. METHODS The expression of markers of aggressiveness Ki67 and Zeb1, and epigenetic marks that could be modified during PCa progression, was analyzed by immunohistochemistry on a tissue-micro-array containing 59 pT3 PCa, including intra-prostatic areas and extra-prostatic foci in contact with PPAT belonging to the same tumor. In addition, we cocultivated PC3 and LNCaP cell lines with PPAT, which were then analyzed for FA composition. RESULTS Although the contact between PPAT and cancer cells led overall to an increase in Ki67 and Zeb1, and a decrease in the epigenetic marks 5MC, 5HMC, and H3K27ac, these effects were highly heterogeneous. Increased proliferation in extra-prostatic areas was associated with the international society of uropathology score. PC3 and LNCaP cocultures with PPAT led to increased Ki67, Zeb1 and H3K27me3, but only for PPAT associated with aggressive PCa. PC3 proliferation was correlated with high 20.2 n-6 and low 20.5n-3 in PPAT. CONCLUSIONS These results suggest that the effects of PPAT on cancer cells may depend on both PCa characteristics and PPAT composition, and could lead to propose nutritional supplementation.
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Affiliation(s)
- Mathilde Cancel
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
- Department of Medical Oncology, CHU Tours, Tours, France
| | - David Crottes
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
| | - Dorine Bellanger
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
| | | | - Coralie Mousset
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
- Department of Pathology, CHU Tours, Tours, France
| | - Michelle Pinault
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
| | - Karine Mahéo
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
| | - Gaëlle Fromont
- Faculté de Médecine, Inserm UMR1069 "Nutrition, Croissance et Cancer" Université François Rabelais, Tours, France
- Department of Pathology, CHU Tours, Tours, France
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3
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Douville C, Lahouel K, Kuo A, Grant H, Avigdor BE, Curtis SD, Summers M, Cohen JD, Wang Y, Mattox A, Dudley J, Dobbyn L, Popoli M, Ptak J, Nehme N, Silliman N, Blair C, Romans K, Thoburn C, Gizzi J, Schoen RE, Tie J, Gibbs P, Ho-Pham LT, Tran BNH, Tran TS, Nguyen TV, Goggins M, Wolfgang CL, Wang TL, Shih IM, Lennon AM, Hruban RH, Bettegowda C, Kinzler KW, Papadopoulos N, Vogelstein B, Tomasetti C. Machine learning to detect the SINEs of cancer. Sci Transl Med 2024; 16:eadi3883. [PMID: 38266106 DOI: 10.1126/scitranslmed.adi3883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
We previously described an approach called RealSeqS to evaluate aneuploidy in plasma cell-free DNA through the amplification of ~350,000 repeated elements with a single primer. We hypothesized that an unbiased evaluation of the large amount of sequencing data obtained with RealSeqS might reveal other differences between plasma samples from patients with and without cancer. This hypothesis was tested through the development of a machine learning approach called Alu Profile Learning Using Sequencing (A-PLUS) and its application to 7615 samples from 5178 individuals, 2073 with solid cancer and the remainder without cancer. Samples from patients with cancer and controls were prespecified into four cohorts used for model training, analyte integration, and threshold determination, validation, and reproducibility. A-PLUS alone provided a sensitivity of 40.5% across 11 different cancer types in the validation cohort, at a specificity of 98.5%. Combining A-PLUS with aneuploidy and eight common protein biomarkers detected 51% of the cancers at 98.9% specificity. We found that part of the power of A-PLUS could be ascribed to a single feature-the global reduction of AluS subfamily elements in the circulating DNA of patients with solid cancer. We confirmed this reduction through the analysis of another independent dataset obtained with a different approach (whole-genome sequencing). The evaluation of Alu elements may therefore have the potential to enhance the performance of several methods designed for the earlier detection of cancer.
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Affiliation(s)
- Christopher Douville
- Division of Quantitative Sciences, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kamel Lahouel
- Center for Cancer Prevention and Early Detection, City of Hope, Duarte, CA 91010, USA
- Center for Cancer Prevention and Early Detection, City of Hope, Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Albert Kuo
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Haley Grant
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Bracha Erlanger Avigdor
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Samuel D Curtis
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mahmoud Summers
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joshua D Cohen
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yuxuan Wang
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Austin Mattox
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan Dudley
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Lisa Dobbyn
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Popoli
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Janine Ptak
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Nadine Nehme
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Natalie Silliman
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Cherie Blair
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Katharine Romans
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher Thoburn
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Jennifer Gizzi
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Robert E Schoen
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
- Department of Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Jeanne Tie
- Division of Personalized Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Oncology, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3011, Australia
| | - Peter Gibbs
- Division of Personalized Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Oncology, Melbourne, VIC 3000, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lan T Ho-Pham
- BioMedical Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 72510, Vietnam
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
| | - Bich N H Tran
- Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
| | - Thach S Tran
- Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
- School of Biomedical Engineering, University of Technology Sydney, NSW 2007, Australia
| | - Tuan V Nguyen
- Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
- School of Biomedical Engineering, University of Technology Sydney, NSW 2007, Australia
- Tâm Anh Research Institute, Ho Chi Minh City, Vietnam
- Centre for Health Technologies, University of Technology, NSW 2007, Australia
- School of Population Health, University of New South Wales, NSW 2003, Australia
| | - Michael Goggins
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins Medical Institutes, 733 N. Broadway, Baltimore, MD 21205, USA
| | | | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Anne Marie Lennon
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins Medical Institutes, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Surgery, Johns Hopkins Medical Institutes, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Ralph H Hruban
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nickolas Papadopoulos
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Cristian Tomasetti
- Center for Cancer Prevention and Early Detection, City of Hope, Duarte, CA 91010, USA
- Center for Cancer Prevention and Early Detection, City of Hope, Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
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4
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Jiraboonsri S, Hemvipat P, Kamolratanakul S, Bhummaphan N, Siritientong T, Kitkumthorn N, Mutirangura A, Meevassana J. CpG methylation changes in Alu repetitive sequences in normal aging due to diastolic hypertension in human dermal fibroblasts from the facial area. Biomed Rep 2024; 20:5. [PMID: 38222864 PMCID: PMC10784876 DOI: 10.3892/br.2023.1693] [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: 06/28/2023] [Accepted: 11/02/2023] [Indexed: 01/16/2024] Open
Abstract
Aging fibroblasts, an important factor contributing to skin aging, are affected by numerous mechanisms, including alterations in DNA methylation and age-related diseases. The current study aimed to investigate the role of Alu methylation in aging fibroblasts and hypertension. The Alu methylation levels in dermal fibroblasts obtained from patients of different ages and blood pressure status were analyzed using the combined bisulfite restriction analysis technique. An inverse correlation was observed between Alu methylation in dermal fibroblasts and patient age. Dermal fibroblasts from the high-normal diastolic blood pressure group had higher Alu methylation levels compared with those from the normal group. The findings of the present study suggest that Alu methylation alterations can be observed with chronological aging and hypertension, and are a potential aging marker or therapeutic target.
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Affiliation(s)
- Suvinai Jiraboonsri
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panicha Hemvipat
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Narumol Bhummaphan
- College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tippawan Siritientong
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiraroch Meevassana
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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5
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Destefanis N, Fiano V, Milani L, Vasapolli P, Fiorentino M, Giunchi F, Lianas L, Del Rio M, Frexia F, Pireddu L, Molinaro L, Cassoni P, Papotti MG, Gontero P, Calleris G, Oderda M, Ricardi U, Iorio GC, Fariselli P, Isaevska E, Akre O, Zelic R, Pettersson A, Zugna D, Richiardi L. Cohort profile: the Turin prostate cancer prognostication (TPCP) cohort. Front Oncol 2023; 13:1242639. [PMID: 37869094 PMCID: PMC10587560 DOI: 10.3389/fonc.2023.1242639] [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: 06/23/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Prostate cancer (PCa) is the most frequent tumor among men in Europe and has both indolent and aggressive forms. There are several treatment options, the choice of which depends on multiple factors. To further improve current prognostication models, we established the Turin Prostate Cancer Prognostication (TPCP) cohort, an Italian retrospective biopsy cohort of patients with PCa and long-term follow-up. This work presents this new cohort with its main characteristics and the distributions of some of its core variables, along with its potential contributions to PCa research. Methods The TPCP cohort includes consecutive non-metastatic patients with first positive biopsy for PCa performed between 2008 and 2013 at the main hospital in Turin, Italy. The follow-up ended on December 31st 2021. The primary outcome is the occurrence of metastasis; death from PCa and overall mortality are the secondary outcomes. In addition to numerous clinical variables, the study's prognostic variables include histopathologic information assigned by a centralized uropathology review using a digital pathology software system specialized for the study of PCa, tumor DNA methylation in candidate genes, and features extracted from digitized slide images via Deep Neural Networks. Results The cohort includes 891 patients followed-up for a median time of 10 years. During this period, 97 patients had progression to metastatic disease and 301 died; of these, 56 died from PCa. In total, 65.3% of the cohort has a Gleason score less than or equal to 3 + 4, and 44.5% has a clinical stage cT1. Consistent with previous studies, age and clinical stage at diagnosis are important prognostic factors: the crude cumulative incidence of metastatic disease during the 14-years of follow-up increases from 9.1% among patients younger than 64 to 16.2% for patients in the age group of 75-84, and from 6.1% for cT1 stage to 27.9% in cT3 stage. Discussion This study stands to be an important resource for updating existing prognostic models for PCa on an Italian cohort. In addition, the integrated collection of multi-modal data will allow development and/or validation of new models including new histopathological, digital, and molecular markers, with the goal of better directing clinical decisions to manage patients with PCa.
