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Ghanem NZ, Yamaguchi M. Regucalcin downregulation in human cancer. Life Sci 2024; 340:122448. [PMID: 38246519 DOI: 10.1016/j.lfs.2024.122448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Regucalcin is a unique calcium-binding protein first discovered in rat liver in 1978. Regucalcin has multiple functions as an inhibitor of various cellular signaling pathways that regulate cell activity. The expression of the regucalcin gene can be altered by various physiological and pathological factors such as diet (nutrients), hormones, diabetes, alcohol and drugs. Several transcription factors have been identified on the regucalcin gene, including AP-1, NF1-A1, RGPR-p117, β-catenin, NF-κB, STAT3 and hypoxia-inducible factor-1α (HIF-1α). Notably, regucalcin plays an important role in the development of several cancers by controlling cell growth. Clinically, many studies have reported that the expression of the regucalcin gene is downregulated in various human cancers. In addition, higher expression of regucalcin in tumor tissue has been associated with longer patient survival, suggesting that regucalcin may act as a potential suppressor of various types of human cancer. Regucalcin may offer a novel therapeutic strategy and diagnostic tool for cancer treatment. However, the underlying mechanism by which regucalcin expression is reduced in human cancer is still unclear. A deeper understanding of regucalcin reduction and function in cancer is needed to discover potential resistance mechanisms and biomarkers, and to improve regucalcin-targeting agents. We review recent findings on regucalcin gene expression in cancer. We discuss the possible mechanisms by which regucalcin expression is downregulated in cancer cells to facilitate understanding of how regucalcin regulates cell growth function. This mini-review may lead to better therapeutic targets with regucalcin.
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Affiliation(s)
- Neda Z Ghanem
- Department of Respiratory Therapy, Mohammed Al-Mana College for Medical Sciences, Dammam, Eastern Province 34222, Saudi Arabia
| | - Masayoshi Yamaguchi
- Cancer Biology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo Street, Hawaii, HI 96813, USA.
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Rossi M, Khalifeh M, Fiori F, Parpinel M, Serraino D, Pelucchi C, Negri E, Giacosa A, Crispo A, Collatuzzo G, Hannun Y, Luberto C, La Vecchia C, Boffetta P. Dietary choline and sphingomyelin choline moiety intake and risk of colorectal cancer: a case-control study. Eur J Clin Nutr 2023; 77:905-910. [PMID: 37479807 DOI: 10.1038/s41430-023-01298-4] [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: 07/11/2022] [Revised: 05/03/2023] [Accepted: 06/05/2023] [Indexed: 07/23/2023]
Abstract
INTRODUCTION Phospholipids are possible favorable agents for colorectal cancer (CRC). Choline has been inversely related to CRC risk but findings are inconsistent. We assessed the effect of dietary sphingomyelin (SM) choline moiety and total choline intake on risk of CRC. METHOD This analysis is based on a multicenter case-control study conducted between 1992 and 1996 in Italy. A total of 6107 subjects were enrolled, including 1225 colon cancer cases, 728 rectal cancer cases and 4154 hospital-based controls. We applied data on the composition of foods in terms of SM choline moiety and choline intake on dietary information collected through a validated food-frequency questionnaire. Odds ratio (OR) for energy-adjusted tertiles of SM choline moiety and choline were estimated through logistic regression models adjusted for sex, age, center, education, alcohol consumption, body mass index, family history of CRC, and physical activity. RESULTS Choline was inversely related to CRC risk (OR for the highest versus the lowest tertile: 0.85; 95% confidence interval [CI]: 0.73-0.99), with a significant trend in risk. The OR for an increment of one standard deviation of energy-adjusted choline intake was 0.93 (95% CI: 0.88-0.98). The association was consistent in colon and rectal cancer and also across colon subsites. SM choline moiety was not associated with CRC risk (OR for the highest versus the lowest tertile: 0.96, 95% CI 0.84-1.11). CONCLUSION This study shows an inverse association between choline intake and CRC but not with SM choline moiety.
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Affiliation(s)
- Marta Rossi
- Department of Clinical Sciences and Community Health, University of Milan, 20133, Milan, Italy
| | - Malak Khalifeh
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Federica Fiori
- Department of Medicine, University of Udine, 33100, Udine, Italy
| | - Maria Parpinel
- Department of Medicine, University of Udine, 33100, Udine, Italy
| | - Diego Serraino
- Unit of Cancer Epidemiology, Centro di Riferimento Oncologico, National Cancer Institute IRCCS, 33108, Aviano, Italy
| | - Claudio Pelucchi
- Department of Clinical Sciences and Community Health, University of Milan, 20133, Milan, Italy
| | - Eva Negri
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy
| | - Attilio Giacosa
- Department of Gastroenterology and Clinical Nutrition, Policlinico di Monza, 20900, Monza, Italy
| | - Anna Crispo
- Epidemiology and Biostatistics Unit, Istituto Nazionale dei Tumori IRCCS, Fondazione G. Pascale, 80131, Naples, Italy
| | | | - Yusuf Hannun
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Chiara Luberto
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Carlo La Vecchia
- Department of Clinical Sciences and Community Health, University of Milan, 20133, Milan, Italy
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, Università di Bologna, 40126, Bologna, Italy.
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Bratei AA, Stefan-van Staden RI. Correlation between Maspin Levels in Different Biological Samples and Pathologic Features in Colorectal Adenocarcinomas. Life (Basel) 2023; 13:life13041060. [PMID: 37109589 PMCID: PMC10143283 DOI: 10.3390/life13041060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Maspin is an important biomarker which was proven to be correlated to many pathological features that can help the oncologists, the surgeons and also the pathologists for choosing the personalized treatment of the patients. Maspin expression correlates with the budding of colorectal adenocarcinomas that is usually used mostly in immunohistochemistry. In this preliminary study, a small number of patients with clinical and pathological features were selected. Four kinds of samples (tumoral tissues, blood, saliva and urine) were analyzed using a stochastic method using stochastic microsensors. Whole blood maspin concentration values were related to budding, molecular subtype and location. Tissular maspin concentrations were related to location, maxi-mum diameter and pN value from TNM staging system. Salivary maspin concentrations were related to budding, mucinous compound and macroscopic features. Urinary maspin concentrations were related to pT value from TNM staging system, budding and molecular subtype. The correlations made in this paper may be used for fast diagnostic of colorectal adenocarcinomas, after which, it will be tested on a significant number of patients confirmed with colon cancer, in different stages of evolution.
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Affiliation(s)
- Alexandru Adrian Bratei
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, 060042 Bucharest, Romania
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 060021 Bucharest, Romania
- Department of Pathology, Emergency University Hospital, 050098 Bucharest, Romania
| | - Raluca-Ioana Stefan-van Staden
- Faculty of Chemical Engineering and Biotechnologies, University Politehnica of Bucharest, 060042 Bucharest, Romania
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, 060021 Bucharest, Romania
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Muylaert C, Van Hemelrijck LA, Maes A, De Veirman K, Menu E, Vanderkerken K, De Bruyne E. Aberrant DNA methylation in multiple myeloma: A major obstacle or an opportunity? Front Oncol 2022; 12:979569. [PMID: 36059621 PMCID: PMC9434119 DOI: 10.3389/fonc.2022.979569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
Drug resistance (DR) of cancer cells leading to relapse is a huge problem nowadays to achieve long-lasting cures for cancer patients. This also holds true for the incurable hematological malignancy multiple myeloma (MM), which is characterized by the accumulation of malignant plasma cells in the bone marrow (BM). Although new treatment approaches combining immunomodulatory drugs, corticosteroids, proteasome inhibitors, alkylating agents, and monoclonal antibodies have significantly improved median life expectancy, MM remains incurable due to the development of DR, with the underlying mechanisms remaining largely ill-defined. It is well-known that MM is a heterogeneous disease, encompassing both genetic and epigenetic aberrations. In normal circumstances, epigenetic modifications, including DNA methylation and posttranslational histone modifications, play an important role in proper chromatin structure and transcriptional regulation. However, in MM, numerous epigenetic defects or so-called ‘epimutations’ have been observed and this especially at the level of DNA methylation. These include genome-wide DNA hypomethylation, locus specific hypermethylation and somatic mutations, copy number variations and/or deregulated expression patterns in DNA methylation modifiers and regulators. The aberrant DNA methylation patterns lead to reduced gene expression of tumor suppressor genes, genomic instability, DR, disease progression, and high-risk disease. In addition, the frequency of somatic mutations in the DNA methylation modifiers seems increased in relapsed patients, again suggesting a role in DR and relapse. In this review, we discuss the recent advances in understanding the involvement of aberrant DNA methylation patterns and/or DNA methylation modifiers in MM development, progression, and relapse. In addition, we discuss their involvement in MM cell plasticity, driving myeloma cells to a cancer stem cell state characterized by a more immature and drug-resistant phenotype. Finally, we briefly touch upon the potential of DNA methyltransferase inhibitors to prevent relapse after treatment with the current standard of care agents and/or new, promising (immuno) therapies.
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6
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Tonmoy MIQ, Fariha A, Hami I, Kar K, Reza HA, Bahadur NM, Hossain MS. Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation. Sci Rep 2022; 12:10260. [PMID: 35715447 PMCID: PMC9205881 DOI: 10.1038/s41598-022-13381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs), caused by alterations in DNA methylation, is a driving factor in several cancers. Interplay between lncRNAs’ aberrant methylation and expression in prostate cancer (PC) progression still remains largely elusive. Therefore, this study characterized the genome-wide epigenetic landscape and expression profiles of lncRNAs and their clinical impact by integrating multi-omics data implementing bioinformatics approaches. We identified 62 differentially methylated CpG-sites (DMCs) and 199 differentially expressed lncRNAs (DElncRNAs), where 32 DElncRNAs contain 32 corresponding DMCs within promoter regions. Significant negative correlation was observed between 8 DElncRNAs-DMCs pairs. 3 (cg23614229, cg23957912, and cg11052780) DMCs and 4 (CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1) DElncRNAs were identified as high-risk factors for poor prognosis of PC patients. Overexpression of hypo-methylated CACNA1G-AS1, F11-AS1, and NNT-AS1 and down-regulation of hyper-methylated MSC-AS1 significantly lower the survival of PC patients and could be a potential prognostic and therapeutic biomarker. These DElncRNAs were found to be associated with several molecular functions whose deregulation can lead to cancer. Involvement of these epigenetically deregulated DElncRNAs in cancer-related biological processes was also noticed. These findings provide new insights into the understanding of lncRNA regulation by aberrant DNA methylation which will help to clarify the epigenetic mechanisms underlying PC.
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Affiliation(s)
- Mahafujul Islam Quadery Tonmoy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Ithmam Hami
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Kumkum Kar
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh. .,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh.