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Affiliation(s)
- Nicolas Destefanis
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Lorenzo Milani
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo Vasapolli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Michelangelo Fiorentino
- DIMEC Department of Medicine and Surgery, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Francesca Giunchi
- Department of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Luca Lianas
- Visual and Data-intensive Computing, CRS4 (Center for Advanced Studies, Research and Development in Sardinia), Pula, Italy
| | - Mauro Del Rio
- Visual and Data-intensive Computing, CRS4 (Center for Advanced Studies, Research and Development in Sardinia), Pula, Italy
| | - Francesca Frexia
- Visual and Data-intensive Computing, CRS4 (Center for Advanced Studies, Research and Development in Sardinia), Pula, Italy
| | - Luca Pireddu
- Visual and Data-intensive Computing, CRS4 (Center for Advanced Studies, Research and Development in Sardinia), Pula, Italy
| | - Luca Molinaro
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Paolo Gontero
- Urology Unit, Department of Surgical Sciences, University of Turin, Molinette Hospital, Turin, Italy
| | - Giorgio Calleris
- Urology Unit, Department of Surgical Sciences, University of Turin, Molinette Hospital, Turin, Italy
| | - Marco Oderda
- Urology Unit, Department of Surgical Sciences, University of Turin, Molinette Hospital, Turin, Italy
| | | | | | - Piero Fariselli
- Computational Biomedicine Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Olof Akre
- Department of Molecular Medicine and Surgery, Section of Urology, Karolinska Institutet, Stockholm, Sweden
| | - Renata Zelic
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Pelvic Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Pettersson
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daniela Zugna
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
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6
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Zhao X, Hao Y, Wang Q, Shen Y, Cheng Y, Li B, Gao Y, Wang T, Qiu Y. Novel deoxyribonucleic acid methylation perturbations in workers exposed to vinyl chloride. Toxicol Ind Health 2022; 38:377-388. [PMID: 35548910 DOI: 10.1177/07482337221098600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To explore the epigenetic mechanism of deoxyribonucleic acid (DNA) damage induced by vinyl chloride (VC), we studied the micronuclei of peripheral blood lymphocytes in 193 subjects (92 in a VC exposure group employed in a chlorine-alkali plant; 101 in a control group employed in a power plant) and selected three pairs from the subjects (exposed and control) for whole-genome bisulfite sequencing (WGBS). The results showed that the rate of micronucleus formation in the VC exposure group was higher than that of control group (6.05 ± 3.28‰ vs. 2.01 ± 1.79‰). A total of 9534 differentially methylated regions (DMRs) were identified by WGBS, of which 4816 were hypomethylated and 4718 were hypermethylated. The Kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) analyses showed the top three KEGG pathways were cancer , neuroactive ligand-receptor interaction, and axon guidance, and the top three GO-BP pathways enriched were multicellular organismal process, developmental process, and anatomical structure development. In the most enriched DMR pathway (pathways in cancer), we found that BCL2, TJP2, TAOK1, PFKFB3, LIPI, and LIPH were hypermethylated, and the methylation levels of BNIP1 and GRPEL2 were decreased. The methylation of differentially methylated genes (DMGs) mentioned above were verified by methylation-specific PCR (MSP) and agarose gel electrophoresis (AGE) in 50 pairs of subjects, where the coincidence rate was 60-100%. In conclusion, the epigenetic perturbations of specific DMGs (BCL2, TJP2, TAOK1, PFKFB3, LIPI, LIPH, BNIP1, and GRPEL2) may be associated with DNA damage from vinyl chloride exposure.
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Affiliation(s)
- Xiaotian Zhao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yan Hao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Qian Wang
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yongmei Shen
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Ying Cheng
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Ben Li
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yi Gao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Tong Wang
- Department of Statistics, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yulan Qiu
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
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7
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Berglund A, Matta J, Encarnación-Medina J, Ortiz-Sanchéz C, Dutil J, Linares R, Marcial J, Abreu-Takemura C, Moreno N, Putney R, Chakrabarti R, Lin HY, Yamoah K, Osterman CD, Wang L, Dhillon J, Kim Y, Kim SJ, Ruiz-Deya G, Park JY. Dysregulation of DNA Methylation and Epigenetic Clocks in Prostate Cancer among Puerto Rican Men. Biomolecules 2021; 12:biom12010002. [PMID: 35053153 PMCID: PMC8773891 DOI: 10.3390/biom12010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
In 2021, approximately 248,530 new prostate cancer (PCa) cases are estimated in the United States. Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. The objective of this study was to assess DNA methylation patterns between aggressive and indolent PCa along with ancestry proportions in 49 H/L men from Puerto Rico (PR). Prostate tumors were classified as aggressive (n = 17) and indolent (n = 32) based on the Gleason score. Genomic DNA samples were extracted by macro-dissection. DNA methylation patterns were assessed using the Illumina EPIC DNA methylation platform. We used ADMIXTURE to estimate global ancestry proportions. We identified 892 differentially methylated genes in prostate tumor tissues as compared with normal tissues. Based on an epigenetic clock model, we observed that the total number of stem cell divisions (TNSC) and stem cell division rate (SCDR) were significantly higher in tumor than adjacent normal tissues. Regarding PCa aggressiveness, 141 differentially methylated genes were identified. Ancestry proportions of PR men were estimated as African, European, and Indigenous American; these were 24.1%, 64.2%, and 11.7%, respectively. The identification of DNA methylation profiles associated with risk and aggressiveness of PCa in PR H/L men will shed light on potential mechanisms contributing to PCa disparities in PR population.
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Affiliation(s)
- Anders Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.B.); (R.P.); (Y.K.)
| | - Jaime Matta
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Jarline Encarnación-Medina
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Carmen Ortiz-Sanchéz
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Julie Dutil
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Raymond Linares
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Joshua Marcial
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Caren Abreu-Takemura
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Natasha Moreno
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
- Correspondence: (N.M.); (J.Y.P.)
| | - Ryan Putney
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.B.); (R.P.); (Y.K.)
| | - Ratna Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA;
| | - Hui-Yi Lin
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Kosj Yamoah
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Carlos Diaz Osterman
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Liang Wang
- Department of Molecular Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Jasreman Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.B.); (R.P.); (Y.K.)
| | - Seung Joon Kim
- Department of Internal Medicine, Catholic University of Korea, Seoul 06591, Korea;
| | - Gilberto Ruiz-Deya
- Department of Basic Sciences, Ponce Research Institute, School of Medicine, Ponce Health Sciences University, Ponce 00716-2347, Puerto Rico; (J.M.); (J.E.-M.); (C.O.-S.); (J.D.); (R.L.); (J.M.); (C.A.-T.); (C.D.O.); (G.R.-D.)
| | - Jong Y. Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Correspondence: (N.M.); (J.Y.P.)
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8
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Sui Y, Peng S. A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons. Front Cell Dev Biol 2021; 9:618113. [PMID: 33644055 PMCID: PMC7905054 DOI: 10.3389/fcell.2021.618113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
In recent years, more and more evidence has emerged showing that changes in copy number variations (CNVs) correlated with the transcriptional level can be found during evolution, embryonic development, and oncogenesis. However, the underlying mechanisms remain largely unknown. The success of the induced pluripotent stem cell suggests that genome changes could bring about transformations in protein expression and cell status; conversely, genome alterations generated during embryonic development and senescence might also be the result of genome changes. With rapid developments in science and technology, evidence of changes in the genome affected by transcriptional level has gradually been revealed, and a rational and concrete explanation is needed. Given the preference of the HIV-1 genome to insert into transposons of genes with high transcriptional levels, we propose a mechanism based on retrotransposons facilitated by specific pre-mRNA splicing style and homologous recombination (HR) to explain changes in CNVs in the genome. This mechanism is similar to that of the group II intron that originated much earlier. Under this proposed mechanism, CNVs on genome are dynamically and spontaneously extended in a manner that is positively correlated with transcriptional level or contract as the cell divides during evolution, embryonic development, senescence, and oncogenesis, propelling alterations in them. Besides, this mechanism explains several critical puzzles in these processes. From evidence collected to date, it can be deduced that the message contained in genome is not just three-dimensional but will become four-dimensional, carrying more genetic information.
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Affiliation(s)
- Yunpeng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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9
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Chen S, Su J, Zhao Z, Shao Y, Dou Y, Li F, Deng W, Shi J, Li Q, Zuo X, Song S, Fan C. DNA Framework-Supported Electrochemical Analysis of DNA Methylation for Prostate Cancers. NANO LETTERS 2020; 20:7028-7035. [PMID: 32857520 DOI: 10.1021/acs.nanolett.0c01898] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Epigenetic alterations hold great promise as biomarkers for early stage cancer diagnosis. Nevertheless, direct identification of rare methylated DNA in the genome remains challenging. Here, we report an ultrasensitive framework nucleic acid-based electrochemical sensor for quantitative and highly selective analysis of DNA methylation. Notably, we can detect 160 fg of methylated DNA in million-fold unmethylated DNA samples using this electrochemical methylation-specific polymerase chain reaction (E-MSP) method. The high sensitivity of E-MSP enables one-step detection of low-abundance methylation at two different genes in patient serum samples. By using a combination test with two methylation alterations, we achieve high accuracy and sensitivity for reliable differentiation of prostate cancer and benign prostate hypertrophy (BPH). This new method sheds new light on translational use in early cancer diagnosis and in monitoring patients' responses to therapeutic agents.
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Affiliation(s)
- Shixing Chen
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Institute of Microsystem and information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Jing Su
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhihan Zhao
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yuan Shao
- Department of Urology, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, Shanghai 201801, China
| | - Yanzhi Dou
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fuwu Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Wangping Deng
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiping Song
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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10
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Zeggar HR, How-Kit A, Daunay A, Bettaieb I, Sahbatou M, Rahal K, Adouni O, Gammoudi A, Douik H, Deleuze JF, Kharrat M. Tumor DNA hypomethylation of LINE-1 is associated with low tumor grade of breast cancer in Tunisian patients. Oncol Lett 2020; 20:1999-2006. [PMID: 32724446 PMCID: PMC7377197 DOI: 10.3892/ol.2020.11745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
DNA hypomethylation of long interspersed repetitive DNA retrotransposon (LINE-1) and Alu repeats elements of short interspersed elements family (SINEs) is an early event in carcinogenesis that causes transcriptional activation and leads to chromosomal instability. In the current study, DNA methylation levels of LINE-1 and Alu repeats were analyzed in tumoral tissues of invasive breast cancer in a Tunisian cohort and its association with the clinicopathological features of patients was defined. DNA methylation of LINE-1 and Alu repeats were analyzed using pyrosequencing in 61 invasive breast cancers. Median values observed for DNA methylation of LINE-1 and Alu repeats were considered as the cut-off (59.81 and 18.49%, respectively). The results of the current study demonstrated a positive correlation between DNA methylation levels of LINE-1 and Alu repeats (rho=0.284; P<0.03). DNA hypomethylation of LINE-1 was also indicated to be associated with low grade (P=0.023). To the best of our knowledge, the current study is the first study regarding DNA methylation of LINE-1 and Alu repeats element in breast cancer of the Tunisian population. The results of the current study suggest that, since hypomethylation of LINE-1 is associated with low grade, it could be used as a biomarker for prognosis for patients with breast cancer.
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Affiliation(s)
- Hayet Radia Zeggar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Antoine Daunay
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Ilhem Bettaieb
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Mourad Sahbatou
- Laboratoire de Biostatistique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Khaled Rahal
- Service de Chirurgie Carcinologique, Institut Salah Azaiz de Tunis, 1006 Tunis, Tunisia
| | - Olfa Adouni
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Amor Gammoudi
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Hayet Douik
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
- Centre National de Recherche en Génomique Humaine, CEA, Le Commissariat à l'énergie atomique et aux énergies alternatives-Institut François Jacob, 92265 Evry, France
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
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11
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Park MK, Lee JC, Lee JW, Kang S, Kim J, Park MH, Hwang SJ, Lee M. Effects of fermented rice bran on DEN-induced oxidative stress in mice: GSTP1, LINE-1 methylation, and telomere length ratio. J Food Biochem 2020; 44:e13274. [PMID: 32468620 DOI: 10.1111/jfbc.13274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/01/2020] [Accepted: 04/18/2020] [Indexed: 12/12/2022]
Abstract
N-diethylnitrosamine (DEN), a well-known carcinogen, not only induces excessive reactive oxygen species but also suppresses DNA methylation. This study investigated the effect of fermented rice bran (FRB) treatment on DEN-induced oxidative stress through DNA methylation and telomere length analysis. To evaluate the potential protective role of FRB in oxidative stress, two different doses of FRB, DEN, and their combination were administered to mice that were preadapted or not to FRB. Glutathione-S-transferase P1 (GSTP1) methylation levels significantly decreased at 2 and 24 hr after FRB and DEN co-administration in mice with and without pre-adaptation. Moreover, GSTP1 mRNA was upregulated under DEN-induced oxidative stress. Furthermore, changes in long interspersed nuclear element-1 methylation were observed from the viewpoint of genomic instability. In addition, FRB preadapted mice displayed a lower telomere length ratio than the non-adapted mice, suggesting that FRB adaptation offers advantages over the non-adapted conditions in terms of inflammation suppression. PRACTICAL APPLICATIONS: DEN induces excessive ROS, which is associated with oxidative stress on DNA and other cellular components, resulting in inflammation. This study shows that FRB may alleviate DEN-triggered oxidative stress, based on changes in GSTP1, LINE-1 methylation, and telomere length ratios, thereby, revealing the potential of dietary intervention during inflammation. Furthermore, this study furthers the current understanding of DNA methylation mechanisms underlying the antioxidant and anti-inflammatory effects of functional food components. These results indicate that dietary inclusion of FRB may help decrease oxidative DNA damage and its associated inflammation at early stages of a disease.