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Cao C, Siegel PB, Gilbert ER, Cline MA. Epigenetic modifiers identified as regulators of food intake in a unique hypophagic chicken model. Animal 2022; 16:100549. [PMID: 35679817 DOI: 10.1016/j.animal.2022.100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/01/2022] Open
Abstract
DNA methylation is an epigenetic modification that influences gene transcription; however, the effects of methylation-influencing chemicals on appetite are unknown. We evaluated the effects of single administration of a methyl donor, S-Adenosylmethionine (SAM), or methylation inhibitor, 5-Azacytidine (AZA), on immediate and later-age food intake in an anorexic chick model. The doses of intracerebroventricularly-injected SAM were 0 (vehicle), 0.1, 1, and 10 μg, and of AZA were 0 (vehicle), 1, 5, and 25 μg. When injected on day 5 posthatch, there was no effect of SAM on food intake in either fed or fasted chicks, whereas AZA increased food consumption in the fasted state but decreased it in fed chicks. We then performed a single injection (same doses) at hatch and measured food intake on day 5 in response to neuropeptide Y (NPY; 0.2 μg) injection. Irrespective of NPY, chicks injected with 1 μg of SAM ate more than others on day 5. In contrast, chicks injected with AZA (5 and 25 μg doses) consumed less on day 5. In conclusion, we identified DNA methylation-regulating chemicals as regulators of food intake. AZA but not SAM affected food intake in the short-term, feeding state dependently. Later, both chemicals injected on the day of hatch were associated with food intake changes at a later age, suggesting that feeding pathways might be altered through changes in methylation.
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Affiliation(s)
- C Cao
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - P B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - E R Gilbert
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - M A Cline
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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8
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5mC-Related lncRNAs as Potential Prognostic Biomarkers in Colon Adenocarcinoma. BIOLOGY 2022; 11:biology11020231. [PMID: 35205097 PMCID: PMC8868594 DOI: 10.3390/biology11020231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/15/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Simple Summary To identify the prognostic significance of 5mC-related lncRNAs in colon adenocarcinoma (COAD), we examined the expression levels and mutations of 21 5mC-regulated genes of COAD in TCGA. We also identified lncRNAs associated with 5mC regulatory genes using Pearson correlation analysis. After the least absolute shrinkage and selection operator (Lasso) Cox regression, the risk signature of 4 5mC-related lncRNAs was selected. Next, the risk signature’s predictive efficacy was proven. Moreover, the biological mechanism and potential immunotherapeutic response of this risk signature were identified. Collectively, we constructed the 5mC-related lncRNA risk signature, which could provide a novel prognostic prediction of COAD patients. Abstract Globally, colon adenocarcinoma (COAD) is one of the most frequent types of malignant tumors. About 40~50% of patients with advanced colon adenocarcinoma die from recurrence and metastasis. Long non-coding RNAs (lncRNAs) and 5-methylcytosine (5mC) regulatory genes have been demonstrated to involve in the progression and prognosis of COAD. The goal of this study was to explore the biological characteristics and potential predictive value of 5mC-related lncRNA signature in COAD. In this research, The Cancer Genome Atlas (TCGA) was utilized to obtain the expression of genes and somatic mutations in COAD, and Pearson correlation analysis was used to select lncRNAs involved in 5mC-regulated genes. Furthermore, we applied univariate Cox regression and Lasso Cox regression to construct 5mC-related lncRNA signature. Then Kaplan–Meier survival analysis, principal components analysis (PCA), receiver operating characteristic (ROC) curve, and a nomogram were performed to estimate the prognostic effect of the risk signature. GSEA was utilized to predict downstream access of the risk signature. Finally, the immune characteristics and immunotherapeutic signatures targeting this risk signature were analyzed. In the results, we obtained 1652 5mC-related lncRNAs by Pearson correlation analysis in the TCGA database. Next, we selected a risk signature that comprised 4 5mC-related lncRNAs by univariate and Lasso Cox regression. The prognostic value of the risk signature was proven. Finally, the biological mechanism and potential immunotherapeutic response of the risk signature were identified. Collectively, we constructed the 5mC-related lncRNA risk signature, which could provide a novel prognostic prediction of COAD patients.
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Heery R, Schaefer MH. DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events. Nucleic Acids Res 2021; 49:12692-12705. [PMID: 34871444 PMCID: PMC8682778 DOI: 10.1093/nar/gkab1167] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
While large-scale studies applying various statistical approaches have identified hundreds of mutated driver genes across various cancer types, the contribution of epigenetic changes to cancer remains more enigmatic. This is partly due to the fact that certain regions of the cancer genome, due to their genomic and epigenomic properties, are more prone to dysregulated DNA methylation than others. Thus, it has been difficult to distinguish which promoter methylation changes are really driving carcinogenesis from those that are mostly just a reflection of their genomic location. By developing a novel method that corrects for epigenetic covariates, we reveal a small, concise set of potential epigenetic driver events. Interestingly, those changes suggest different modes of epigenetic carcinogenesis: first, we observe recurrent inactivation of known cancer genes across tumour types suggesting a higher convergence on common tumour suppressor pathways than previously anticipated. Second, in prostate cancer, a cancer type with few recurrently mutated genes, we demonstrate how the epigenome primes tumours towards higher tolerance of other aberrations.
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Affiliation(s)
- Richard Heery
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
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10
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Arumugam T, Ramphal U, Adimulam T, Chinniah R, Ramsuran V. Deciphering DNA Methylation in HIV Infection. Front Immunol 2021; 12:795121. [PMID: 34925380 PMCID: PMC8674454 DOI: 10.3389/fimmu.2021.795121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
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Affiliation(s)
- Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Romona Chinniah
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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11
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Liu Z, Lu T, Wang L, Liu L, Li L, Han X. Comprehensive Molecular Analyses of a Novel Mutational Signature Classification System with Regard to Prognosis, Genomic Alterations, and Immune Landscape in Glioma. Front Mol Biosci 2021; 8:682084. [PMID: 34307451 PMCID: PMC8293748 DOI: 10.3389/fmolb.2021.682084] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/28/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Glioma is the most common malignant brain tumor with complex carcinogenic process and poor prognosis. The current molecular classification cannot fully elucidate the molecular diversity of glioma. Methods: Using broad public datasets, we performed cluster analysis based on the mutational signatures and further investigated the multidimensional heterogeneity of the novel glioma molecular subtypes. The clinical significance and immune landscape of four clusters also investigated. The nomogram was developed using the mutational clusters and clinical characteristics. Results: Four heterogenous clusters were identified, termed C1, C2, C3, and C4, respectively. These clusters presented distinct molecular features: C1 was characterized by signature 1, PTEN mutation, chromosome seven amplification and chromosome 10 deletion; C2 was characterized by signature 8 and FLG mutation; C3 was characterized by signature 3 and 13, ATRX and TP53 mutations, and 11p15.1, 11p15.5, and 13q14.2 deletions; and C4 was characterized by signature 16, IDH1 mutation and chromosome 1p and 19q deletions. These clusters also varied in biological functions and immune status. We underlined the potential immune escape mechanisms: abundant stromal and immunosuppressive cells infiltration and immune checkpoints (ICPs) blockade in C1; lack of immune cells, low immunogenicity and antigen presentation defect in C2 and C4; and ICPs blockade in C3. Moreover, C4 possessed a better prognosis, and C1 and C3 were more likely to benefit from immunotherapy. A nomogram with excellent performance was also developed for assessing the prognosis of patients with glioma. Conclusion: Our results can enhance the mastery of molecular features and facilitate the precise treatment and clinical management of glioma.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Taoyuan Lu
- Department of Cerebrovascular Disease, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
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12
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Moderate DNA hypomethylation suppresses intestinal tumorigenesis by promoting caspase-3 expression and apoptosis. Oncogenesis 2021; 10:38. [PMID: 33947834 PMCID: PMC8096944 DOI: 10.1038/s41389-021-00328-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/18/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Global DNA hypomethylation is a most common epigenetic alteration in human neoplasia. However, accumulative evidence shows that global DNA hypomethylation impacts tumorigenesis in a tissue-specific manner, promoting tumorigenesis in some but suppressing tumorigenesis in others including colorectal cancer. The underlying mechanisms, especially how DNA hypomethylation suppresses tumorigenesis, remain largely unknown. Here, we investigate how DNA hypomethylation affects intestinal tumorigenesis by using an Uhrf1 tandem tudor domain knockin mutant mouse model (Uhrf1ki/ki) that exhibits a moderate ~10% reduction of global DNA methylation. We found that both chemical-induced colorectal carcinogenesis and Apc loss of heterozygosity (LOH)-induced intestinal tumorigenesis are substantially suppressed in the Uhrf1 mutant mice. Furthermore, unlike Dnmt1 hypomorphic mice in which DNA hypomethylation suppresses the incidence of macroscopic intestinal tumors but promotes the formation of microadenoma in ApcMin/+ background, Uhrf1ki/ki/ApcMin/+ mice have markedly reduced incidence of both microadenoma and macroadenoma. DNA hypomethylation does not appear to affect Apc LOH, activation of the Wnt or Hippo pathway, or tumor cell proliferation, but acts cooperatively with activated Wnt pathway to enhance the caspase-3 gene expression, activation, and apoptosis. Furthermore, increased caspase-3 expression correlates with DNA hypomethylation within the caspase-3 enhancer regions. Taken together, we present a new mouse model for investigating the role of and the molecular mechanisms by which DNA hypomethylation suppresses intestinal tumorigenesis. Our finding that a moderate DNA hypomethylation is sufficient to suppress intestinal tumorigenesis by promoting caspase-3 expression and apoptosis sheds new light on DNA-methylation inhibitor-based colorectal cancer therapeutics.
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Sorin M, Watkins D, Gilfix BM, Rosenblatt DS. Methionine dependence in tumor cells: The potential role of cobalamin and MMACHC. Mol Genet Metab 2021; 132:155-161. [PMID: 33487542 DOI: 10.1016/j.ymgme.2021.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/27/2022]
Abstract
Methionine dependence of tumor cell lines, the inability to grow in tissue culture media lacking methionine but supplemented with homocysteine, has been known for decades, but an understanding of the mechanism underlying this phenomenon remains incomplete. Methionine dependence of certain glioma and melanoma cell lines has been linked to alterations in the metabolism of cobalamin (vitamin B12). In the MeWo LC1 melanoma line, complementation analysis demonstrated that the genetic defect affected the same locus mutated in the cblC inborn error of cobalamin metabolism; hypermethylation of the MMACHC promoter was subsequently demonstrated. Analysis of data in the Cancer Cell Line Encyclopedia showed increased MMACHC methylation levels in melanoma lines compared to other types of cancer. RNA sequencing data from isolated tumors, tabulated at the cBioPortal for Cancer Genomics website, showed decreased MMACHC expression compared to other tumors; and methylation data tabulated at the TGGA Wanderer website demonstrated increased MMACHC methylation. These data suggest that disruptions in cobalamin metabolism might play a more general role in methionine dependence, and potentially in the pathogenesis of melanoma cell lines and primary tumors.
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Affiliation(s)
- Mark Sorin
- Department of Human Genetics, McGill University and Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - David Watkins
- Department of Human Genetics, McGill University and Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.
| | - Brian M Gilfix
- Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University and Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada; Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada; Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
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Chen X, Wu X, Lei W. USP44 hypermethylation promotes cell proliferation and metastasis in breast cancer. Future Oncol 2020; 17:279-289. [PMID: 32956592 DOI: 10.2217/fon-2020-0415] [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] [Indexed: 12/25/2022] Open
Abstract
Aim: The methylation and expression levels of USP44 in breast cancer were investigated and their effects on tumor cells were researched. Materials & methods: Bioinformatics was employed to identify the target gene from TCGA database. Sodium bisulfite and decitabine were used for DNA modification and demethylation, and methylation-specific PCR and reverse transcriptase PCR were performed to assess USP44 methylation and expression levels. Tumor cell behaviors were assayed via several in vitro experiments. Results: USP44 was hypermethylated, which caused its poor expression in breast cancer, whereas its overexpression significantly suppressed cancer cell proliferation, migration and invasion and induced apoptosis. Conclusion: USP44 negatively functions in cancer progression upon overexpression, indicating its potential as a therapeutic target for clinical treatment of breast cancer.
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Affiliation(s)
- Xin Chen
- Department of Surgical Oncology, Taizhou Municipal Hospital, Taizhou University, Taizhou, Zhejiang, 318000, PR China
| | - Xiaotang Wu
- Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, 200000, PR China
| | - Wen Lei
- Department of Breast Surgical Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian, 350014, PR China
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15
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The DNA methylation landscape in cancer. Essays Biochem 2020; 63:797-811. [PMID: 31845735 PMCID: PMC6923322 DOI: 10.1042/ebc20190037] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
As one of the most abundant and well-studied epigenetic modifications, DNA methylation plays an essential role in normal development and cellular biology. Global alterations to the DNA methylation landscape contribute to alterations in the transcriptome and deregulation of cellular pathways. Indeed, improved methods to study DNA methylation patterning and dynamics at base pair resolution and across individual DNA molecules on a genome-wide scale has highlighted the scope of change to the DNA methylation landscape in disease states, particularly during tumorigenesis. More recently has been the development of DNA hydroxymethylation profiling techniques, which allows differentiation between 5mC and 5hmC profiles and provides further insights into DNA methylation dynamics and remodeling in tumorigenesis. In this review, we describe the distribution of DNA methylation and DNA hydroxymethylation in different genomic contexts, first in normal cells, and how this is altered in cancer. Finally, we discuss DNA methylation profiling technologies and the most recent advances in single-cell methods, bisulfite-free approaches and ultra-long read sequencing techniques.
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Castle JR, Lin N, Liu J, Storniolo AMV, Shendre A, Hou L, Horvath S, Liu Y, Wang C, He C. Estimating breast tissue-specific DNA methylation age using next-generation sequencing data. Clin Epigenetics 2020; 12:45. [PMID: 32164769 PMCID: PMC7282053 DOI: 10.1186/s13148-020-00834-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/01/2020] [Indexed: 12/20/2022] Open
Abstract
Background DNA methylation (DNAm) age has been widely accepted as an epigenetic biomarker for biological aging. Emerging evidence suggests that DNAm age can be tissue-specific and female breast tissue ages faster than other parts of the body. The Horvath clock, which estimates DNAm age across multiple tissues, has been shown to be poorly calibrated in breast issue. We aim to develop a model to estimate breast tissue-specific DNAm age. Methods Genome-wide DNA methylation sequencing data were generated for 459 normal, 107 tumor, and 45 paired adjacent-normal breast tissue samples. We determined a novel set of 286 breast tissue-specific clock CpGs using penalized linear regression and developed a model to estimate breast tissue-specific DNAm age. The model was applied to estimate breast tissue-specific DNAm age in different breast tissue types and in tumors with distinct clinical characteristics to investigate cancer-related aging effects. Results Our estimated breast tissue-specific DNAm age was highly correlated with chronological age (r = 0.88; p = 2.9 × 10−31) in normal breast tissue. Breast tumor tissue samples exhibited a positive epigenetic age acceleration, where DNAm age was on average 7 years older than respective chronological age (p = 1.8 × 10−8). In age-matched analyses, tumor breast tissue appeared 12 and 13 years older in DNAm age than adjacent-normal and normal breast tissue (p = 4.0 × 10−6 and 1.0 × 10−6, respectively). Both HER2+ and hormone-receptor positive subtypes demonstrated significant acceleration in DNAm ages (p = 0.04 and 3.8 × 10−6, respectively), while no apparent DNAm age acceleration was observed for triple-negative breast tumors. We observed a non-linear pattern of epigenetic age acceleration with breast tumor grade. In addition, early-staged tumors showed a positive epigenetic age acceleration (p = 0.003) while late-staged tumors exhibited a non-significant negative epigenetic age acceleration (p = 0.10). Conclusions The intended applications for this model are wide-spread and have been shown to provide biologically meaningful results for cancer-related aging effects in breast tumor tissue. Future studies are warranted to explore whether breast tissue-specific epigenetic age acceleration is predictive of breast cancer development, treatment response, and survival as well as the clinical utility of whether this model can be extended to blood samples.
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Affiliation(s)
- James R Castle
- University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY, 40536, USA
| | - Nan Lin
- University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY, 40536, USA
| | - Jinpeng Liu
- University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY, 40536, USA
| | - Anna Maria V Storniolo
- Susan G. Komen Tissue Bank at Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Aditi Shendre
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Steve Horvath
- Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA, USA
| | - Yunlong Liu
- Department of Molecular and Medical Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Wang
- University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY, 40536, USA
| | - Chunyan He
- University of Kentucky Markey Cancer Center, 800 Rose Street, Lexington, KY, 40536, USA. .,Department of Internal Medicine, Division of Medical Oncology, University of Kentucky College of Medicine, Lexington, KY, USA.
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17
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Wang Y, Wang T, Xu M, Yu H, Ding C, Wang Z, Pan X, Li Y, Niu Y, Yan R, Song J, Yan H, Dai Y, Sun Z, Su W, Duan H. Independent effect of main components in particulate matter on DNA methylation and DNA methyltransferase: A molecular epidemiology study. ENVIRONMENT INTERNATIONAL 2020; 134:105296. [PMID: 31759273 DOI: 10.1016/j.envint.2019.105296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/09/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND There is a paucity of mechanistic information on the DNA methylation and particulate matter (PM) exposure. This study aimed to investigate the association of PM and its component with DNA methylation, and the roles of DNA methyltransferase (DNMTs). METHODS There were 240 high-exposed, 318 low-exposed and 210 non-exposed participants in this study. Individual concentrations of PM, polycyclic aromatic hydrocarbons (PAHs) and metals were identified by the monitoring data in their workplaces. Urinary 1-OHP and metals were determined as exposure markers. The global DNA methylation (% 5mC) and the mRNA expression of DNMT1, DNMT3A and DNMT3B were measured. We used mediation analysis to evaluate the role of DNMTs expression on DNA methylation alteration induced by PAHs and metals components. RESULTS The decreasing trend of % 5mC was associated with increment of PM exposure in all subjects. We found that one IQR increase in total PAHs (3.82 μg/m3) and urinary 1-OHP (1.06 μmol/mol creatinine) were associated with a separate 6.08% and 7.26% decrease in % 5mC (P = 0.009, P < 0.001), and one IQR increase in urinary Ni (27.75 μmol/mol creatinine) was associated with a 3.29% decrease in % 5mC (P = 0.03). The interaction of urinary 1-OHP with Ni on global DNA methylation (%5mC) was not found (P interaction = 0.89). PM exposure was significantly associated with decreased mRNA level of DNMT3B, but the mediated effect of the PAHs and Ni levels on % 5mC through the DNMT3B pathway was not observed. CONCLUSIONS We found the decrement of global DNA methylation and DNMT3B expression with elevated PM levels in population. The independent mode of action on DNA hypomethylation was found from PAHs and metal components. Global DNA hypomethylation might be a potential biomarker for evaluation of adverse health effects in response to PM exposure.
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Affiliation(s)
- Yanhua Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ting Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengmeng Xu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China; School of Public Health, Shandong University, Jinan, China
| | - Haitao Yu
- Laigang Hospital Affiliated to Taishan Medical University, Laiwu, China
| | - Chunguang Ding
- National Center for Occupational Safety and Health, National Health Commission of the People's Republic of China, Beijing, China
| | - Zhenjie Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xingfu Pan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanbo Li
- School of Public Health, Capital Medical University, Beijing, China
| | - Yong Niu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruixue Yan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiayang Song
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huifang Yan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yufei Dai
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhiwei Sun
- School of Public Health, Capital Medical University, Beijing, China
| | - Wenge Su
- Laigang Hospital Affiliated to Taishan Medical University, Laiwu, China
| | - Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China.
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18
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Zhang Y, Yang L, Kucherlapati M, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Park PJ, Kucherlapati R, Creighton CJ. Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol 2019; 20:209. [PMID: 31610796 PMCID: PMC6792267 DOI: 10.1186/s13059-019-1818-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored. Results By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration. Conclusion Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lixing Yang
- Ben May Department for Cancer Research and Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Melanie Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angela Hadjipanayis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Christopher A Bristow
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Harshad S Mahadeshwar
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jiabin Tang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sahil Seth
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Semin Lee
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaojia Ren
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xingzhi Song
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huandong Sun
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lovelace J Luquette
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruibin Xi
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lynda Chin
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Eli and Edythe L. Broad Institute of Massachusetts Institute Of Technology and Harvard University, Cambridge, MA, 02142, USA
| | | | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Center for Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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DNA Methylation Status in Cancer Disease: Modulations by Plant-Derived Natural Compounds and Dietary Interventions. Biomolecules 2019; 9:biom9070289. [PMID: 31323834 PMCID: PMC6680848 DOI: 10.3390/biom9070289] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/24/2022] Open
Abstract
The modulation of the activity of DNA methyltransferases (DNMTs) represents a crucial epigenetic mechanism affecting gene expressions or DNA repair mechanisms in the cells. Aberrant modifications in the function of DNMTs are a fundamental event and part of the pathogenesis of human cancer. Phytochemicals, which are biosynthesized in plants in the form of secondary metabolites, represent an important source of biomolecules with pleiotropic effects and thus provide a wide range of possible clinical applications. It is well documented that phytochemicals demonstrate significant anticancer properties, and in this regard, rapid development within preclinical research is encouraging. Phytochemicals affect several epigenetic molecular mechanisms, including DNA methylation patterns such as the hypermethylation of tumor-suppressor genes and the global hypomethylation of oncogenes, that are specific cellular signs of cancer development and progression. This review will focus on the latest achievements in using plant-derived compounds and plant-based diets targeting epigenetic regulators and modulators of gene transcription in preclinical and clinical research in order to generate novel anticancer drugs as sensitizers for conventional therapy or compounds suitable for the chemoprevention clinical setting in at-risk individuals. In conclusion, indisputable anticancer activities of dietary phytochemicals linked with proper regulation of DNA methylation status have been described. However, precisely designed and well-controlled clinical studies are needed to confirm their beneficial epigenetic effects after long-term consumption in humans.