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Affiliation(s)
- Min-Koo Park
- Nutrigenetics Institute, Bio-Innovation Park, Erom, Inc., Uiwang, Republic of Korea
| | - Jeong-Chan Lee
- Nutrigenetics Institute, Bio-Innovation Park, Erom, Inc., Uiwang, Republic of Korea
| | - Ji-Won Lee
- Nutrigenetics Institute, Bio-Innovation Park, Erom, Inc., Uiwang, Republic of Korea
| | - Sujin Kang
- Bio R&D Division, Bio-Innovation Park, Erom, Inc., Chuncheon, Republic of Korea
| | - JoongHark Kim
- Bio R&D Division, Bio-Innovation Park, Erom, Inc., Chuncheon, Republic of Korea
| | - Mi Houn Park
- Bio R&D Division, Bio-Innovation Park, Erom, Inc., Chuncheon, Republic of Korea
| | - Sung-Joo Hwang
- Integrated Medicine Institute, Loving Care Hospital, Sampyeong, Republic of Korea
| | - MinJae Lee
- College of Veterinary Medicine, Kangwon National University, Chuncheon, Republic of Korea
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12
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Ye D, Jiang D, Zhang X, Mao Y. Alu Methylation and Risk of Cancer: A Meta-analysis. Am J Med Sci 2020; 359:271-280. [PMID: 32268941 DOI: 10.1016/j.amjms.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The association between Alu methylation and risk of cancer remains uncertain. This meta-analysis was conducted to elucidate this issue. MATERIALS AND METHODS PubMed and Web of Science up to December 31, 2018, and the reference lists of studies, as well as those presented in relevant meta-analyses and reviews were systematically searched. Standardized mean difference (SMD) in Alu methylation level between cases and controls were pooled using random effects model and assessed heterogeneity between strata by stratified factors using meta-regression model. Sensitivity analysis and publication bias test were also conducted. RESULTS Twenty-five articles, including 2719 cases and 3018 controls were included in the meta-analysis. The significant difference in Alu methylation level between cancer cases and controls was greater in tissue (SMD = -1.89, 95% CI: -2.72, -1.05) than blood (SMD = -0.46, 95% CI: -0.82, -0.09), and heterogeneity was found in materials (P = 0.038). In tissue samples, Alu hypomethylation was found in carcinoma (SMD = -2.50, 95% CI: -3.51, -1.48), while not in non-carcinoma. The inverse associations were consistently found in subgroups stratified by data sources and quality score in tissue samples, and publication year was considered to be the potential source of between-study heterogeneity. Moreover, reduced Alu methylation level was found in the European subgroup, detection method of SIRPH and COBRA, and original data source in blood samples. CONCLUSIONS Alu hypomethylation was associated with increased risk of cancer, which could be a potential biomarker for cancer.
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Affiliation(s)
- Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China
| | - Danjie Jiang
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Xinhan Zhang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Yingying Mao
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China.
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13
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Jiang Y, Zong W, Ju S, Jing R, Cui M. Promising member of the short interspersed nuclear elements ( Alu elements): mechanisms and clinical applications in human cancers. J Med Genet 2019; 56:639-645. [PMID: 30852527 DOI: 10.1136/jmedgenet-2018-105761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022]
Abstract
Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
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Affiliation(s)
- Yun Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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14
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Molecular Mechanisms and Bioavailability of Polyphenols in Prostate Cancer. Int J Mol Sci 2019; 20:ijms20051062. [PMID: 30823649 PMCID: PMC6429226 DOI: 10.3390/ijms20051062] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer is the one of the most frequently diagnosed cancers among men over the age of 50. Several lines of evidence support the observation that polyphenols have preventive and therapeutic effects in prostate cancer. Moreover, prostate cancer is ideal for chemoprevention due to its long latency. We propose here an equilibrated lifestyle with a diet rich in polyphenols as prophylactic attempts to slow down the progression of localized prostate cancer or prevent the occurrence of the disease. In this review, we will first summarize the molecular mechanisms of polyphenols in prostate cancer with a focus on the antioxidant and pro-oxidant effects, androgen receptors (AR), key molecules involved in AR signaling and their transactivation pathways, cell cycle, apoptosis, angiogenesis, metastasis, genetic aspects, and epigenetic mechanisms. The relevance of the molecular mechanisms is discussed in light of current bioavailability data regarding the activity of polyphenols in prostate cancer. We also highlight strategies for improving the bioavailability of polyphenols. We hope that this review will lead to further research regarding the bioavailability and the role of polyphenols in prostate cancer prevention and treatment.
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Rubicz R, Zhao S, Geybels M, Wright JL, Kolb S, Klotzle B, Bibikova M, Troyer D, Lance R, Ostrander EA, Feng Z, Fan JB, Stanford JL. DNA methylation profiles in African American prostate cancer patients in relation to disease progression. Genomics 2019; 111:10-16. [PMID: 26902887 PMCID: PMC4992660 DOI: 10.1016/j.ygeno.2016.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 12/02/2015] [Accepted: 02/18/2016] [Indexed: 12/25/2022]
Abstract
This study examined whether differential DNA methylation is associated with clinical features of more aggressive disease at diagnosis and prostate cancer recurrence in African American men, who are more likely to die from prostate cancer than other populations. Tumor tissues from 76 African Americans diagnosed with prostate cancer who had radical prostatectomy as their primary treatment were profiled for epigenome-wide DNA methylation levels. Long-term follow-up identified 19 patients with prostate cancer recurrence. Twenty-three CpGs were differentially methylated (FDR q≤0.25, mean methylation difference≥0.10) in patients with vs. without recurrence, including CpGs in GCK, CDKL2, PRDM13, and ZFR2. Methylation differences were also observed between men with metastatic-lethal prostate cancer vs. no recurrence (five CpGs), regional vs. local pathological stage (two CpGs), and higher vs. lower tumor aggressiveness (one CpG). These results indicate that differentially methylated CpG sites identified in tumor tissues of African American men may contribute to prostate cancer aggressiveness.
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Affiliation(s)
- Rohina Rubicz
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Milan Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jonathan L. Wright
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA,Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Dean Troyer
- Departments of Pathology and Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA
| | - Raymond Lance
- Department of Urology, Eastern Virginia Medical School, Norfolk, VA
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD
| | - Ziding Feng
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA,Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
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Hernandez-Cortes D, Alvarado-Cruz I, Solís-Heredia MJ, Quintanilla-Vega B. Epigenetic modulation of Nrf2 and Ogg1 gene expression in testicular germ cells by methyl parathion exposure. Toxicol Appl Pharmacol 2018. [PMID: 29540303 DOI: 10.1016/j.taap.2018.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methyl parathion (Me-Pa) is an oxidizing organophosphate (OP) pesticide that generates reactive oxygen species (ROS) through its biotransformation. Some studies have also suggested that OP pesticides have the capacity to alkylate biomolecules, including DNA. In general, DNA methylation in gene promoters represses transcription. NRF2 is a key transcription factor that regulates the expression of antioxidant, metabolic and detoxifying genes through the antioxidant response element (ARE) situated in promoters of regulated genes. Furthermore, DNA repair genes, including 8-oxoguanine DNA glycosidase (OGG1), have been proposed as NRF2 target genes. Me-Pa exposure produces poor semen quality, genetic and oxidative damage in sperm cells, and reduced fertility. However, the Me-Pa effects on the methylation status and the expression of antioxidant (Nrf2) or DNA repair (Ogg1) genes in male germ cells have not been investigated. Therefore, mice were exposed to Me-Pa to evaluate the global (%5-mC) and specific methylation of Nrf2 and Ogg1 genes using pyrosequencing, gene expression, and total protein carbonylation in male germ cells. The results showed that Me-Pa significantly decreased the global DNA methylation pattern and significantly increased the methylation of two CpG sites within Ogg1 promoter and one CpG site within Nrf2 promoter. In addition, Ogg1 or Nrf2 expression did not change after Me-Pa exposure despite the oxidative damage produced. Altogether, our data suggest that Me-Pa toxicity alters Ogg1 and Nrf2 promoter methylation in male germ cells that may be modulating their gene expression.
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Affiliation(s)
| | - I Alvarado-Cruz
- Department of Toxicology, Cinvestav, Mexico City 07360, Mexico
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Cao Z, Wei L, Zhu W, Yao X. Meta-analysis of CDKN2A methylation to find its role in prostate cancer development and progression, and also to find the effect of CDKN2A expression on disease-free survival (PRISMA). Medicine (Baltimore) 2018; 97:e0182. [PMID: 29561434 PMCID: PMC5895353 DOI: 10.1097/md.0000000000010182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Reduction of cyclin-dependent kinase inhibitor 2A (CDKN2A) (p16 and p14) expression through DNA methylation has been reported in prostate cancer (PCa). This meta-analysis was conducted to assess the difference of p16 and p14 methylation between PCa and different histological types of nonmalignant controls and the correlation of p16 or p14 methylation with clinicopathological features of PCa. METHODS According to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement criteria, articles were searched in PubMed, Embase, EBSCO, Wanfang, and CNKI databases. The strength of correlation was calculated by the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). Trial sequential analysis (TSA) was used to estimate the required population information for significant results. RESULTS A total of 20 studies published from 1997 to 2017 were identified in this meta-analysis, including 1140 PCa patients and 530 cases without cancer. Only p16 methylation in PCa was significantly higher than in benign prostatic lesions (OR = 4.72, P = .011), but had a similar level in PCa and adjacent tissues or high-grade prostatic intraepithelial neoplasias (HGPIN). TSA revealed that this analysis on p16 methylation is a false positive result in cancer versus benign prostatic lesions (the estimated required information size of 5116 participants). p16 methylation was not correlated with PCa in the urine and blood. Besides, p16 methylation was not linked to clinical stage, prostate-specific antigen (PSA) level, and Gleason score (GS) of patients with PCa. p14 methylation was not correlated with PCa in tissue and urine samples. No correlation was observed between p14 methylation and clinical stage or GS. CDKN2A mutation and copy number alteration were not associated with prognosis of PCa in overall survival and disease-free survival. CDKN2A expression was not correlated with the prognosis of PCa in overall survival (492 cases) (P > .1), while CDKN2A expression was significantly associated with a poor disease-free survival (P < .01). CONCLUSION CDKN2A methylation may not be significantly associated with the development, progression of PCa. Although CDKN2A expression had an unfavorable prognosis in disease-free survival. More studies are needed to confirm our results.