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20
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Han P, Bidulescu A, Barber JR, Zeisel SH, Joshu CE, Prizment AE, Vitolins MZ, Platz EA. Dietary choline and betaine intakes and risk of total and lethal prostate cancer in the Atherosclerosis Risk in Communities (ARIC) Study. Cancer Causes Control 2019; 30:343-354. [PMID: 30825046 DOI: 10.1007/s10552-019-01148-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/16/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE Two prior cohort studies suggested that choline, but not betaine intake, is associated with an increased risk of advanced prostate cancer (PCa). Given that evidence remains limited, we evaluated whether intakes of choline and derivative betaine are associated with total and lethal PCa risk and PCa death in men with PCa. METHODS We included 6,528 men (24.4% African American) without a cancer diagnosis at baseline (1987-1989) followed through 2012. Dietary intake was assessed using a food frequency questionnaire coupled with a nutrient database. We used Cox proportional hazards regression to estimate hazards ratios (HRs) and 95% confidence intervals (CIs) of total and lethal PCa risk overall and by race. RESULTS Choline intake was not associated with total (n = 811) or lethal (n = 95) PCa risk overall or by race. Betaine intake was inversely associated with lethal (tertile 3 vs 1, HR 0.59, 95% CI 0.35-1.00, p trend = 0.04), but not total PCa risk; patterns for lethal PCa were similar by race. Neither nutrient was associated with PCa death in men with PCa. CONCLUSIONS Choline intake was not associated with total or lethal PCa or with PCa death in men with PCa. Betaine intake was inversely associated with lethal, but not total PCa risk or with PCa death in men with PCa. Our results do not support the hypothesis that higher choline intake increases lethal PCa risk, but do suggest that higher betaine intake may be associated with lower lethal PCa risk. Further investigation with a larger number of lethal cases is needed.
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Affiliation(s)
- Peijin Han
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Aurelian Bidulescu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington School of Public Health, Bloomington, IN, USA
| | - John R Barber
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Steven H Zeisel
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Corinne E Joshu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Anna E Prizment
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Mara Z Vitolins
- Epidemiology & Prevention Office of Women in Medicine and Science Center on Diabetes, Obesity, and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. .,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA. .,Department of Urology and the James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,, 615 N. Wolfe Street Room E6132, Baltimore, MD, 21205, USA.
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21
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Liu X, Li C, Zhang R, Xiao W, Niu X, Ye X, Li Z, Guo Y, Tan J, Li Y. The EZH2- H3K27me3-DNMT1 complex orchestrates epigenetic silencing of the wwc1 gene, a Hippo/YAP pathway upstream effector, in breast cancer epithelial cells. Cell Signal 2018; 51:243-256. [PMID: 30121333 DOI: 10.1016/j.cellsig.2018.08.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 02/06/2023]
Abstract
It is well known that epithelial-mesenchymal transition (EMT) can confer cancer cells with invasive and migratory capabilities associated with distant metastasis. As a key upstream factor in the Hippo pathway, Kibra (wwc1 gene) has been shown to suppress EMT in breast cancer cells, and we have found that its expression is reduced or lost completely in both human breast cancer cell lines and clinical tissue samples, particularly in triple negative breast cancer (TNBC). Unfortunately, the molecular mechanisms underlying this progression-associated event remain to be elucidated. Epigenetic gene silencing is one of the most common causes of suppressed expression of tumor suppressor genes. Furthermore, recent studies have demonstrated that EZH2 can recruit DNA methyltransferases, resulting in DNA methylation and subsequent gene silencing in certain circumstances. Thus, we hypothesized that there may exist a link between EZH2 and DNA methylation in association with wwc1 silencing in breast cancer. To test this hypothesis, we performed bisulfite sequencing, shRNA, co-IP, ChIP, MeDIP and ChIP-qPCR. As expected, RG108 or 5-Aza treatment improved the wwc1 gene transcription and Kibra protein expression. Both bisulfite sequencing and MeDIP demonstrated higher CpG methylation of the wwc1 promoter the TNBC cells (MDA-MB-231) than in luminal breast cancer cells (MCF7). It is noteworthy that ChIP and co-IP assays showed that EZH2, H3K27me3 and DNMT1 are enriched at the wwc1 promoter, and there exist physiologically relevant protein-protein interactions between them. We also found that EZH2 knockdown leads to a partial increase in Kibra expression and a considerable reduction in H3K27 and DNMT1 trimethylation. Moreover, ChIP-qPCR revealed more DNA fragments containing the wwc1 promoter in MDA-MB-231 than in MCF7 cells after immunoprecipitation with EZH2, DNMT1 and H3K27me3 antibodies. Collectively, our results reveal crosstalk between H3K27me3 inhibition catalyzed by EZH2 and CpG island methylation mediated by DNMT1 within the wwc1 promoter, which synergistically silence wwc1 gene expression in TNBC. Based on these results, we conclude that EZH2 shows promise as a potential anti-tumor target.
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Affiliation(s)
- Xiong Liu
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China; Present address: Shenzhen Key Lab of Neuropsychiatric Modulation and Collaborative Innovation Center for Brain Science, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Center for Excellence in Brain Science and Intelligence Technology, The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun Li
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China; Department of Pathology, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Rendong Zhang
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Wenjun Xiao
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Xia Niu
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Xiajun Ye
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Zijia Li
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Yuxian Guo
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Junyu Tan
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China
| | - Yaochen Li
- The central Laboratory, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, China.
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Abstract
Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. While survival rates are high if RCC is diagnosed when still confined to the kidney and treated definitively, there are no specific diagnostic screening tests available and symptoms are rare in early stages of the disease. Management of advanced RCC has changed significantly with the advent of targeted therapies, yet survival is usually increased by months due to acquired resistance to these therapies. DNA methylation, the covalent addition of a methyl group to a cytosine, is essential for normal development and transcriptional regulation, but becomes altered commonly in cancer. These alterations result in broad transcriptional changes, including in tumor suppressor genes. Because DNA methylation is one of the earliest molecular changes in cancer and is both widespread and stable, its role in cancer biology, including RCC, has been extensively studied. In this review, we examine the role of DNA methylation in RCC disease etiology and progression, the preclinical use of DNA methylation alterations as diagnostic, prognostic and predictive biomarkers, and the potential for DNA methylation-directed therapies.
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Affiliation(s)
- Brittany N Lasseigne
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806-2908, USA.
| | - James D Brooks
- Department of Urology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA, 94305-5118, USA
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23
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Pajares MA, Pérez-Sala D. Mammalian Sulfur Amino Acid Metabolism: A Nexus Between Redox Regulation, Nutrition, Epigenetics, and Detoxification. Antioxid Redox Signal 2018; 29:408-452. [PMID: 29186975 DOI: 10.1089/ars.2017.7237] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Transsulfuration allows conversion of methionine into cysteine using homocysteine (Hcy) as an intermediate. This pathway produces S-adenosylmethionine (AdoMet), a key metabolite for cell function, and provides 50% of the cysteine needed for hepatic glutathione synthesis. The route requires the intake of essential nutrients (e.g., methionine and vitamins) and is regulated by their availability. Transsulfuration presents multiple interconnections with epigenetics, adenosine triphosphate (ATP), and glutathione synthesis, polyol and pentose phosphate pathways, and detoxification that rely mostly in the exchange of substrates or products. Major hepatic diseases, rare diseases, and sensorineural disorders, among others that concur with oxidative stress, present impaired transsulfuration. Recent Advances: In contrast to the classical view, a nuclear branch of the pathway, potentiated under oxidative stress, is emerging. Several transsulfuration proteins regulate gene expression, suggesting moonlighting activities. In addition, abnormalities in Hcy metabolism link nutrition and hearing loss. CRITICAL ISSUES Knowledge about the crossregulation between pathways is mostly limited to the hepatic availability/removal of substrates and inhibitors. However, advances regarding protein-protein interactions involving oncogenes, identification of several post-translational modifications (PTMs), and putative moonlighting activities expand the potential impact of transsulfuration beyond methylations and Hcy. FUTURE DIRECTIONS Increasing the knowledge on transsulfuration outside the liver, understanding the protein-protein interaction networks involving these enzymes, the functional role of their PTMs, or the mechanisms controlling their nucleocytoplasmic shuttling may provide further insights into the pathophysiological implications of this pathway, allowing design of new therapeutic interventions. Antioxid. Redox Signal. 29, 408-452.
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Affiliation(s)
- María A Pajares
- 1 Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC) , Madrid, Spain .,2 Molecular Hepatology Group, Instituto de Investigación Sanitaria La Paz (IdiPAZ) , Madrid, Spain
| | - Dolores Pérez-Sala
- 1 Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC) , Madrid, Spain
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24
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Liu Z, Cui C, Wang X, Fernandez-Escobar A, Wu Q, Xu K, Mao J, Jin M, Wang K. Plasma Levels of Homocysteine and the Occurrence and Progression of Rectal Cancer. Med Sci Monit 2018; 24:1776-1783. [PMID: 29581416 PMCID: PMC5883868 DOI: 10.12659/msm.909217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Zhi Liu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Chunhui Cui
- Department of Gynecologic Oncology, Shandong Cancer Hospital and Institute, Jinan, Shandong, China (mainland)
| | - Xiaoyang Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | | | - Qunzheng Wu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Kai Xu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China (mainland)
| | - Jiajia Mao
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Minxin Jin
- General Surgery, Qilu Hospital of Shandong University, , China (mainland)
| | - Kexin Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
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25
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Kotelnikova EA, Pyatnitskiy M, Paleeva A, Kremenetskaya O, Vinogradov D. Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. Oncotarget 2018; 7:52493-52516. [PMID: 27191992 PMCID: PMC5239569 DOI: 10.18632/oncotarget.9370] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/18/2016] [Indexed: 12/17/2022] Open
Abstract
Nowadays, the personalized approach to health care and cancer care in particular is becoming more and more popular and is taking an important place in the translational medicine paradigm. In some cases, detection of the patient-specific individual mutations that point to a targeted therapy has already become a routine practice for clinical oncologists. Wider panels of genetic markers are also on the market which cover a greater number of possible oncogenes including those with lower reliability of resulting medical conclusions. In light of the large availability of high-throughput technologies, it is very tempting to use complete patient-specific New Generation Sequencing (NGS) or other "omics" data for cancer treatment guidance. However, there are still no gold standard methods and protocols to evaluate them. Here we will discuss the clinical utility of each of the data types and describe a systems biology approach adapted for single patient measurements. We will try to summarize the current state of the field focusing on the clinically relevant case-studies and practical aspects of data processing.
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Affiliation(s)
- Ekaterina A Kotelnikova
- Personal Biomedicine, Moscow, Russia.,A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Institute Biomedical Research August Pi Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Barcelona, Spain
| | - Mikhail Pyatnitskiy
- Personal Biomedicine, Moscow, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Olga Kremenetskaya
- Personal Biomedicine, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy Vinogradov
- Personal Biomedicine, Moscow, Russia.,A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
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26
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Pajares MÁ. PDRG1 at the interface between intermediary metabolism and oncogenesis. World J Biol Chem 2017; 8:175-186. [PMID: 29225734 PMCID: PMC5714802 DOI: 10.4331/wjbc.v8.i4.175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/14/2017] [Accepted: 11/19/2017] [Indexed: 02/05/2023] Open
Abstract
PDRG1 is a small oncogenic protein of 133 residues. In normal human tissues, the p53 and DNA damage-regulated gene 1 (PDRG1) gene exhibits maximal expression in the testis and minimal levels in the liver. Increased expression has been detected in several tumor cells and in response to genotoxic stress. High-throughput studies identified the PDRG1 protein in a variety of macromolecular complexes involved in processes that are altered in cancer cells. For example, this oncogene has been found as part of the RNA polymerase II complex, the splicing machinery and nutrient sensing machinery, although its role in these complexes remains unclear. More recently, the PDRG1 protein was found as an interaction target for the catalytic subunits of methionine adenosyltransferases. These enzymes synthesize S-adenosylmethionine, the methyl donor for, among others, epigenetic methylations that occur on the DNA and histones. In fact, downregulation of S-adenosylmethionine synthesis is the first functional effect directly ascribed to PDRG1. The existence of global DNA hypomethylation, together with increased PDRG1 expression, in many tumor cells highlights the importance of this interaction as one of the putative underlying causes for cell transformation. Here, we will review the accumulated knowledge on this oncogene, emphasizing the numerous aspects that remain to be explored.
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Affiliation(s)
- María Ángeles Pajares
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas (CSIC), Madrid 28040, Spain
- Instituto de Investigación Sanitaria La Paz (IdiPAZ), Madrid 28046, Spain
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27
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Schlosberg CE, VanderKraats ND, Edwards JR. Modeling complex patterns of differential DNA methylation that associate with gene expression changes. Nucleic Acids Res 2017; 45:5100-5111. [PMID: 28168293 PMCID: PMC5435975 DOI: 10.1093/nar/gkx078] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/26/2017] [Indexed: 12/15/2022] Open
Abstract
Numerous genomic studies are underway to determine which genes are abnormally regulated by DNA methylation in disease. However, we have a poor understanding of how disease-specific methylation changes affect expression. We thus developed an integrative analysis tool, Methylation-based Gene Expression Classification (ME-Class), to explain specific variation in methylation that associates with expression change. This model captures the complexity of methylation changes around a gene promoter. Using 17 whole-genome bisulfite sequencing and RNA-seq datasets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms standard methods using methylation to predict differential gene expression change. To demonstrate its utility, we used ME-Class to analyze 32 datasets from different hematopoietic cell types from the Blueprint Epigenome project. Expression-associated methylation changes were predominantly found when comparing cells from distantly related lineages, implying that changes in the cell's transcriptional program precede associated methylation changes. Training ME-Class on normal-tumor pairs from The Cancer Genome Atlas indicated that cancer-specific expression-associated methylation changes differ from tissue-specific changes. We further show that ME-Class can detect functionally relevant cancer-specific, expression-associated methylation changes that are reversed upon the removal of methylation. ME-Class is thus a powerful tool to identify genes that are dysregulated by DNA methylation in disease.
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Affiliation(s)
- Christopher E Schlosberg
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Nathan D VanderKraats
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - John R Edwards
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
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28
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Singh P, Sailu S, Palchamy E, Coumar MS, Baluchamy S. Identification of a novel leukemic-specific splice variant of DNMT3B and its stability. Med Oncol 2017; 34:145. [PMID: 28730333 DOI: 10.1007/s12032-017-1008-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022]
Abstract
DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon-exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines. However, DNMT3B9 expression was less in other tested cancer cell lines indicating that DNMT3B9 might serve as a leukemic-specific biomarker. Surprisingly, endogenous protein for DNMT3B9 was not detected in leukemic cells suggesting the unidentified RNA-related function(s) for DNMT3B9. In addition, we showed that DNMT3B9 protein lacks PWWP domain is less stable compared to other DNMT3B variants which contain PWWP domain through computational predictions and by cycloheximide half-life experiment. Taken together, we demonstrated the existence of novel leukemic-specific splice variant of DNMT3B and provide the evidence for the role of PWWP domain in the stability of DNMT3B. The findings reported here have relevance in epigenetic therapy, which is aimed to target the DNMT3B in cancer cells.
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Affiliation(s)
- Prachi Singh
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sarvagalla Sailu
- Centre for Bioinformatics, Pondicherry Central University, Pondicherry, 605014, India
| | - Elango Palchamy
- Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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29
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Piyathilake CJ, Badiga S, Borak SG, Weragoda J, Bae S, Matthews R, Bell WC, Partridge EE. A higher degree of expression of DNA methyl transferase 1 in cervical cancer is associated with poor survival outcome. Int J Womens Health 2017; 9:413-420. [PMID: 28652820 PMCID: PMC5476577 DOI: 10.2147/ijwh.s133441] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Even though novel therapies based on aberrant DNA methylation could be of particular importance for the treatment of cervical cancer (CC) because the oncoproteins E6/E7 of high-risk human papillomaviruses, the causative agents for developing CC, have the capacity to bind and upregulate DNA methyltransferases (DNMTs), to our knowledge, no previous studies have evaluated the expression of this enzyme in CC in relation to survival outcomes. The purpose of the study was to evaluate the expression of DNMT1 in CC and its association with survival outcomes. Methods The study population consisted of 76 women treated for primary CC and followed up by the University of Alabama at Birmingham (UAB) cancer registry. The expression of DNMT1 was examined using immunohistochemistry, and the degree of expression of DNMT1 was expressed as a percentage of cells positive for DNMT1 and its intensity. Cox proportional hazards model was used to assess the relationship between the degree of expression of DNMT1 and overall survival after adjusting for relevant covariates. Results The expression of DNMT1 was significantly higher in CC cells compared to that in the normal cervical epithelium. A higher percentage of cells positive for DNMT1 and a higher intensity score for DNMT1 were significantly associated with poor survival outcome (hazard ratio [HR] =4.3, P=0.03 and HR =4.9, P=0.02, respectively). Conclusion Our findings suggested that the degree of expression of DNMT1 could be considered as a target in the epigenetic treatment of CC. Replication of our results in other study populations with CC could create the opportunity of using DNMT inhibitors to treat CC.
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Affiliation(s)
| | | | | | | | - Sejong Bae
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL
| | - Roland Matthews
- Department of Obstetrics and Gynecology, Morehouse School of Medicine, Atlanta, GA
| | | | - Edward E Partridge
- Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL, USA
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30
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Fantony JJ, Longo TA, Gopalakrishna A, Owusu R, Lance RS, Foo WC, Inman BA, Abern MR. Urinary NID2 and TWIST1 methylation to augment conventional urine cytology for the detection of bladder cancer. Cancer Biomark 2017; 18:381-387. [DOI: 10.3233/cbm-160261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Joseph J. Fantony
- Division of Urology, Duke University Medical Center, Durham, NC, USA
| | - Thomas A. Longo
- Division of Urology, Duke University Medical Center, Durham, NC, USA
| | | | - Richmond Owusu
- Division of Urology, Duke University Medical Center, Durham, NC, USA
| | | | - Wen-Chi Foo
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Brant A. Inman
- Division of Urology, Duke University Medical Center, Durham, NC, USA
| | - Michael R. Abern
- Department of Urology, University of Illinois Chicago, Chicago, IL, USA
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31
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Krishna SM, Seto SW, Jose RJ, Li J, Morton SK, Biros E, Wang Y, Nsengiyumva V, Lindeman JHN, Loots GG, Rush CM, Craig JM, Golledge J. Wnt Signaling Pathway Inhibitor Sclerostin Inhibits Angiotensin II-Induced Aortic Aneurysm and Atherosclerosis. Arterioscler Thromb Vasc Biol 2016; 37:553-566. [PMID: 28062506 DOI: 10.1161/atvbaha.116.308723] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 12/07/2016] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Sclerostin (SOST) has been identified as an important regulator of bone formation; however, it has not been previously implicated in arterial disease. The aim of this study was to assess the role of SOST in aortic aneurysm (AA) and atherosclerosis using human samples, a mouse model, and in vitro investigations. APPROACH AND RESULTS SOST protein was downregulated in human and mouse AA samples compared with controls. Transgenic introduction of human SOST in apolipoprotein E-deficient (ApoE-/-) mice (SOSTTg .ApoE-/-) and administration of recombinant mouse Sost inhibited angiotensin II-induced AA and atherosclerosis. Serum concentrations of several proinflammatory cytokines were significantly reduced in SOSTTg .ApoE-/- mice. Compared with controls, the aortas of mice receiving recombinant mouse Sost and SOSTTg .ApoE-/- mice showed reduced matrix degradation, reduced elastin breaks, and preserved collagen. Decreased inflammatory cell infiltration and a reduction in the expression of wingless-type mouse mammary virus integration site/β-catenin responsive genes, including matrix metalloproteinase-9, osteoprotegerin, and osteopontin, were observed in the aortas of SOSTTg .ApoE-/- mice. SOST expression was downregulated and the wingless-type mouse mammary virus integration site/β-catenin pathway was activated in human AA samples. The cytosine-phosphate-guanine islands in the SOST gene promoter showed significantly higher methylation in human AA samples compared with controls. Incubation of vascular smooth muscle cells with the demethylating agent 5-azacytidine resulted in upregulation of SOST, suggesting that SOST is epigenetically regulated. CONCLUSIONS This study identifies that SOST is expressed in the aorta and downregulated in human AA possibly because of epigenetic silencing. Upregulating SOST inhibits AA and atherosclerosis development, with potential important implications for treating these vascular diseases.
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Affiliation(s)
- Smriti Murali Krishna
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Sai-Wang Seto
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Roby J Jose
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Jiaze Li
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Susan K Morton
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Erik Biros
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Yutang Wang
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Vianne Nsengiyumva
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Jan H N Lindeman
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Gabriela G Loots
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Catherine M Rush
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Jeffrey M Craig
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.)
| | - Jonathan Golledge
- From the Vascular Biology Unit, Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, Australia (S.M.K., S.-W.S., R.J.J., J.L., S.K.M., E.B., Y.W., V.N., J.G.); National Institute of Complementary Medicine (NICM), School of Science and Health, Western Sydney University, Campbelltown, NSW, Australia (S.-W.S.); School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia (Y.W.); Department of Vascular and Transplant Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.); Physical and Life Sciences Division, Lawrence Livermore National Laboratory, CA (G.G.L.); Discipline of Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia (C.M.R.); Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia (J.M.C.); and Department of Vascular and Endovascular Surgery, The Townsville Hospital, Queensland, Australia (J.G.).