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Affiliation(s)
| | - Lijuan Wei
- Department of Respiratory Medicine, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang, China
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MIEN1 is tightly regulated by SINE Alu methylation in its promoter. Oncotarget 2018; 7:65307-65319. [PMID: 27589566 PMCID: PMC5323157 DOI: 10.18632/oncotarget.11675] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/18/2016] [Indexed: 01/26/2023] Open
Abstract
Migration and invasion enhancer 1 (MIEN1) is a novel gene involved in prostate cancer progression by enhancing prostate cancer cell migration and invasion. DNA methylation, an important epigenetic regulation, is one of the most widely altered mechanisms in prostate cancer. This phenomenon frames the basis to study the DNA methylation patterns in the promoter region of MIEN1. Bisulfite pyrosequencing demonstrates the MIEN1 promoter contains a short interspersed nuclear Alu element (SINE Alu) repeat sequence. Validation of methylation inhibition on MIEN1 was performed using nucleoside analogs and non-nucleoside inhibitors and resulted in an increase in both MIEN1 RNA and protein in normal cells. MIEN1 mRNA and protein increases upon inhibition of individual DNA methyltransferases using RNA interference technologies. Furthermore, dual luciferase reporter assays, in silico analysis, and chromatin immunoprecipitation assays identified a sequence upstream of the transcription start site that has a site for binding of the USF transcription factors. These results suggest the MIEN1 promoter has a SINE Alu region that is hypermethylated in normal cells leading to repression of the gene. In cancer, the hypomethylation of a part of this repeat, in addition to the binding of USF, results in MIEN1 expression.
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Klein Hesselink EN, Zafon C, Villalmanzo N, Iglesias C, van Hemel BM, Klein Hesselink MS, Montero-Conde C, Buj R, Mauricio D, Peinado MA, Puig-Domingo M, Riesco-Eizaguirre G, Reverter JL, Robledo M, Links TP, Jordà M. Increased Global DNA Hypomethylation in Distant Metastatic and Dedifferentiated Thyroid Cancer. J Clin Endocrinol Metab 2018; 103:397-406. [PMID: 29165662 DOI: 10.1210/jc.2017-01613] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022]
Abstract
CONTEXT Global DNA hypomethylation is a major event for the development and progression of cancer, although the significance in thyroid cancer remains unclear. Therefore, we aimed to investigate its role in thyroid cancer progression and its potential as a prognostic marker. METHODS Global hypomethylation of Alu repeats was used as a surrogate marker for DNA global hypomethylation, and was assessed using the Quantification of Unmethylated Alu technique. Mutations in BRAF and RAS were determined by Sanger sequencing. RESULTS Ninety primary thyroid tumors were included [28 low-risk differentiated thyroid cancer (DTC), 13 pediatric DTC, 33 distant metastatic DTC, 7 poorly differentiated thyroid cancer (PDTC), and 9 anaplastic thyroid cancer (ATC)], as well as 24 distant metastases and 20 normal thyroid tissues. An increasing hypomethylation was found for distant metastatic DTC [median, 4.0; interquartile range (IQR), 3.1 to 6.2] and PDTC/ATC (median, 9.3; IQR, 7.0 to 12.1) as compared with normal thyroid tissue (median, 2.75; IQR, 2.30 to 3.15), whereas low-risk and pediatric DTC were not affected by hypomethylation. Alu hypomethylation was similar between distant metastases and matched primary tumors. Within distant metastatic DTC, Alu hypomethylation was increased in BRAF vs RAS mutated tumors. Kaplan-Meier and Cox regression analyses showed that thyroid cancer-related and all-cause mortality were associated with tumor hypomethylation, but this association was lost after adjustment for thyroid cancer risk category. CONCLUSION Distant metastatic DTC, PDTC, and ATC were increasingly affected by global Alu hypomethylation, suggesting that this epigenetic entity may be involved in thyroid cancer progression and dedifferentiation.
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Affiliation(s)
- Esther N Klein Hesselink
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Carles Zafon
- Diabetes and Metabolism Research Unit, Vall d'Hebron University Hospital, Barcelona, Spain
- Department of Endocrinology, Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
- Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
| | - Núria Villalmanzo
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
| | - Carmela Iglesias
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Pathology, Vall D'Hebron University Hospital, Barcelona, Spain
| | - Bettien M van Hemel
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mariëlle S Klein Hesselink
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Raquel Buj
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
| | - Dídac Mauricio
- Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital, Badalona, Spain
| | - Miguel A Peinado
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
| | - Manel Puig-Domingo
- Biomedical Research Networking Center in Diabetes and Associated Metabolic Diseases, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital, Badalona, Spain
- Biomedical Research Networking Center in Rare Diseases, CIBERER, Institute of Health Carlos III, Madrid, Spain
| | - Garcilaso Riesco-Eizaguirre
- Department of Endocrinology and Nutrition, Hospital Universitario de Móstoles, Madrid, Spain
- Biomedical Research Networking Center in Oncology, CIBERONC, Institute of Health Carlos III, Madrid, Spain
| | - Jordi L Reverter
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Department of Endocrinology and Nutrition, Germans Trias i Pujol Research Institute and University Hospital, Badalona, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center, Madrid, Spain
- Biomedical Research Networking Center in Rare Diseases, CIBERER, Institute of Health Carlos III, Madrid, Spain
| | - Thera P Links
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mireia Jordà
- Consortium for the Study of Thyroid Cancer, CECaT, Barcelona, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Barcelona, Spain
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Alu RNA accumulation induces epithelial-to-mesenchymal transition by modulating miR-566 and is associated with cancer progression. Oncogene 2017; 37:627-637. [PMID: 28991230 PMCID: PMC5799714 DOI: 10.1038/onc.2017.369] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/08/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2022]
Abstract
Alu sequences are the most abundant short interspersed repeated elements in the human genome. Here we show that in a cell culture model of colorectal cancer (CRC) progression, we observe accumulation of Alu RNA that is associated with reduced DICER1 levels. Alu RNA induces epithelial-to-mesenchymal transition (EMT) by acting as a molecular sponge of miR-566. Moreover, Alu RNA accumulates as consequence of DICER1 deficit in colorectal, ovarian, renal and breast cancer cell lines. Interestingly, Alu RNA knockdown prevents DICER1 depletion-induced EMT despite global microRNA (miRNA) downregulation. Alu RNA expression is also induced by transforming growth factor-β1, a major driver of EMT. Corroborating this data, we found that non-coding Alu RNA significantly correlates with tumor progression in human CRC patients. Together, these findings reveal an unexpected DICER1-dependent, miRNA-independent role of Alu RNA in cancer progression that could bring mobile element transcripts in the fields of cancer therapeutic and prognosis.
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Vryer R, Saffery R. What's in a name? Context-dependent significance of 'global' methylation measures in human health and disease. Clin Epigenetics 2017; 9:2. [PMID: 28149330 PMCID: PMC5270354 DOI: 10.1186/s13148-017-0311-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/04/2017] [Indexed: 12/20/2022] Open
Abstract
The study of DNA methylation in development and disease has 'exploded' as a field in recent years, with three major classes of measurement now routine. These encompass (i) locus-specific, (ii) genome-scale/wide and (iii) 'global' methylation approaches. Measures of global methylation refer to the level of 5-methylcytosine (5mC) content in a sample relative to total cytosine. Despite this, several other measures are often referred to as 'global', with the underlying assumption that they accurately reflect 5mC content. The two most common surrogate, or proxy, measures include generating a mean or median methylation value from (i) the average measure in thousands of highly repetitive genomic elements and (ii) many thousands to several million primarily unique CpG sites throughout the genome. Numerous lines of evidence suggest the underlying assumption of equivalence of these measures is flawed, with considerable variation in the regulation of different 'flavours' of DNA methylation throughout the genome depending on cell type, differentiation and disease state. As such, the regulation of methylation 'types' is often uncoupled. The emerging picture suggests that no approach can accurately detect all biologically important differences in 5mC variation and distribution in all instances, with this needing to be ascertained on a case-by-case basis. Thus, it is important to clearly elaborate the genomic context and content of DNA methylation being analysed, the sample and developmental stage in which it is being examined and to remember that in most instances, the most common measures are not a true representation of 'global' 5mC content as orginally defined.
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Affiliation(s)
- Regan Vryer
- Murdoch Childrens Research Institute, 50 Flemington Rd, Parkville, Victoria 3052 Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute, 50 Flemington Rd, Parkville, Victoria 3052 Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria Australia
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Fiano V, Zugna D, Grasso C, Trevisan M, Delsedime L, Molinaro L, Gillio-Tos A, Merletti F, Richiardi L. LINE-1 methylation status in prostate cancer and non-neoplastic tissue adjacent to tumor in association with mortality. Epigenetics 2016; 12:11-18. [PMID: 27892790 DOI: 10.1080/15592294.2016.1261786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aberrant DNA methylation seems to be associated with prostate cancer behavior. We investigated LINE-1 methylation in prostate cancer and non-neoplastic tissue adjacent to tumor (NTAT) in association with mortality from prostate cancer. We selected 157 prostate cancer patients with available NTAT from 2 cohorts of patients diagnosed between 1982-1988 and 1993-1996, followed up until 2010. An association between LINE-1 hypomethylation and prostate cancer mortality in tumor was suggested [hazard ratio per 5% decrease in LINE-1 methylation levels: 1.40, 95% confidence interval (CI): 0.95-2.01]. After stratification of the patients for Gleason score, the association was present only for those with a Gleason score of at least 8. Among these, low (<75%) vs. high (>80%) LINE-1 methylation was associated with a hazard ratio of 4.68 (95% CI: 1.03-21.34). LINE-1 methylation in the NTAT was not associated with prostate cancer mortality. Our results are consistent with the hypothesis that tumor tissue global hypomethylation may be a late event in prostate cancerogenesis and is associated with tumor progression.
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Affiliation(s)
- Valentina Fiano
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
| | - Daniela Zugna
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
| | - Chiara Grasso
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
| | - Morena Trevisan
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
| | - Luisa Delsedime
- b Division of Pathology, A.O. Città della Salute e della Scienza Hospital , Turin , Italy
| | - Luca Molinaro
- b Division of Pathology, A.O. Città della Salute e della Scienza Hospital , Turin , Italy
| | - Anna Gillio-Tos
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
| | - Franco Merletti
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
| | - Lorenzo Richiardi
- a Cancer Epidemiology Unit-CERMS , Department of Medical Sciences , University of Turin and CPO-Piemonte , Turin , Italy
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Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case-control study. Br J Cancer 2016; 115:664-73. [PMID: 27490804 PMCID: PMC5023776 DOI: 10.1038/bjc.2016.237] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/13/2016] [Accepted: 07/08/2016] [Indexed: 12/23/2022] Open
Abstract
Background: Global DNA methylation has been reported to be associated with urothelial cell carcinoma (UCC) by studies using blood samples collected at diagnosis. Using the Illumina HumanMethylation450 assay, we derived genome-wide measures of blood DNA methylation and assessed them for their prospective association with UCC risk. Methods: We used 439 case–control pairs from the Melbourne Collaborative Cohort Study matched on age, sex, country of birth, DNA sample type, and collection period. Conditional logistic regression was used to compute odds ratios (OR) of UCC risk per s.d. of each genome-wide measure of DNA methylation and 95% confidence intervals (CIs), adjusted for potential confounders. We also investigated associations by disease subtype, sex, smoking, and time since blood collection. Results: The risk of superficial UCC was decreased for individuals with higher levels of our genome-wide DNA methylation measure (OR=0.71, 95% CI: 0.54–0.94; P=0.02). This association was particularly strong for current smokers at sample collection (OR=0.47, 95% CI: 0.27–0.83). Intermediate levels of our genome-wide measure were associated with decreased risk of invasive UCC. Some variation was observed between UCC subtypes and the location and regulatory function of the CpGs included in the genome-wide measures of methylation. Conclusions: Higher levels of our genome-wide DNA methylation measure were associated with decreased risk of superficial UCC and intermediate levels were associated with reduced risk of invasive disease. These findings require replication by other prospective studies.