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Huang YW, Gu F, Dombkowski A, Wang LS, Stoner GD. Black raspberries demethylate Sfrp4, a WNT pathway antagonist, in rat esophageal squamous cell papilloma. Mol Carcinog 2016; 55:1867-1875. [PMID: 27696538 DOI: 10.1002/mc.22435] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/26/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022]
Abstract
Aberrant methylation of DNA is a common event in the development of cancers, including squamous cell carcinoma (SCC) of the human esophagus. In the present study, we determined: (a) whether aberrant DNA methylation also occurs in the development of N-nitrosomethylbenzylamine (NMBA)-induced tumorigenesis in the rat esophagus, a model of human esophageal SCC; and (b) if so, whether dietary black raspberries (BRBs) are capable of preventing this aberrant DNA methylation. A diet containing 5% BRBs inhibited the development of NMBA-induced tumors in the rat esophagus. This inhibition was associated with reduced mRNA levels of the DNA methyltransferases, Dnmt1 and Dnmt3b, in both dysplastic lesions and in papillomas of the esophagus. In addition, promoter methylation of Sfrp4, a WNT pathway antagonist, was significantly reduced by the berry diet, and this was associated with decreased nuclear localization of β-CATENIN and reduced expression of c-MYC protein in NMBA-treated esophagi. Decreased promoter methylation of Sfrp4 correlated with decreased expression of Dmnt3b and, ultimately, with increased Sfrp4 mRNA expression. This suggests that epigenetic alterations in NMBA-induced rat esophageal tumorigenesis recapitulate epigenetic events in human esophageal SCC, and that BRBs could be useful in preventing the aberrant DNA methylation involved in the development of human esophageal SCC. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin.
| | - Fei Gu
- Department of Pediatrics, Children's Hospital Boston, Boston, Massachusetts
| | - Alan Dombkowski
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan
| | - Li-Shu Wang
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Gary D Stoner
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
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Qi D, Li J, Que B, Su J, Li M, Zhang C, Yang M, Zhou G, Ji W. Long non-coding RNA DBCCR1-003 regulate the expression of DBCCR1 via DNMT1 in bladder cancer. Cancer Cell Int 2016; 16:81. [PMID: 27777512 PMCID: PMC5069854 DOI: 10.1186/s12935-016-0356-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 10/03/2016] [Indexed: 01/17/2023] Open
Abstract
Background Many long non coding RNAs have been identified as key modulators in cancer development. A lncRNA, DBCCR1-003, derived from the locus of tumor suppressor gene DBCCR1 (deleted in bladder cancer chromosome region 1), has unknown function. In the present study, we explored function and molecular mechanism of DBCCR1-003 in bladder cancer (BC) development. Methods We evaluated the expression levels of DBCCR1-003 in tissues and cells with western blot and quantitative real-time polymerase chain reaction. Multiple approaches including chromatin immunoprecipitation assay and RNA immunoprecipitation were used to confirm the direct binding of DBCCR1-003 to DNMT1. The recombinant vector overexpressing DBCCR1-003 was constructed. Cell proliferation assay, colony formation assay and flow cytometric analysis were employed to measure the role of DBCCR1-003 in regulation of cell proliferation, cycle and apoptosis. Results Firstly we detected the expression of DBCCR1-003, DBCCR1, DNMT1 (DNA methyltransferase 1) and DNA methylation in the promoter of DBCCR1. We found low expression of DBCCR1-003, same as DBCCR1, while high expression of DNMT1 and hypermethylation of DBCCR1 gene promoter in BC tissues and T24 cells line. Further studies revealed that treatment of DNMT inhibitor, 5-aza-2-deoxycytidine(DAC), or overexpression of DBCCR1-003 led to increased DBCCR1 expression by reversion of promoter hypermethylation and DNMT1 binding to DBCCR1 promoter in T24 cells. Importantly, RNA immunoprecipitation (RIP) showed that DBCCR1-003 physically associates with DNMT1. The binding of them was increased with the inhibition of DBCCR1 promoter methylation, indicating that DBCCR1-003 may bind to DNMT1 and prevent DNMT1-mediated the methylation of DBCCR1. Furthermore, overexpression of DBCCR1-003 resulted in significant inhibition of T24 cells growth through the inducing G0/G1 arrest and apoptosis. Conclusions Taken together, these findings demonstrated that a novel tumor suppressor DBCCR1-003 regulates the expression of DBCCR1 via binding to DNMT1 and preventing DNMT1-mediated the methylation of DBCCR1 in BC. LncRNA DBCCR1-003 may serve as a novel biomarker and therapeutic target for BC in future cancer clinic. Electronic supplementary material The online version of this article (doi:10.1186/s12935-016-0356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Defeng Qi
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Jinhui Li
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.,The Affiliated Hospital of School of Medicine of Ningbo University, Zhejiang, 315000 China
| | - Biao Que
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Jialin Su
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China.,The First Affiliated Hospital, Center for Translational Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Mengxi Li
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Chaofeng Zhang
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Kangda Road 1#, Haizhu District, Guangzhou, 510230 Guangdong China
| | - Mei Yang
- Breast Disease Center, Guangdong Women and Children Hospital of Guangzhou Medical University, Guangzhou, 510010 Guangdong China.,Department of General Surgery, General Hospital of Guangzhou Military Command of PLA, Guangzhou, 510010 Guangdong China
| | - Guoren Zhou
- Department of Medical Oncology, Jiangsu Cancer Hospital, Nanjing, 210009 Jiangsu China
| | - Weidong Ji
- The First Affiliated Hospital, Center for Translational Medicine, Sun Yat-sen University, Guangzhou, 510080 China
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Cai XC, Kapilashrami K, Luo M. Synthesis and Assays of Inhibitors of Methyltransferases. Methods Enzymol 2016; 574:245-308. [DOI: 10.1016/bs.mie.2016.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Duenas-Gonzalez A, Medina-Franco JL, Chavez-Blanco A, Dominguez-Gomez G, Fernández-de Gortari E. Developmental DNA methyltransferase inhibitors in the treatment of gynecologic cancers. Expert Opin Pharmacother 2015; 17:323-38. [PMID: 26559668 DOI: 10.1517/14656566.2016.1118053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION DNA methylation has become an attractive target for the treatment of cancer. DNA methyltransferase inhibitors have proven useful for the treatment of myelodysplastic syndrome and are being evaluated in gynecological neoplasias. AREAS COVERED We provide an overview of the current knowledge on DNA methylation and cancer and the role of DNA methylation in cervical, ovarian and endometrial carcinomas. The results of recent clinical trials with demethylating agents for cervical and ovarian cancer treatment are also discussed. EXPERT OPINION There are few studies of DNA demethylating agents for cervical and ovarian cancer treatment; nevertheless, the results are promising. To accelerate these advances, there are at least two actions that can be simultaneously pursued. One is to greatly increase the number of small clinical exploratory trials with existing demethylating drugs and using methylome analyses to identify predictive factors for response and/or toxicity. The second is finding out epigenetic 'drivers' unique to gynecological cancers and their subtypes, and then proceed to clinical trials in a highly selected population of patients. It is expected that in the future, DNA demethylation could have a role in the treatment of gynecologic cancers.
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Affiliation(s)
- Alfonso Duenas-Gonzalez
- a Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México/Instituto Nacional de Cancerología , Mexico City , Mexico
| | - José L Medina-Franco
- b Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México City , México
| | - Alma Chavez-Blanco
- c Division of Basic Research , Instituto Nacional de Cancerología , Mexico City , México
| | | | - Eli Fernández-de Gortari
- b Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México City , México
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Moarii M, Boeva V, Vert JP, Reyal F. Changes in correlation between promoter methylation and gene expression in cancer. BMC Genomics 2015; 16:873. [PMID: 26510534 PMCID: PMC4625954 DOI: 10.1186/s12864-015-1994-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/06/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Methylation of high-density CpG regions known as CpG Islands (CGIs) has been widely described as a mechanism associated with gene expression regulation. Aberrant promoter methylation is considered a hallmark of cancer involved in silencing of tumor suppressor genes and activation of oncogenes. However, recent studies have also challenged the simple model of gene expression control by promoter methylation in cancer, and the precise mechanism of and role played by changes in DNA methylation in carcinogenesis remains elusive. RESULTS Using a large dataset of 672 matched cancerous and healthy methylomes, gene expression, and copy number profiles accross 3 types of tissues from The Cancer Genome Atlas (TCGA), we perform a detailed meta-analysis to clarify the interplay between promoter methylation and gene expression in normal and cancer samples. On the one hand, we recover the existence of a CpG island methylator phenotype (CIMP) with prognostic value in a subset of breast, colon and lung cancer samples, where a common subset of promoter CGIs hypomethylated in normal samples become hypermethylated. However, this hypermethylation is not accompanied by a decrease in expression of the corresponding genes, which are already lowly expressed in the normal genes. On the other hand, we identify tissue-specific sets of genes, different between normal and cancer samples, whose inter-individual variation in expression is significantly correlated with the variation in methylation of the 3' flanking regions of the promoter CGIs. These subsets of genes are not the same in the different tissues, nor between normal and cancerous samples, but transcription factors are over-represented in all subsets. CONCLUSION Our results suggest that epigenetic reprogramming in cancer does not contribute to cancer development via direct inhibition of gene expression through promoter hypermethylation. It may instead modify how the expression of a few specific genes, particularly transcription factors, are associated with DNA methylation variations in a tissue-dependent manner.
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Affiliation(s)
- Matahi Moarii
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Valentina Boeva
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Jean-Philippe Vert
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Fabien Reyal
- UMR932, Immunity and Cancer Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France. .,Department of Translational Research, Residual Tumor and Response to Treatment Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France. .,Department of Surgery, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France.
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DNA methyltransferase 3A promotes cell proliferation by silencing CDK inhibitor p18INK4C in gastric carcinogenesis. Sci Rep 2015; 5:13781. [PMID: 26350239 PMCID: PMC4563369 DOI: 10.1038/srep13781] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 08/05/2015] [Indexed: 01/13/2023] Open
Abstract
Little is known about the roles of DNA methyltransferase 3A (DNMT3A) in gastric carcinogenesis. Here, we reported that the exogenous expression of DNMT3A promoted gastric cancer (GC) cell proliferation by accelerating the G1/S transition. Subsequently, p18INK4C was identified as a downstream target of DNMT3A. The elevated expression of DNMT3A suppressed p18INK4C at least at the transcriptional level. Depletion of p18INK4C expression in GC cells induced cell cycle progression, whereas its re-expression alleviated the effect of DNMT3A overexpression on G1/S transition. Furthermore, we found that DNMT3A modulated p18INK4C by directly binding to and silencing the p18INK4C gene via promoter hypermethylation. In clinical GC tissue specimens analyzed, the level of methylation of p18INK4C detected in tumor tissues was significantly higher than that in paired non-tumor tissues. Moreover, elevated level of DNMT3A expression was associated with the differentiation of GC tissues and was negatively correlated with the p18INK4C expression level. Taken together, our results found that DNMT3A contributes to the dysregulation of the cell cycle by repressing p18INK4C in a DNA methylation-dependent manner, suggesting that DNMT3A-p18INK4C axis involved in GC. These findings provide new insights into gastric carcinogenesis and a potential therapeutic target for GC that may be further investigated in the future.
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Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JPA, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Res 2015; 43:6945-58. [PMID: 25916844 PMCID: PMC4538798 DOI: 10.1093/nar/gkv111] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/23/2015] [Accepted: 02/02/2015] [Indexed: 12/30/2022] Open
Abstract
To determine early somatic changes in high-grade serous ovarian cancer (HGSOC), we performed whole genome sequencing on a rare collection of 16 low stage HGSOCs. The majority showed extensive structural alterations (one had an ultramutated profile), exhibited high levels of p53 immunoreactivity, and harboured a TP53 mutation, deletion or inactivation. BRCA1 and BRCA2 mutations were observed in two tumors, with nine showing evidence of a homologous recombination (HR) defect. Combined Analysis with The Cancer Genome Atlas (TCGA) indicated that low and late stage HGSOCs have similar mutation and copy number profiles. We also found evidence that deleterious TP53 mutations are the earliest events, followed by deletions or loss of heterozygosity (LOH) of chromosomes carrying TP53, BRCA1 or BRCA2. Inactivation of HR appears to be an early event, as 62.5% of tumours showed a LOH pattern suggestive of HR defects. Three tumours with the highest ploidy had little genome-wide LOH, yet one of these had a homozygous somatic frame-shift BRCA2 mutation, suggesting that some carcinomas begin as tetraploid then descend into diploidy accompanied by genome-wide LOH. Lastly, we found evidence that structural variants (SV) cluster in HGSOC, but are absent in one ultramutated tumor, providing insights into the pathogenesis of low stage HGSOC.
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Affiliation(s)
- Jeremy Chien
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Sean Humphray
- Illumina Cambridge Ltd, Little Chesterford, Essex CB10 1, UK
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Ying Li
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jaime I Davila
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Sabine Dietmann
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Debra A Bell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Takayo Ota
- Department of Internal Medicine, Rinku General Medical Center, Izumi-sano, 598-8577, Japan
| | - Yaman Tarabishy
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Rui Kuang
- Department of Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55414, USA
| | | | | | | | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98109, USA
| | - John Peden
- Illumina Cambridge Ltd, Little Chesterford, Essex CB10 1, UK
| | - David Bentley
- Illumina Cambridge Ltd, Little Chesterford, Essex CB10 1, UK
| | | | | | - Lynn C Hartmann
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Viji Shridhar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors. Genome Med 2015; 7:87. [PMID: 26257827 PMCID: PMC4528310 DOI: 10.1186/s13073-015-0210-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/23/2015] [Indexed: 12/12/2022] Open
Abstract
Background Mucinous ovarian tumors are an unusual group of rare neoplasms with an apparently clear progression from benign to borderline to carcinoma, yet with a controversial cell of origin in the ovarian surface epithelium. They are thought to be molecularly distinct from other ovarian tumors but there have been no exome-level sequencing studies performed to date. Methods To understand the genetic etiology of mucinous ovarian tumors and assess the presence of novel therapeutic targets or pathways, we undertook exome sequencing of 24 tumors encompassing benign (5), borderline (8) and carcinoma (11) histologies and also assessed a validation cohort of 58 tumors for specific gene regions including exons 4–9 of TP53. Results The predominant mutational signature was of C>T transitions in a NpCpG context, indicative of deamination of methyl-cytosines. As well as mutations in known drivers (KRAS, BRAF and CDKN2A), we identified a high percentage of carcinomas with TP53 mutations (52 %), and recurrent mutations in RNF43, ELF3, GNAS, ERBB3 and KLF5. Conclusions The diversity of mutational targets suggests multiple routes to tumorigenesis in this heterogeneous group of tumors that is generally distinct from other ovarian subtypes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0210-y) contains supplementary material, which is available to authorized users.
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Pathania R, Ramachandran S, Elangovan S, Padia R, Yang P, Cinghu S, Veeranan-Karmegam R, Arjunan P, Gnana-Prakasam JP, Sadanand F, Pei L, Chang CS, Choi JH, Shi H, Manicassamy S, Prasad PD, Sharma S, Ganapathy V, Jothi R, Thangaraju M. DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nat Commun 2015; 6:6910. [PMID: 25908435 PMCID: PMC4410389 DOI: 10.1038/ncomms7910] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/09/2015] [Indexed: 02/07/2023] Open
Abstract
Mammary stem/progenitor cells (MaSCs) maintain self-renewal of the mammary epithelium during puberty and pregnancy. DNA methylation provides a potential epigenetic mechanism for maintaining cellular memory during self-renewal. Although DNA methyltransferases (DNMTs) are dispensable for embryonic stem cell maintenance, their role in maintaining MaSCs and cancer stem cells (CSCs) in constantly replenishing mammary epithelium is unclear. Here we show that DNMT1 is indispensable for MaSC maintenance. Furthermore, we find that DNMT1 expression is elevated in mammary tumors, and mammary gland-specific DNMT1 deletion protects mice from mammary tumorigenesis by limiting the CSC pool. Through genome-scale methylation studies, we identify ISL1 as a direct DNMT1 target, hypermethylated and downregulated in mammary tumors and CSCs. DNMT inhibition or ISL1 expression in breast cancer cells limits CSC population. Altogether, our studies uncover an essential role for DNMT1 in MaSC and CSC maintenance and identify DNMT1-ISL1 axis as a potential therapeutic target for breast cancer treatment.
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Affiliation(s)
- Rajneesh Pathania
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Sabarish Ramachandran
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Selvakumar Elangovan
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Ravi Padia
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Pengyi Yang
- System Biology Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Senthilkumar Cinghu
- System Biology Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Rajalakshmi Veeranan-Karmegam
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Pachiappan Arjunan
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Jaya P Gnana-Prakasam
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Fulzele Sadanand
- Department of Orthopedic Surgery, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Lirong Pei
- Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Chang-Sheng Chang
- Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Jeong-Hyeon Choi
- Department of Biostatistics, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA.,Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Huidong Shi
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA.,Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Santhakumar Manicassamy
- Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Puttur D Prasad
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA.,Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Suash Sharma
- Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA.,Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Vadivel Ganapathy
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA.,Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
| | - Raja Jothi
- System Biology Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA.,Cancer Research Center, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
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Lu MS, Fang YJ, Pan ZZ, Zhong X, Zheng MC, Chen YM, Zhang CX. Choline and betaine intake and colorectal cancer risk in Chinese population: a case-control study. PLoS One 2015; 10:e0118661. [PMID: 25785727 PMCID: PMC4364675 DOI: 10.1371/journal.pone.0118661] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background Few studies have examined the association of choline and betaine intake with colorectal cancer risk, although they might play an important role in colorectal cancer development because of their role as methyl donors. The aim of this study was to examine the relationship between consumption of choline and betaine and colorectal cancer risk in a Chinese population. Methodology/Principal Findings A case-control study was conducted between July 2010 and December 2013 in Guangzhou, China. Eight hundred and ninety consecutively recruited colorectal cancer cases were frequency matched to 890 controls by age (5-year interval) and sex. Dietary information was assessed with a validated food frequency questionnaire by face-to-face interviews. The logistic regression model was used to estimate multivariate odds ratios (ORs) and 95% confidence intervals (CIs). Total choline intake was inversely associated with colorectal cancer risk after adjustment for various lifestyle and dietary factors. The multivariate-adjusted OR was 0.54 (95%CI = 0.37-0.80, Ptrend <0.01) comparing the highest with the lowest quartile. No significant associations were observed for betaine or total choline+betaine intakes. For choline-containing compounds, lower colorectal cancer risk was associated with higher intakes of choline from phosphatidylcholine, glycerophosphocholine and sphingomyelin but not for free choline and phosphocholine. The inverse association of total choline intake with colorectal cancer risk was observed in both men and women, colon and rectal cancer. These inverse associations were not modified by folate intake. Conclusions These results indicate that high intake of total choline is associated with a lower risk of colorectal cancer.
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Affiliation(s)
- Min-Shan Lu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Jing Fang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhi-Zhong Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiao Zhong
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Mei-Chun Zheng
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-Ming Chen
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- * E-mail: (CXZ); (YMC)
| | - Cai-Xia Zhang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- * E-mail: (CXZ); (YMC)
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42
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Figueroa JD, Yang H, Garcia-Closas M, Davis S, Meltzer P, Lissowska J, Horne HN, Sherman ME, Lee M. Integrated analysis of DNA methylation, immunohistochemistry and mRNA expression, data identifies a methylation expression index (MEI) robustly associated with survival of ER-positive breast cancer patients. Breast Cancer Res Treat 2015; 150:457-466. [PMID: 25773928 DOI: 10.1007/s10549-015-3314-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/18/2015] [Indexed: 12/17/2022]
Abstract
Identification of prognostic gene expression signatures may enable improved decisions about management of breast cancer. To identify a prognostic signature for breast cancer, we performed DNA methylation profiling and identified methylation markers that were associated with expression of ER, PR, HER2, CK5/6, and EGFR proteins. Methylation markers that were correlated with corresponding mRNA expression levels were identified using 208 invasive tumors from a population-based case-control study conducted in Poland. Using this approach, we defined the methylation expression index (MEI) signature that was based on a weighted sum of mRNA levels of 57 genes. Classification of cases as low or high MEI scores was related to survival using Cox regression models. In the Polish study, women with ER-positive low MEI cancers had reduced survival at a median of 5.20 years of follow-up, HR = 2.85 95 % CI = 1.25-6.47. Low MEI was also related to decreased survival in four independent datasets totaling over 2500 ER-positive breast cancers. These results suggest that integrated analysis of tumor expression markers, DNA methylation, and mRNA data may be an important approach for identifying breast cancer prognostic signatures. Prospective assessment of MEI along with other prognostic signatures should be evaluated in future studies.
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Affiliation(s)
| | - Howard Yang
- National Cancer Institute, NIH, HHS, Bethesda, MD
| | | | - Sean Davis
- National Cancer Institute, NIH, HHS, Bethesda, MD
| | - Paul Meltzer
- National Cancer Institute, NIH, HHS, Bethesda, MD
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Cancer Center and M. Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | | | | | - Maxwell Lee
- National Cancer Institute, NIH, HHS, Bethesda, MD
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43
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CpG hypermethylation contributes to decreased expression of PTEN during acquired resistance to gefitinib in human lung cancer cell lines. Lung Cancer 2015; 87:265-71. [DOI: 10.1016/j.lungcan.2015.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/29/2014] [Accepted: 01/13/2015] [Indexed: 11/20/2022]
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44
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Pinna A, Zinellu A, Tendas D, Blasetti F, Carru C, Castiglia P. Plasma Homocysteine and Asymmetrical Dimethyl-l-Arginine (ADMA) and Whole Blood DNA Methylation in Early and Neovascular Age-Related Macular Degeneration: A Pilot Study. Curr Eye Res 2015; 41:88-96. [PMID: 25611924 DOI: 10.3109/02713683.2014.1002044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PURPOSE/AIM To compare the plasma levels of homocysteine and asymmetrical dimethyl-l-arginine (ADMA) and the degree of whole blood DNA methylation in patients with early and neovascular age-related macular degeneration (AMD) and in controls without maculopathy of any sort. MATERIALS AND METHODS This observational case-control pilot study included 39 early AMD patients, 27 neovascular AMD patients and 132 sex- and age-matched controls without maculopathy. Plasma homocysteine and ADMA concentrations and the degree of whole blood DNA methylation were measured. Quantitative variables were compared by Student's t-test or Mann-Whitney test. Logistic regression models were used to investigate the significance of the association between early or wet AMD and some variables. RESULTS There were no significant differences in mean plasma homocysteine and ADMA concentrations and in the degree of whole blood DNA methylation between patients with early or neovascular AMD and their controls. Similarly, logistic regression analysis disclosed that plasma homocysteine and ADMA levels were not associated with an increased risk for early or neovascular AMD. CONCLUSIONS We failed to demonstrate an association between early or neovascular AMD and increased plasma homocysteine and/or ADMA. Results also suggest that the degree of whole blood DNA methylation is not a marker of AMD.