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Badiga S, Siddiqui NR, Macaluso M, Johanning GL, Piyathilake CJ. Homocysteinemia is Associated with a Lower Degree of PBMC LINE-1 Methylation and a Higher Risk of CIN 2C in the U.S. Post-Folic Acid Fortification Era. Nutr Cancer 2016; 68:446-55. [DOI: 10.1080/01635581.2016.1152388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ghorbani M, Themis M, Payne A. Genome wide classification and characterisation of CpG sites in cancer and normal cells. Comput Biol Med 2015; 68:57-66. [PMID: 26615449 DOI: 10.1016/j.compbiomed.2015.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/16/2015] [Accepted: 09/29/2015] [Indexed: 11/30/2022]
Abstract
This study identifies common methylation patterns across different cancer types in an effort to identify common molecular events in diverse types of cancer cells and provides evidence for the sequence surrounding a CpG to influence its susceptibility to aberrant methylation. CpG sites throughout the genome were divided into four classes: sites that either become hypo or hyper-methylated in a variety cancers using all the freely available microarray data (HypoCancer and HyperCancer classes) and those found in a constant hypo (Never methylated class) or hyper-methylated (Always methylated class) state in both normal and cancer cells. Our data shows that most CpG sites included in the HumanMethylation450K microarray remain unmethylated in normal and cancerous cells; however, certain sites in all the cancers investigated become specifically modified. More detailed analysis of the sites revealed that majority of those in the never methylated class were in CpG islands whereas those in the HyperCancer class were mostly associated with miRNA coding regions. The sites in the Hypermethylated class are associated with genes involved in initiating or maintaining the cancerous state, being enriched for processes involved in apoptosis, and with transcription factors predicted to bind to these genes linked to apoptosis and tumourgenesis (notably including E2F). Further we show that more LINE elements are associated with the HypoCancer class and more Alu repeats are associated with the HyperCancer class. Motifs that classify the classes were identified to distinguish them based on the surrounding DNA sequence alone, and for the identification of DNA sequences that could render sites more prone to aberrant methylation in cancer cells. This provides evidence that the sequence surrounding a CpG site has an influence on whether a site is hypo or hyper methylated.
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Affiliation(s)
- Mohammadmersad Ghorbani
- Department of Computer Science, Brunel University, Uxbridge, Middlesex UB8 3PH, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute
| | - Michael Themis
- Department of Biosciences, Brunel University, Uxbridge, Middlesex UB8 3PH, UK
| | - Annette Payne
- Department of Computer Science, Brunel University, Uxbridge, Middlesex UB8 3PH, UK.
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Global Hypomethylation (LINE-1) and Gene-Specific Hypermethylation (GSTP1) on Initial Negative Prostate Biopsy as Markers of Prostate Cancer on a Rebiopsy. Clin Cancer Res 2015; 22:984-92. [DOI: 10.1158/1078-0432.ccr-15-0606] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/07/2015] [Indexed: 11/16/2022]
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Hiwi Promotes the Proliferation of Colorectal Cancer Cells via Upregulating Global DNA Methylation. DISEASE MARKERS 2015; 2015:383056. [PMID: 26355242 PMCID: PMC4556077 DOI: 10.1155/2015/383056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 01/18/2023]
Abstract
Hiwi is well known for its role in stem cell renewal, maintaining the resting stage, and downregulating cell cycle of stem cells via RNA silencing. And Hiwi overexpression has been recognized in several types of cancers. In the present study, we examined the Hiwi expression in colorectal cancer (CRC) specimens in both mRNA and protein levels via real-time quantitative PCR, western blot assay, and immunohistochemical staining. Then we explored the role of Hiwi in the cancer cell proliferation and in the DNA methylation in human CRC Caro-2 and HT-29 cell lines. Results demonstrated that both mRNA and protein levels of Hiwi were significantly higher in 38 CRC tissues than in 38 peritumor tissues. Moreover, the Hiwi overexpression with an adenovirus vector significantly promoted the proliferation of Caro-2 and HT-29 cells, associated with significant increase in the global DNA methylation levels. And the chemical inhibition of DNA methylation significantly restrained such proliferation promotion. In summary, we confirmed that Hiwi was overexpressed in CRC tissues and that the forced Hiwi overexpression promoted the proliferation and global DNA methylation of CRC cell lines. Our results imply for the first time that Hiwi promotes the proliferation of CRC cells via promoting global DNA methylation.
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Abstract
Alu element is the most successful transposon and it maintains a high level of content in primate genome. However, despite the fact that the expression level of independent Alu element is rather low under common condition, an increasing number of the observations for the Alu transcripts in cells and tissues have been reported recently. Alu transcripts play key roles in the network of gene expression regulation. The main functions of Alu transcript focus on gene regulation both at transcriptional and post-transcriptional levels. This review summarizes major functions of Alu transcripts on gene expression and highlights molecular mechanisms dependent on conserved sequence or secondary structure in order to unravel a relative ubiquitous way that Alu transcript uses to affect the whole genome.
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Affiliation(s)
- Li Zhang
- Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.
| | - Ju-Gao Chen
- Department of Oncology, The Second Clinical Medical college (Shenzhen People׳s Hospital), Jinan University, Shenzhen, Guangdong, China
| | - Qi Zhao
- Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.
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Keelawat S, Thorner PS, Shuangshoti S, Bychkov A, Kitkumthorn N, Rattanatanyong P, Boonyayothin W, Poumsuk U, Ruangvejvorachai P, Mutirangura A. Detection of global hypermethylation in well-differentiated thyroid neoplasms by immunohistochemical (5-methylcytidine) analysis. J Endocrinol Invest 2015; 38:725-32. [PMID: 25740063 DOI: 10.1007/s40618-015-0246-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/20/2015] [Indexed: 12/13/2022]
Abstract
PURPOSE While global hypomethylation of DNA has been found in several malignancies, studies on thyroid tumours have shown controversial results using different techniques. To help resolve this issue, we assessed methylation status using two different techniques in papillary thyroid carcinomas (PTC) and follicular adenomas (FA) and carcinomas (FTC), comparing adjacent non-neoplastic thyroid tissue. METHODS A series of 15 FA, 18 FTC and 17 PTC were assessed by: (1) measurement of methylation levels of long interspersed nuclear elements (LINE-1) using a combined bisulfite restriction analysis polymerase chain reaction protocol and (2) immunostaining with an anti-5-methylcytidine antibody that detects methylated DNA regardless of the DNA sequence. Immunostaining was scored by image analysis. RESULTS Methylation levels of LINE-1 in FA, FTC and PTC were not significantly different from adjacent normal tissue. There was no significant difference in methylation levels of LINE-1 between FA, FTC and PTC (p = 0.44). By immunohistochemical staining for methylation, the 5-methylcytidine score was significantly higher in tumours than in normal tissue counterparts, for FA (p < 0.001), FTC (p = 0.04) and PTC (p = 0.02). PTC showed the highest 5-methylcytidine expression amongst all tumours which was significantly different from FTC (p = 0.015), but not FA (p = 0.09). There was no correlation in methylation level between LINE-1 and 5-methylcytidine scores for each group and overall. CONCLUSIONS Well-differentiated thyroid neoplasms (FA, FTC and PTC) were not found by two independent methods to undergo global hypomethylation as part of an oncogenic sequence from normal tissue to carcinoma. Instead, hypermethylation was detected in all types of tumours, implying that this epigenetic event may contribute to oncogenic development of thyroid neoplasms (both benign and malignant).
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Affiliation(s)
- S Keelawat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
| | - P S Thorner
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
- Division of Pathology, Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - S Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - A Bychkov
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - N Kitkumthorn
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - P Rattanatanyong
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - W Boonyayothin
- Department of Pathology, Chonburi Hospital, 69 Moo 2, Tambon Baan Seaun, Ampur Mueung, Chonburi, Thailand
| | - U Poumsuk
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - P Ruangvejvorachai
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - A Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Lidocaine sensitizes the cytotoxicity of cisplatin in breast cancer cells via up-regulation of RARβ2 and RASSF1A demethylation. Int J Mol Sci 2014; 15:23519-36. [PMID: 25526566 PMCID: PMC4284778 DOI: 10.3390/ijms151223519] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 12/24/2022] Open
Abstract
It has been reported that lidocaine is toxic to various types of cells. And a recent study has confirmed that lidocaine exerts a demethylation effect and regulates the proliferation of human breast cancer cell lines. To recognize a potential anti-tumor effect of lidocaine, we evaluated the DNA demethylation by lidocaine in human breast cancer lines, MCF-7 and MDA-MB-231 cells, and determined the influence of demethylation on the toxicity to these cells of cisplatin, which is a commonly utilized anti-tumor agent for breast cancer. Results demonstrated that lidocaine promoted a significant global genomic demethylation, and particularly in the promoters of tumor suppressive genes (TSGs), RARβ2 and RASSF1A. Further, the lidocaine treatment increased cisplatin-induced apoptosis and enhanced cisplatin-induced cytotoxicity. The combined treatment with both lidocaine and cisplatin promoted a significantly higher level of MCF-7 cell apoptosis than singular lidocaine or cisplatin treatment. Moreover, the abrogation of RARβ2 or RASSF1A expression inhibited such apoptosis. In conclusion, the present study confirms the demethylation effect of lidocaine in breast cancer cells, and found that the demethylation of RARβ2 and RASSF1A sensitized the cytotoxicity of cisplatin in breast cancer cells.
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Jiang R, Jones MJ, Sava F, Kobor MS, Carlsten C. Short-term diesel exhaust inhalation in a controlled human crossover study is associated with changes in DNA methylation of circulating mononuclear cells in asthmatics. Part Fibre Toxicol 2014; 11:71. [PMID: 25487561 PMCID: PMC4268899 DOI: 10.1186/s12989-014-0071-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/24/2014] [Indexed: 11/10/2022] Open
Abstract
Background Changes in DNA methylation have been associated with traffic-related air pollution in observational studies, but the specific mechanisms and temporal dynamics therein have not been explored in a controlled study of asthmatics. In this study, we investigate short-term effects of diesel exhaust inhalation on DNA methylation levels at CpG sites across the genome in circulating blood in asthmatics. Methods A double-blind crossover study of filtered air and diesel exhaust exposures was performed on sixteen non-smoking asthmatic subjects. Blood samples were collected pre-exposure, and then 6 and 30 hours post-exposure. Peripheral blood mononuclear cell DNA methylation was interrogated using the Illumina Infinium HumanMethylation450 Array. Exposure-related changes in DNA methylation were identified. In addition, CpG sites overlapping with Alu or LINE1 repetitive elements and candidate microRNA loci were also analyzed. Results DNA methylation at 2827 CpG sites were affected by exposure to diesel exhaust but not filtered air; these sites enriched for genes involved in protein kinase and NFkB pathways. CpG sites with significant changes in response to diesel exhaust exposure primarily became less methylated, with a site residing within GSTP1 being among the significant hits. Diesel exhaust-associated change was also found for CpG sites overlapping with Alu and LINE1 elements as well as for a site within miR-21. Conclusion Short-term exposure to diesel exhaust resulted in DNA methylation changes at CpG sites residing in genes involved in inflammation and oxidative stress response, repetitive elements, and microRNA. This provides plausibility for the role of DNA methylation in pathways by which airborne particulate matter impacts gene expression and offers support for including DNA methylation analysis in future efforts to understand the interactions between environmental exposures and biological systems. Electronic supplementary material The online version of this article (doi:10.1186/s12989-014-0071-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruiwei Jiang
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 west 28th Avenue, Vancouver, V5Z4H4, Canada.
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 west 28th Avenue, Vancouver, V5Z4H4, Canada.
| | - Francesco Sava
- Air Pollution Exposure Laboratory, Chan-Yeung Centre for Occupational and Environmental Lung Disease, Department of Medicine, Division of Respiratory Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, British Columbia, V5Z1L9, Canada.
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 west 28th Avenue, Vancouver, V5Z4H4, Canada. .,Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, 2206 East Mall, Vancouver, British Columbia, V6T1Z3, Canada.
| | - Christopher Carlsten
- Air Pollution Exposure Laboratory, Chan-Yeung Centre for Occupational and Environmental Lung Disease, Department of Medicine, Division of Respiratory Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, British Columbia, V5Z1L9, Canada.
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Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nat Genet 2014; 47:22-30. [PMID: 25485837 DOI: 10.1038/ng.3165] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/17/2014] [Indexed: 12/14/2022]
Abstract
Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.
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Affiliation(s)
- Lei Gu
- 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra C Frommel
- 1] Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland. [2] Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Christopher C Oakes
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Grupp
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cristina Y Gerig
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Dominik Bär
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- 1] Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. [2] Swiss Institute of Bioinformatics (SIB), University of Zurich, Zurich, Switzerland
| | - Constance Baer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Weiss
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthieu Schapira
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Ruprecht Kuner
- Unit of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center of Tumour Diseases, Heidelberg, Germany
| | - Holger Sültmann
- Unit of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center of Tumour Diseases, Heidelberg, Germany
| | - Maurizio Provenzano
- Oncology Research Unit, Division of Urology, University Hospital of Zurich, Zurich, Switzerland
| | | | | | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thorsten Schlomm
- Martini Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roland Eils
- 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raffaella Santoro
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
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Global DNA hypomethylation in prostate cancer development and progression: a systematic review. Prostate Cancer Prostatic Dis 2014; 18:1-12. [PMID: 25384337 DOI: 10.1038/pcan.2014.45] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/10/2014] [Accepted: 09/16/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND The role of global DNA methylation in prostate cancer (PCa) remains largely unknown. Our aim was to summarize evidence on the role of global DNA hypomethylation in PCa development and progression. METHODS We searched PubMed through December 2013 for all studies containing information on global methylation levels in PCa tissue and at least one non-tumor comparison tissue and/or studies reporting association between global methylation levels in PCa tissue and survival, disease recurrence or at least one clinicopathological prognostic factor. We summarized results using non-parametric comparisons and P-value summary methods. RESULTS We included 15 studies in the review: 6 studies with both diagnostic and prognostic information, 5 studies with only diagnostic information and 4 studies with only prognostic information. Quantitative meta-analysis was not possible because of the large heterogeneity in molecular techniques, types of tissues analyzed, aims and study designs. Summary statistical tests showed association of DNA hypomethylation with PCa diagnosis (P<0.006) and prognosis (P<0.001). Restriction to studies assessing 5-methylcytosine or long interspersed nucleotide element-1 revealed results in the same direction. Analyses restricted to specific clinicopathological features showed association with the presence of metastasis and tumor stage in all tests with P<0.03, and no association with Gleason score (all tests P>0.1 except for the weighted Z-test, P=0.05). CONCLUSION DNA hypomethylation was associated with PCa development and progression. However, due to the heterogeneity and small sample sizes of the included studies, along with the possibility of publication bias, this association requires additional assessment.
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Harada K, Baba Y, Ishimoto T, Chikamoto A, Kosumi K, Hayashi H, Nitta H, Hashimoto D, Beppu T, Baba H. LINE-1 methylation level and patient prognosis in a database of 208 hepatocellular carcinomas. Ann Surg Oncol 2014; 22:1280-7. [PMID: 25319577 DOI: 10.1245/s10434-014-4134-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND The level of long interspersed nucleotide element-1 (LINE-1) methylation has become regarded as a surrogate marker of global DNA methylation. Previously, we demonstrated that LINE-1 hypomethylation might contribute to the acquisition of aggressive tumor behavior through genomic gains of oncogenes such as cyclin-dependent kinase 6 (CDK6) in esophageal squamous cell carcinoma. However, the relationship between LINE-1 hypomethylation and clinical outcome in hepatocellular carcinoma (HCC) remains unclear. METHODS LINE-1 methylation level in 208 samples of curatively resected HCCs was measured by pyrosequencing assay, and the prognostic value of LINE-1 methylation level in HCC was examined. RESULTS LINE-1 methylation levels in the 208 HCC patients investigated were distributed as follows: mean 64.7; median 64.6; standard deviation (SD) 13.6; range 21.5-99.1; interquartile range 62.9-66.6. Univariate Cox regression analysis revealed a significantly higher cancer recurrence rate in the low-methylation-level group than in the high-methylation-level group (hazard ratio 1.58; 95 % CI 1.05-2.47; p = 0.028). Interestingly, the influence of LINE-1 hypomethylation on patient outcome was modified by hepatitis virus infection (p of interaction = 0.023); LINE-1 hypomethylation was associated with a higher cancer recurrence rate in patients without hepatitis virus infection (log-rank p = 0.0047). CDK6 messenger RNA expression levels were inversely associated with LINE-1 methylation levels (p = 0.0075; R = -0.37). CONCLUSIONS Genome-wide DNA hypomethylation, as measured by LINE-1 levels, might be associated with poor disease-free survival in HCC patients, suggesting a potential role for LINE-1 methylation level as a biomarker for identifying patients who will experience an unfavorable clinical outcome.
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Affiliation(s)
- Kazuto Harada
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
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Dynamic Alu methylation during normal development, aging, and tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:784706. [PMID: 25243180 PMCID: PMC4163490 DOI: 10.1155/2014/784706] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/16/2014] [Indexed: 12/15/2022]
Abstract
DNA methylation primarily occurs on CpG dinucleotides and plays an important role in transcriptional regulations during tissue development and cell differentiation. Over 25% of CpG dinucleotides in the human genome reside within Alu elements, the most abundant human repeats. The methylation of Alu elements is an important mechanism to suppress Alu transcription and subsequent retrotransposition. Decades of studies revealed that Alu methylation is highly dynamic during early development and aging. Recently, many environmental factors were shown to have a great impact on Alu methylation. In addition, aberrant Alu methylation has been documented to be an early event in many tumors and Alu methylation levels have been associated with tumor aggressiveness. The assessment of the Alu methylation has become an important approach for early diagnosis and/or prognosis of cancer. This review focuses on the dynamic Alu methylation during development, aging, and tumor genesis. The cause and consequence of Alu methylation changes will be discussed.
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Luo W, Hu Q, Wang D, Deeb KK, Ma Y, Morrison CD, Liu S, Johnson CS, Trump DL. Isolation and genome-wide expression and methylation characterization of CD31+ cells from normal and malignant human prostate tissue. Oncotarget 2014; 4:1472-83. [PMID: 23978847 PMCID: PMC3824530 DOI: 10.18632/oncotarget.1269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endothelial cells (ECs) are an important component involved in the angiogenesis. Little is known about the global gene expression and epigenetic regulation in tumor endothelial cells. The identification of gene expression and epigenetic difference between human prostate tumor-derived endothelial cells (TdECs) and those in normal tissues may uncover unique biological features of TdEC and facilitate the discovery of new anti-angiogenic targets. We established a method for isolation of CD31+ endothelial cells from malignant and normal prostate tissues obtained at prostatectomy. TdECs and normal-derived ECs (NdECs) showed >90% enrichment in primary culture and demonstrated microvascular endothelial cell characteristics such as cobblestone morphology in monolayer culture, diI-acetyl-LDL uptake and capillary-tube like formation in Matrigel®. In vitro primary cultures of ECs maintained expression of endothelial markers such as CD31, von Willebrand factor, intercellular adhesion molecule, vascular endothelial growth factor receptor 1, and vascular endothelial growth factor receptor 2. We then conducted a pilot study of transcriptome and methylome analysis of TdECs and matched NdECs from patients with prostate cancer. We observed a wide spectrum of differences in gene expression and methylation patterns in endothelial cells, between malignant and normal prostate tissues. Array-based expression and methylation data were validated by qRT-PCR and bisulfite DNA pyrosequencing. Further analysis of transcriptome and methylome data revealed a number of differentially expressed genes with loci whose methylation change is accompanied by an inverse change in gene expression. Our study demonstrates the feasibility of isolation of ECs from histologically normal prostate and prostate cancer via CD31+ selection. The data, although preliminary, indicates that there exist widespread differences in methylation and transcription between TdECs and NdECs. Interestingly, only a small proportion of perturbed genes were overlapped between American (AA) and Caucasian American (CA) patients with prostate cancer. Our study indicates that identifying gene expression and/or epigenetic differences between TdECs and NdECs may provide us with new anti-angiogenic targets. Future studies will be required to further characterize the isolated ECs and determine the biological features that can be exploited in the prognosis and therapy of prostate cancer.
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Affiliation(s)
- Wei Luo
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York
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Stott-Miller M, Zhao S, Wright JL, Kolb S, Bibikova M, Klotzle B, Ostrander EA, Fan JB, Feng Z, Stanford JL. Validation study of genes with hypermethylated promoter regions associated with prostate cancer recurrence. Cancer Epidemiol Biomarkers Prev 2014; 23:1331-9. [PMID: 24718283 PMCID: PMC4082437 DOI: 10.1158/1055-9965.epi-13-1000] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND One challenge in prostate cancer is distinguishing indolent from aggressive disease at diagnosis. DNA promoter hypermethylation is a frequent epigenetic event in prostate cancer, but few studies of DNA methylation in relation to features of more aggressive tumors or prostate cancer recurrence have been completed. METHODS We used the Infinium HumanMethylation450 BeadChip to assess DNA methylation in tumor tissue from 407 patients with clinically localized prostate cancer who underwent radical prostatectomy. Recurrence status was determined by follow-up patient surveys, medical record review, and linkage with the Surveillance, Epidemiology, and End Results (SEER) registry. The methylation status of 14 genes for which promoter hypermethylation was previously correlated with advanced disease or biochemical recurrence was evaluated. Average methylation level for promoter region CpGs in patients who recurred compared with those with no evidence of recurrence was analyzed. For two genes with differential methylation, time to recurrence was examined. RESULTS During an average follow-up of 11.7 years, 104 (26%) patients recurred. Significant promoter hypermethylation in at least 50% of CpG sites in two genes, ABHD9 and HOXD3, was found in tumors from patients who recurred compared with those without recurrence. Evidence was strongest for HOXD3 (lowest P = 9.46 × 10(-6)), with higher average methylation across promoter region CpGs associated with reduced recurrence-free survival (P = 2 × 10(-4)). DNA methylation profiles did not differ by recurrence status for the other genes. CONCLUSIONS These results validate the association between promoter hypermethylation of ADHB9 and HOXD3 and prostate cancer recurrence. IMPACT Tumor DNA methylation profiling may help to distinguish patients with prostate cancer at higher risk for disease recurrence.