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Affiliation(s)
- Antonio Pinna
- a Department of Surgical , Microsurgical, and Medical Sciences, Section of Ophthalmology, University of Sassari , Sassari , Italy .,b Azienda Ospedaliero-Universitaria di Sassari , Sassari , Italy
| | - Angelo Zinellu
- c Department of Biomedical Sciences , Section of Clinical Biochemistry, University of Sassari , Sassari , Italy and
| | - Donatella Tendas
- a Department of Surgical , Microsurgical, and Medical Sciences, Section of Ophthalmology, University of Sassari , Sassari , Italy
| | - Francesco Blasetti
- a Department of Surgical , Microsurgical, and Medical Sciences, Section of Ophthalmology, University of Sassari , Sassari , Italy
| | - Ciriaco Carru
- b Azienda Ospedaliero-Universitaria di Sassari , Sassari , Italy .,c Department of Biomedical Sciences , Section of Clinical Biochemistry, University of Sassari , Sassari , Italy and
| | - Paolo Castiglia
- b Azienda Ospedaliero-Universitaria di Sassari , Sassari , Italy .,d Department of Biomedical Sciences, Laboratory of Epidemiology and Biostatistics , University of Sassari , Sassari , Italy
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45
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Abstract
We provide an overview covering the existing challenges and latest developments in achieving high selectivity and sensitivity cancer-biomarker detection.
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Affiliation(s)
- Li Wu
- Laboratory of Chemical Biology and Division of Biological Inorganic Chemistry
- State Key laboratory of Rare Earth Resource Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
| | - Xiaogang Qu
- Laboratory of Chemical Biology and Division of Biological Inorganic Chemistry
- State Key laboratory of Rare Earth Resource Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
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46
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47
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Zhang B, Xing X, Li J, Lowdon RF, Zhou Y, Lin N, Zhang B, Sundaram V, Chiappinelli KB, Hagemann IS, Mutch DG, Goodfellow PJ, Wang T. Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. BMC Genomics 2014; 15:868. [PMID: 25286960 PMCID: PMC4198682 DOI: 10.1186/1471-2164-15-868] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), or Type II. However, the whole genome DNA methylation changes in these two classical types of endometrial cancer is still unknown. RESULTS Here we described complete genome-wide DNA methylome maps of EAC, UPSC, and normal endometrium by applying a combined strategy of methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme digestion sequencing (MRE-seq). We discovered distinct genome-wide DNA methylation patterns in EAC and UPSC: 27,009 and 15,676 recurrent differentially methylated regions (DMRs) were identified respectively, compared with normal endometrium. Over 80% of DMRs were in intergenic and intronic regions. The majority of these DMRs were not interrogated on the commonly used Infinium 450K array platform. Large-scale demethylation of chromosome X was detected in UPSC, accompanied by decreased XIST expression. Importantly, we discovered that the majority of the DMRs harbored promoter or enhancer functions and are specifically associated with genes related to uterine development and disease. Among these, abnormal methylation of transposable elements (TEs) may provide a novel mechanism to deregulate normal endometrium-specific enhancers derived from specific TEs. CONCLUSIONS DNA methylation changes are an important signature of endometrial cancer and regulate gene expression by affecting not only proximal promoters but also distal enhancers.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Aldehyde Dehydrogenase 1 Family
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/metabolism
- Chromosomes, Human, X
- CpG Islands
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- DNA Transposable Elements/genetics
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/physiopathology
- Enhancer Elements, Genetic/genetics
- Female
- Humans
- Kruppel-Like Factor 4
- Kruppel-Like Transcription Factors/genetics
- MutL Protein Homolog 1
- Nuclear Proteins/genetics
- Polymorphism, Single Nucleotide
- Promoter Regions, Genetic/genetics
- RNA, Long Noncoding/genetics
- Retinal Dehydrogenase/genetics
- Sequence Analysis, DNA
- Uterine Neoplasms/genetics
- Uterine Neoplasms/physiopathology
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Affiliation(s)
- Bo Zhang
- />Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108 USA
| | - XiaoYun Xing
- />Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108 USA
| | - Jing Li
- />Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108 USA
- />Shanghai International Joint Cancer Institute, The Second Military Medical University, Shanghai, 200433 P. R. China
| | - Rebecca F Lowdon
- />Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108 USA
| | - Yan Zhou
- />Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun, Jilin Province 130024 P. R. China
| | - Nan Lin
- />Department of Mathematics and Division of Biostatistics, Washington University in Saint Louis, Saint Louis, MO 63130 USA
| | - Baoxue Zhang
- />Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun, Jilin Province 130024 P. R. China
| | - Vasavi Sundaram
- />Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108 USA
| | - Katherine B Chiappinelli
- />Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21231 USA
| | - Ian S Hagemann
- />Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - David G Mutch
- />Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St Louis, MO 63124 USA
| | - Paul J Goodfellow
- />The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA
| | - Ting Wang
- />Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108 USA
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48
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Barchitta M, Quattrocchi A, Maugeri A, Vinciguerra M, Agodi A. LINE-1 hypomethylation in blood and tissue samples as an epigenetic marker for cancer risk: a systematic review and meta-analysis. PLoS One 2014; 9:e109478. [PMID: 25275447 PMCID: PMC4183594 DOI: 10.1371/journal.pone.0109478] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/31/2014] [Indexed: 01/07/2023] Open
Abstract
Objective A systematic review and a meta-analysis were carried out in order to summarize the current published studies and to evaluate LINE-1 hypomethylation in blood and other tissues as an epigenetic marker for cancer risk. Methods A systematic literature search in the Medline database, using PubMed, was conducted for epidemiological studies, published before March 2014. The random-effects model was used to estimate weighted mean differences (MDs) with 95% Confidence Intervals (CIs). Furthermore, subgroup analyses were conducted by sample type (tissue or blood samples), cancer types, and by assays used to measure global DNA methylation levels. The Cochrane software package Review Manager 5.2 was used. Results A total of 19 unique articles on 6107 samples (2554 from cancer patients and 3553 control samples) were included in the meta-analysis. LINE-1 methylation levels were significantly lower in cancer patients than in controls (MD: −6.40, 95% CI: −7.71, −5.09; p<0.001). The significant difference in methylation levels was confirmed in tissue samples (MD −7.55; 95% CI: −9.14, −65.95; p<0.001), but not in blood samples (MD: −0.26, 95% CI: −0.69, 0.17; p = 0.23). LINE-1 methylation levels were significantly lower in colorectal and gastric cancer patients than in controls (MD: −8.33; 95% CI: −10.56, −6.10; p<0.001 and MD: −5.75; 95% CI: −7.75, −3.74; p<0.001) whereas, no significant difference was observed for hepatocellular cancer. Conclusions The present meta-analysis adds new evidence to the growing literature on the role of LINE-1 hypomethylation in human cancer and demonstrates that LINE-1 methylation levels were significantly lower in cancer patients than in control samples, especially in certain cancer types. This result was confirmed in tissue samples, both fresh/frozen or FFPE specimens, but not in blood. Further studies are needed to better clarify the role of LINE-1 methylation in specific subgroups, considering both cancer and sample type, and the methods of measurement.
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Affiliation(s)
| | | | - Andrea Maugeri
- Department GF Ingrassia, University of Catania, Catania, Italy
| | - Manlio Vinciguerra
- University College London, Institute for Liver and Digestive Health, Royal Free Campus, London, United Kingdom
- Gastroenterology Unit, Department of Medical Sciences, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- * E-mail: (AA); (MV)
| | - Antonella Agodi
- Department GF Ingrassia, University of Catania, Catania, Italy
- * E-mail: (AA); (MV)
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49
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Baulcombe DC, Dean C. Epigenetic regulation in plant responses to the environment. Cold Spring Harb Perspect Biol 2014; 6:a019471. [PMID: 25183832 DOI: 10.1101/cshperspect.a019471] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications. Heritable epigenetic marks may result in heritable phenotypic variation, influencing fitness, and so be subject to natural selection. However, unlike genetic inheritance, the epigenetic modifications show instability and are influenced by the environment. These two case histories are then compared with other phenomena in plant biology that are likely to represent epigenetic regulation in response to the environment.
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Affiliation(s)
- David C Baulcombe
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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50
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Moarii M, Pinheiro A, Sigal-Zafrani B, Fourquet A, Caly M, Servant N, Stoven V, Vert JP, Reyal F. Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences. PLoS One 2014; 9:e103986. [PMID: 25098247 PMCID: PMC4123987 DOI: 10.1371/journal.pone.0103986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/04/2014] [Indexed: 01/19/2023] Open
Abstract
Introduction Epigenetic modifications such as aberrant DNA methylation has long been associated with tumorogenesis. Little is known, however, about how these modifications appear in cancer progression. Comparing the methylome of breast carcinomas and locoregional evolutions could shed light on this process. Methods The methylome profiles of 48 primary breast carcinomas (PT) and their matched axillary metastases (PT/AM pairs, 20 cases), local recurrences (PT/LR pairs, 17 cases) or contralateral breast carcinomas (PT/CL pairs, 11 cases) were analyzed. Univariate and multivariate analyzes were performed to determine differentially methylated probes (DMPs), and a similarity score was defined to compare methylation profiles. Correlation with copy-number based score was calculated and metastatic-free survival was compared between methods. Results 49 DMPs were found for the PT/AM set, but none for the others (FDR ). Hierarchical clustering clustered 75% of the PT/AM, 47% of the PT/LR, and none of the PT/CL pairs together. A methylation-based score (MS) was defined as a clonality measure. The PT/AM set contained a high proportion of clonal pairs while PT/LR pairs were evenly split between high and low MS score, suggesting two groups: true recurrences (TR) and new primary tumors (NP). CL were classified as new tumors. MS score was significantly correlated with copy-number based scores. There was no significant difference between the metastatic-free survival of groups of patients based on different classifications. Conclusion Epigenomic alterations are well suited to study clonality and track cancer progression. Methylation-based classification of TR and NP performed as well as clinical and copy-number based methods suggesting that these phenomenons are tightly linked.
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Affiliation(s)
- Matahi Moarii
- Centre for Computational Biology, Mines ParisTech, Fontainebleau, France
- Institut Curie, Paris, France
- U900, INSERM, Paris, France
| | - Alice Pinheiro
- UMR144, Oncology Molecular Team, Institut Curie, Paris, France
- Department of translational research, Residual Tumor and Response to Treatment Team, Institut Curie, Paris, France
| | | | - Alain Fourquet
- Department of Radiotherapy, Institut Curie, Paris, France
| | - Martial Caly
- Department of Tumor Biology, Institut Curie, Paris, France
| | - Nicolas Servant
- Centre for Computational Biology, Mines ParisTech, Fontainebleau, France
- Institut Curie, Paris, France
- U900, INSERM, Paris, France
| | - Véronique Stoven
- Centre for Computational Biology, Mines ParisTech, Fontainebleau, France
- Institut Curie, Paris, France
- U900, INSERM, Paris, France
| | - Jean-Philippe Vert
- Centre for Computational Biology, Mines ParisTech, Fontainebleau, France
- Institut Curie, Paris, France
- U900, INSERM, Paris, France
| | - Fabien Reyal
- UMR144, Oncology Molecular Team, Institut Curie, Paris, France
- Department of translational research, Residual Tumor and Response to Treatment Team, Institut Curie, Paris, France
- Department of Surgery, Institut Curie, Paris, France
- * E-mail:
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