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Affiliation(s)
- Marni Stott-Miller
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Shanshan Zhao
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Jonathan L Wright
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Department of Urology, University of Washington School of Medicine; Departments of
| | - Suzanne Kolb
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | | | | | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | - Ziding Feng
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Biostatistics and
| | - Janet L Stanford
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Epidemiology, University of Washington, Seattle, Washington;
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Bujko M, Musialik E, Olbromski R, Przestrzelska M, Libura M, Pastwińska A, Juszczyński P, Zwierzchowski L, Baranowski P, Siedlecki JA. Repetitive genomic elements and overall DNA methylation changes in acute myeloid and childhood B-cell lymphoblastic leukemia patients. Int J Hematol 2014; 100:79-87. [PMID: 24841671 DOI: 10.1007/s12185-014-1592-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 12/30/2022]
Abstract
Aberrant epigenetic regulation is a hallmark of neoplastic cells. Increased DNA methylation of individual genes' promoter regions and decreases in overall DNA methylation level are both generally observed in cancer. In solid tumors, this global DNA hypomethylation is related to reduced methylation of repeated DNA elements (REs) and contributes to genome instability. The aim of the present study was to assess methylation level of LINE-1 and ALU REs and total 5-methylcytosine (5metC) content in adult acute myeloid leukemia (AML) (n = 58), childhood B-cell acute lymphoblastic leukemia (ALL) (n = 32), as the most frequent acute leukemias in two age categories and in normal adult bone marrow and children's blood samples. DNA pyrosequencing and ELISA assays were used, respectively. Global DNA hypomethylation was not observed in leukemia patients. Results revealed higher DNA methylation of LINE-1 in AML and ALL samples compared to corresponding normal controls. Elevated methylation of ALU and overall 5metC level were also observed in B-cell ALL patients. Differences of REs and global DNA methylation between AML cytogenetic-risk groups were observed, with the lowest methylation levels in intermediate-risk/cytogenetically normal patients. B-cell ALL is characterized by the highest DNA methylation level compared to AML and controls and overall DNA methylation is correlated with leukocyte count.
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Affiliation(s)
- Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, W.K. Roentgena 5, 02-781, Warsaw, Poland,
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Prostate cancer epigenetic biomarkers: next-generation technologies. Oncogene 2014; 34:1609-18. [PMID: 24837368 DOI: 10.1038/onc.2014.111] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 03/14/2014] [Accepted: 03/20/2014] [Indexed: 12/15/2022]
Abstract
Cancer is caused by a combination of genetic alterations and gross changes to the epigenetic landscape that together result in aberrant cancer gene regulation. Therefore, we need to fully sequence both the cancer genome and the matching cancer epigenomes before we can fully integrate the suite of molecular mechanisms involved in initiation and progression of cancer. A further understanding of epigenetic aberrations has a great potential in the next era of molecular genomic pathology in cancer detection and treatment in all types of cancer, including prostate cancer. In this review, we discuss the most common epigenetic aberrations identified in prostate cancer with the biomarker potential. We also describe the innovative and current epigenomic technologies used for the identification of epigenetic-associated changes in prostate cancer and future translational applications in molecular pathology for cancer detection and prognosis.
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Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Goggins M, Shih IM, Duffield AS, Montgomery EA, Gabrielson E, Netto GJ, Lotan TL, De Marzo AM, Westra W, Binder ZA, Orr BA, Gallia GL, Eberhart CG, Boeke JD, Harris CR, Burns KH. Long interspersed element-1 protein expression is a hallmark of many human cancers. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1280-6. [PMID: 24607009 PMCID: PMC4005969 DOI: 10.1016/j.ajpath.2014.01.007] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 01/16/2014] [Accepted: 01/27/2014] [Indexed: 01/08/2023]
Abstract
Cancers comprise a heterogeneous group of human diseases. Unifying characteristics include unchecked abilities of tumor cells to proliferate and spread anatomically, and the presence of clonal advantageous genetic changes. However, universal and highly specific tumor markers are unknown. Herein, we report widespread long interspersed element-1 (LINE-1) repeat expression in human cancers. We show that nearly half of all human cancers are immunoreactive for a LINE-1-encoded protein. LINE-1 protein expression is a common feature of many types of high-grade malignant cancers, is rarely detected in early stages of tumorigenesis, and is absent from normal somatic tissues. Studies have shown that LINE-1 contributes to genetic changes in cancers, with somatic LINE-1 insertions seen in selected types of human cancers, particularly colon cancer. We sought to correlate this observation with expression of the LINE-1-encoded protein, open reading frame 1 protein, and found that LINE-1 open reading frame 1 protein is a surprisingly broad, yet highly tumor-specific, antigen.
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Affiliation(s)
- Nemanja Rodić
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Reema Sharma
- Department of Biochemistry and Molecular Biology, University of Maryland Baltimore County, Baltimore, Maryland
| | - Rajni Sharma
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John Zampella
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lixin Dai
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Martin S Taylor
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anirban Maitra
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael S Torbenson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael Goggins
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amy S Duffield
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth A Montgomery
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - George J Netto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angelo M De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William Westra
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zev A Binder
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Gary L Gallia
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jef D Boeke
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chris R Harris
- Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers University Cancer Institute of New Jersey, Raymond and Beverly Sackler Foundation, New Brunswick, New Jersey; Cancer Institute of New Jersey, Rutgers University of Medicine and Dentistry, New Brunswick, New Jersey
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Abstract
Epigenetic change is part of the carcinogenic process and a deep reservoir for biomarker discovery. Reversible methylation of cytosines is noteworthy because it can be measured accurately and easily by various molecular methods and DNA methylation patterns are linked to important tumourigenic pathways. Clinically relevant methylation changes are known in common human cancers such as cervix, prostate, breast, colon, bladder, stomach and lung. Differential methylation may have a central role in the development and outcome of most if not all human malignancies. The advent of deep sequencing holds great promise for epigenomics, with bioinformatics tools ready to reveal large numbers of new targets for prognosis and therapeutic intervention. This review focuses on two selected cancers, namely cervix and prostate, which illustrate the more general themes of epigenetic diagnostics in cancer. Also discussed is differential methylation of specific human and viral DNA targets and laboratory methods for measuring methylation biomarkers.
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Affiliation(s)
- Attila T Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, EC1M 6BQ, UK
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Eskola PJ, Männikkö M, Samartzis D, Karppinen J. Genome-wide association studies of lumbar disc degeneration--are we there yet? Spine J 2014; 14:479-82. [PMID: 24210639 DOI: 10.1016/j.spinee.2013.07.437] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/14/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Pasi J Eskola
- Department of Physical and Rehabilitation Medicine, Institute of Clinical Medicine, University of Oulu, and Medical Research Center Oulu, Box 5000, 90014 Oulu, Finland
| | - Minna Männikkö
- Institute of Health Sciences, Biocenter Oulu, University of Oulu, Box 5000, 90014 Oulu, Finland
| | - Dino Samartzis
- Department of Orthopaedics and Traumatology, University of Hong Kong, Professorial Block, 5th Floor, 102 Pokfulam Rd, Pokfulam, Hong Kong, SAR, China
| | - Jaro Karppinen
- Department of Physical and Rehabilitation Medicine, Institute of Clinical Medicine, University of Oulu, and Medical Research Center Oulu, Box 5000, 90014 Oulu, Finland.
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Moison C, Assemat F, Daunay A, Tost J, Guieysse-Peugeot AL, Arimondo PB. Synergistic chromatin repression of the tumor suppressor gene RARB in human prostate cancers. Epigenetics 2014; 9:477-82. [PMID: 24492483 PMCID: PMC4121358 DOI: 10.4161/epi.27869] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation and polycomb proteins are well-known mediators of epigenetic silencing in mammalian cells. Usually described as mutually exclusive, this statement is today controversial and recent in vitro studies suggest the co-existence of both repressor systems. We addressed this issue in the study of Retinoic Acid Receptor β (RARβ), a tumor suppressor gene frequently silenced in prostate cancer. We found that the RARβ promoter is hypermethylated in all studied prostate tumors and methylation levels are positively correlated with H3K27me3 enrichments. Thus, by using bisulfite conversion and pyrosequencing of immunoprecipitated H3K27me3 chromatin, we demonstrated that DNA methylation and polycomb repression co-exist in vivo at this locus. We found this repressive association in 6/6 patient tumor samples of different Gleason score, suggesting a strong interplay of DNA methylation and EZH2 to silence RARβ during prostate tumorigenesis.
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Affiliation(s)
- Céline Moison
- CNRS-Pierre Fabre USR3388; Epigenetic Targeting of Cancer (ETaC); Toulouse, France; MNHN CNRS UMR7196; Paris, France; INSERM U565; Paris, France; Université Pierre et Marie Curie; Paris, France
| | - Fanny Assemat
- CNRS-Pierre Fabre USR3388; Epigenetic Targeting of Cancer (ETaC); Toulouse, France
| | - Antoine Daunay
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH; Paris, France
| | - Jörg Tost
- Laboratory for Functional Genomics; Fondation Jean Dausset - CEPH; Paris, France; Laboratory for Epigenetics and Environment; Centre National de Génotypage; CEA-Institut de Génomique; Evry, France
| | | | - Paola B Arimondo
- CNRS-Pierre Fabre USR3388; Epigenetic Targeting of Cancer (ETaC); Toulouse, France
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Verdugo AD, Crona J, Starker L, Stålberg P, Åkerström G, Westin G, Hellman P, Björklund P. Global DNA methylation patterns through an array-based approach in small intestinal neuroendocrine tumors. Endocr Relat Cancer 2014; 21:L5-7. [PMID: 24192231 DOI: 10.1530/erc-13-0481] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alberto Delgado Verdugo
- Department of Surgical Sciences Uppsala University Hospital, Uppsala University, Entre 7075185, Uppsala Sweden Department of Surgery Yale University, New Haven, Connecticut USA
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Baba Y, Watanabe M, Murata A, Shigaki H, Miyake K, Ishimoto T, Iwatsuki M, Iwagami S, Yoshida N, Oki E, Sakamaki K, Nakao M, Baba H. LINE-1 hypomethylation, DNA copy number alterations, and CDK6 amplification in esophageal squamous cell carcinoma. Clin Cancer Res 2014; 20:1114-24. [PMID: 24423610 DOI: 10.1158/1078-0432.ccr-13-1645] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE Global DNA hypomethylation plays a crucial role in genomic instability and carcinogenesis. DNA methylation of the long interspersed nucleotide element-1, L1 (LINE-1) repetitive element is a good indicator of the global DNA methylation level, and is attracting interest as a useful marker for predicting cancer prognosis. Our previous study using more than 200 esophageal squamous cell carcinoma (ESCC) specimens demonstrated the significant relationship between LINE-1 hypomethylation and poor prognosis. However, the mechanism by which LINE-1 hypomethylation affects aggressive tumor behavior has yet to be revealed. EXPERIMENTAL DESIGN To examine the relationship between LINE-1 hypomethylation and DNA copy number variations, we investigated LINE-1-hypomethylated and LINE-1-hypermethylated ESCC tumors by comparative genomic hybridization array. RESULTS LINE-1-hypomethylated tumors showed highly frequent genomic gains at various loci containing candidate oncogenes such as CDK6. LINE-1 methylation levels were significantly associated with CDK6 mRNA and CDK6 protein expression levels in ESCC specimens. In our cohort of 129 patients with ESCC, cases with CDK6-positive expression experienced worse clinical outcome compared with those with CDK6-negative expression, supporting the oncogenic role of CDK6 in ESCC. In addition, we found that the prognostic impact of LINE-1 hypomethylation might be attenuated by CDK6 expression. CONCLUSION LINE-1 hypomethylation (i.e., global DNA hypomethylation) in ESCC might contribute to the acquisition of aggressive tumor behavior through genomic gains of oncogenes such as CDK6.
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Affiliation(s)
- Yoshifumi Baba
- Authors' Affiliations: Department of Gastroenterological Surgery, Graduate School of Medical Sciences; Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto; Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka; and Department of Biostatistics and Epidemiology, Yokohama City University Medical Center, Yokohama, Japan
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Abstract
Cancer is a disease that results from the successive accumulation of genetic and epigenetic alterations. Despite intense study, many unanswered questions about the nature of the contribution of epigenetic changes to carcinogenesis remain. In this review, we describe principles of epigenetics as they relate to our current understanding of carcinogenesis. There are a number of in vivo models of specific pathways of carcinogenesis that are very useful for the characterization of epigenetic mechanisms that link environmental exposures or genetic susceptibility and cancer progression. Because epigenetic alterations are thought to be reversible, they offer great promise for treatment of cancer. The use of animal models to evaluate the effects of decitabine and zebularine has elucidated the mechanisms of action and indicated the potential for these types of treatment. Ultimately, the greatest challenge lies in the integration of laboratory and epidemiologic data to best prevent and treat this deadly disease.
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Affiliation(s)
| | - Shami Virani
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor 48109, USA
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47
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Fu LJ, Ding YB, Wu LX, Wen CJ, Qu Q, Zhang X, Zhou HH. The Effects of Lycopene on the Methylation of the GSTP1 Promoter and Global Methylation in Prostatic Cancer Cell Lines PC3 and LNCaP. Int J Endocrinol 2014; 2014:620165. [PMID: 25389438 PMCID: PMC4217342 DOI: 10.1155/2014/620165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 11/18/2022] Open
Abstract
DNA (cytosine-5-) methylation silencing of GSTP1 function occurs in prostate adenocarcinoma (PCa). Previous studies have shown that there is an inverse relationship between dietary lycopene intake and the risk of PCa. However, it is unknown whether lycopene reactivates the tumor suppressor gene glutathioneS-transferase-π (GSTP1) by demethylation of the hypermethylated CpGs that act to silence the GSTP1 promoter. Here, we demonstrated that lycopene treatment significantly decreased the methylation levels of the GSTP1 promoter and increased the mRNA and protein levels of GSTP1 in an androgen-independent PC-3 cell line. In contrast, lycopene treatment did not demethylate the GSTP1 promoter or increase GSTP1 expression in the androgen-dependent LNCaP cell line. DNA methyltransferase (DNMT) 3A protein levels were downregulated in PC-3 cells following lycopene treatment; however, DNMT1 and DNMT3B levels were unchanged. Furthermore, the long interspersed element (LINE-1) and short interspersed element ALU were not demethylated when treated by lycopene. In LNCaP cells, lycopene treatment did not affect any detected DNMT protein expression, and the methylation levels of LINE-1 and ALU were decreased. These results indicated that the protective effect of lycopene on the prostate is different between androgen-dependent and androgen-independent derived PCa cells. Further, in vivo studies should be conducted to confirm these promising results and to evaluate the potential role of lycopene in the protection of the prostate.
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Affiliation(s)
- Li-Juan Fu
- Institute of Life Sciences, Chongqing Medical University, No. 1 Yixueyuan Road, Chongqing 400016, China
- Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yu-Bin Ding
- Institute of Life Sciences, Chongqing Medical University, No. 1 Yixueyuan Road, Chongqing 400016, China
| | - Lan-Xiang Wu
- Institute of Life Sciences, Chongqing Medical University, No. 1 Yixueyuan Road, Chongqing 400016, China
| | - Chun-Jie Wen
- Institute of Life Sciences, Chongqing Medical University, No. 1 Yixueyuan Road, Chongqing 400016, China
| | - Qiang Qu
- Pharmacogenetics Research Institute, Central South University, Changsha, Hunan 410078, China
| | - Xue Zhang
- Institute of Life Sciences, Chongqing Medical University, No. 1 Yixueyuan Road, Chongqing 400016, China
| | - Hong-Hao Zhou
- Institute of Life Sciences, Chongqing Medical University, No. 1 Yixueyuan Road, Chongqing 400016, China
- *Hong-Hao Zhou:
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Gao XD, Qu JH, Chang XJ, Lu YY, Bai WL, Wang H, Xu ZX, An LJ, Wang CP, Zeng Z, Yang YP. Hypomethylation of long interspersed nuclear element-1 promoter is associated with poor outcomes for curative resected hepatocellular carcinoma. Liver Int 2014; 34:136-46. [PMID: 23875825 PMCID: PMC4238827 DOI: 10.1111/liv.12264] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 06/12/2013] [Accepted: 06/20/2013] [Indexed: 12/19/2022]
Abstract
BACKGROUND Epigenetic alterations are well documented in hepatocarcinogenesis. However, hypomethylation of long interspersed nuclear element 1(LINE-1) promoter and its relationship with clinicopathological features in hepatocellular carcinoma(HCC) remain unknown. METHODS The bisulfite-specific PCR and DNA sequencing analysis was performed to assess the methylation status of LINE-1 promoter in a pilot cohort of 71 patients with HCC. Additionally,methylation levels of two hot CpG sites of LINE-1 promoter, site 7 and 18 were measured by real-time PCR and compared with clinicopathological parameters in a cohort of 172 HCC. All the patients included were in BCLC stage A or B. RESULTS Most patients with HCC (87.3%) showed hypomethylation of LINE-1 promoter compared with HBV-related cirrhosis and normal controls (P < 0.001). The HCC patients with LINE-1 promoter hypomethylation had a median tumour-free survival (TFS) and overall survival (OS)post-resection of 22.0 (95% CI: 13.3–30.7) months and 35.0 (95% CI: 24.0–46.1) months, respectively, compared with 40 months and ~60 months for those with LINE-1 promoter hypermethylation (P < 0.05). Multivariate analyses showed that the hypomethylation level at CpG site 7 and 18 of LINE-1 promoter, along with tumour size and tumour differentiation, was independently associated with both TFS and OS for patients with HCC after resection. CONCLUSION Promoter hypomethylation of LINE-1, especially at the CpG site 7 and 18, was associated with a poor prognosis in HCC.
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Affiliation(s)
- Xu-dong Gao
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China,* Both authors contributed equally to this work
| | - Jian-hui Qu
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China,Beijing Institute for Infectious DiseaseBeijing, China,* Both authors contributed equally to this work
| | - Xiu-juan Chang
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Yin-ying Lu
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Wen-lin Bai
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Hong Wang
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Zhong-xian Xu
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Lin-jing An
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Chun-ping Wang
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Zhen Zeng
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China
| | - Yong-ping Yang
- Department of Hepatology, Center of Therapeutic Research for Liver Cancer, The 302nd HospitalBeijing, China,Beijing Institute for Infectious DiseaseBeijing, China
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49
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The association between RASSF1A promoter methylation and prostate cancer: evidence from 19 published studies. Tumour Biol 2013; 35:3881-90. [PMID: 24353088 DOI: 10.1007/s13277-013-1515-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 12/03/2013] [Indexed: 11/26/2022] Open
Abstract
Ras-associated domain family 1A (RASSF1A) is a putative tumor suppressor gene located at 3p21.3, and the epigenetic inactivation of RASSF1A by hypermethylation of CpG islands within the promoter region has been observed in various cancer types, including prostate cancer (PCa). However, results from published studies on the association between RASSF1A promoter methylation and PCa risk are conflicting and inconclusive. Hence, we conducted a meta-analysis of 19 eligible studies with odds ratio (OR) and its corresponding 95% confidence intervals (95% CI) in order to investigate the strength of relationship of RASSF1A promoter methylation with PCa risk and its clinicopathological variables. Overall, the RASSF1A promoter methylation was significantly associated with PCa risk (OR = 9.58, 95% CI 5.64-16.88, P heterogeneity <0.001) and Gleason score (GS) (OR = 2.58, 95% CI 1.64-4.04, P(heterogeneity) = 0.019). In addition, subgroup analysis by testing material demonstrated the significant association between RASSF1A methylation and GS (OR = 3.09, 95% CI 1.92-4.97, P heterogeneity =0.042), PSA level (OR = 2.75, 95% CI 1.67-4.52, P(heterogeneity) = 0.639), and tumor stage (OR = 1.74, 95% CI 1.05-2.87, P(heterogeneity) = 0.026) in tissue rather than urine samples. In conclusion, this meta-analysis suggested that RASSF1A promoter methylation was significantly associated with an increased risk for PCa; furthermore, the RASSF1A methylation status in tissue rather than urine was positively correlated with GS, serum PSA level, and tumor stage, which can be utilized for the early detection and prognosis prediction of PCa.
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50
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Benard A, van de Velde CJH, Lessard L, Putter H, Takeshima L, Kuppen PJK, Hoon DSB. Epigenetic status of LINE-1 predicts clinical outcome in early-stage rectal cancer. Br J Cancer 2013; 109:3073-83. [PMID: 24220694 PMCID: PMC3859941 DOI: 10.1038/bjc.2013.654] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND We evaluated the clinical prognostic value of methylation of two non-coding repeat sequences, long interspersed element 1 (LINE-1) and Alu, in rectal tumour tissues. In addition to DNA methylation, expression of histone modifications H3K27me3 and H3K9Ac was studied in this patient cohort. METHODS LINE-1 and Alu methylation were assessed in DNA extracted from formalin-fixed paraffin-embedded tissues. A pilot (30 tumour and 25 normal tissues) and validation study (189 tumour and 53 normal tissues) were performed. Histone modifications H3K27me3 and H3K9Ac were immunohistochemically stained on tissue microarrays of the study cohort. RESULTS In early-stage rectal cancer (stage I-II), hypomethylation of LINE-1 was an independent clinical prognostic factor, showing shorter patient survival (P=0.014; HR: 4.6) and a higher chance of tumour recurrence (P=0.001; HR: 9.6). Alu methylation did not show any significant correlation with clinical parameters, suggesting an active role of LINE-1 in tumour development. Expression of H3K27me3 (silencing gene expression) and H3K9Ac (activating gene expression) in relation to methylation status of LINE-1 and Alu supported this specific role of LINE-1 methylation. CONCLUSION The epigenetic status of LINE-1, but not of Alu, is prognostic in rectal cancer, indicating an active role for LINE-1 in determining clinical outcome.
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Affiliation(s)
- A Benard
- 1] Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA 90404, USA [2] Department of Surgery, Leiden University Medical Center, Leiden 2300RC, The Netherlands
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