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Vatanmakanian M, Tavallaie M, Ghadami S. Imatinib independent aberrant methylation of NOV/CCN3 in chronic myelogenous leukemia patients: a mechanism upstream of BCR-ABL1 function? Cell Commun Signal 2019; 17:38. [PMID: 31014357 PMCID: PMC6480731 DOI: 10.1186/s12964-019-0350-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Background The NOV gene product, CCN3, has been reported in a diverse range of tumors to serve as a negative growth regulator, while acting as a tumor suppressor in Chronic Myelogenous Leukemia (CML). However, the precise mechanism of its silencing in CML is poorly understood. In the current study, we aimed to query if the gene regulation of CCN3 is mediated by the promoter methylation in the patients with CML. In addition, to clarify whether the epigenetic silencing is affected by BCR-ABL1 inhibition, we assessed the methylation status in the patients at different time intervals following the tyrosine kinase inhibition using imatinib therapy, as the first-line treatment for this type of leukemia. Methods To address this issue, we applied bisulfite-sequencing technique as a high-resolution method to study the regulatory segment of the CCN3 gene. The results were analyzed in newly diagnosed CML patients as well as following imatinib therapy. We also evaluated the correlation of CCN3 promoter methylation with BCR-ABL1 levels. Results Our findings revealed that the methylation occurs frequently in the promoter region of CML patients showing a significant increase of the methylated percentage at the CpG sites compared to normal individuals. Interestingly, this hypermethylation was indicated to be independent of BCR-ABL1 titers in both groups, which might suggest a mechanism beyond the BCR-ABL1 function. Conclusion Despite suggesting that the CCN3 hypermethylation acts as a molecular mechanism independent of BCR-ABL1 function in CML patients, this scenario requires further validation by complementary experiments. In the case of acting upstream of BCR-ABL1 signaling, the methylation marker can provide early detection and a novel platform for targeted epigenetic modifiers for efficient treatment in imatinib resistant patients.
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Affiliation(s)
- Mousa Vatanmakanian
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran
| | - Mahmood Tavallaie
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran
| | - Shirin Ghadami
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran.
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102
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Methylation of SPARCL1 Is Associated with Oncologic Outcome of Advanced Upper Urinary Tract Urothelial Carcinoma. Int J Mol Sci 2019; 20:ijms20071653. [PMID: 30987093 PMCID: PMC6480388 DOI: 10.3390/ijms20071653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022] Open
Abstract
Advanced upper urinary tract urothelial carcinoma (UTUC) is often associated with poor oncologic outcomes. The secreted protein acidic and rich in cysteine-like 1 (SPARCL1) protein, belongs to the SPARC-related family of matricellular proteins. Much literature has been published describing the role of SPARCL1 in the prognosis many cancers. In this study, methylated promoter regions in high-grade and high-stage upper urinary urothelial tumours compared with normal urothelium were analyzed and revealed that SPARCL1 was the most significantly hypermethylated gene in UTUC tissues. Then we prospectively collected UTUC samples and adjacent normal urothelium for pyrosequencing validation, identifying significant CpG site methylation in UTUC tissues. In addition, SPARCL1 RNA levels were significantly lower in UTUC samples. Multivariate Cox regression analysis from 78 patients with solitary renal pelvic or ureteral pT3N0M0 urothelial carcinomas revealed that only negative SPARCL1 expression and nonpapillary tumour architecture were independently associated with systemic recurrence (p = 0.011 and 0.008, respectively). In vitro studies revealed that the behaviour of BFTC-909 cells was less aggressive and more sensitive to radiation or chemotherapy after SPARCL1 overexpression. Thus, SPARCL1 could be considered as a prognostic marker and help decision-making in clinical practice.
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103
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Klein CB. Emerging confluences of epigenetics and DNA repair in cancer and disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2019; 780:11-14. [PMID: 31395354 DOI: 10.1016/j.mrrev.2019.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Catherine B Klein
- Department of Environmental Medicine, NYU School of Medicine, 341 East 25 Street, New York, NY, 10010, United States.
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104
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Zeng Y, Chen T. DNA Methylation Reprogramming during Mammalian Development. Genes (Basel) 2019; 10:E257. [PMID: 30934924 PMCID: PMC6523607 DOI: 10.3390/genes10040257] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methylation (5-methylcytosine, 5mC) is a major form of DNA modification in the mammalian genome that plays critical roles in chromatin structure and gene expression. In general, DNA methylation is stably maintained in somatic tissues. However, DNA methylation patterns and levels show dynamic changes during development. Specifically, the genome undergoes two waves of global demethylation and remethylation for the purpose of producing the next generation. The first wave occurs in the germline, initiated with the erasure of global methylation in primordial germ cells (PGCs) and completed with the establishment of sex-specific methylation patterns during later stages of germ cell development. The second wave occurs after fertilization, including the erasure of most methylation marks inherited from the gametes and the subsequent establishment of the embryonic methylation pattern. The two waves of DNA methylation reprogramming involve both distinct and shared mechanisms. In this review article, we provide an overview of the key reprogramming events, focusing on the important players in these processes, including DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) family of 5mC dioxygenases.
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Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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105
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Fu Y, Zhang L, Zhang R, Xu S, Wang H, Jin Y, Wu Z. Enterovirus 71 Suppresses miR-17-92 Cluster Through Up-Regulating Methylation of the miRNA Promoter. Front Microbiol 2019; 10:625. [PMID: 30984146 PMCID: PMC6447709 DOI: 10.3389/fmicb.2019.00625] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
Enterovirus 71 (EV71), the etiological agent of hand-foot-and-mouth disease, has become an increasing public health challenge worldwide. Accumulating evidence suggests that mammalian microRNAs (miRNAs), a class of non-coding RNAs of 18 to 24 nucleotides (nt) with important regulatory roles in cellular processes, participate in host antiviral defense and studies have suggested roles of miRNAs in EV71 replication and pathogenesis. In the current study, we reported that the expression of hsa-miR-17∼92 cluster was significantly downregulated during EV71 infection. Overexpression of hsa-miR-17∼92 inhibited, while inhibition of endogenous hsa-miR-17∼92 facilitated EV71 replication. We identified two sequences located at nt 3024 to 3038 and nt 2838 to 2862 of the EV71 (strain FY0805) genome as potential targets for hsa-miR-17-5p and miR-19a/b, respectively, which were validated by luciferase reporter assays and Western blot. Meanwhile, we identified DNA methylation as a novel mechanism of hsa-miR-17∼92 regulatory roles. The methylation of the miR-17-92 promoter was significantly increased (50%) upon EV71 infection, which appeared to be caused by the increased expression of DNMT3B but not DNMT1 and DNMT3A. Furthermore, we demonstrated that the members of miR-17-92 cluster were decreased in the sera of EV71 infected patients, suggesting the clinical implication and the potential therapeutic application of miR-17-92.
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Affiliation(s)
- Yuxuan Fu
- School of Life Sciences, Ningxia University, Yinchuan, China.,Center for Public Health Research, Medical School of Nanjing University, Nanjing, China.,Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Li Zhang
- Center for Public Health Research, Medical School of Nanjing University, Nanjing, China
| | - Rui Zhang
- Center for Public Health Research, Medical School of Nanjing University, Nanjing, China
| | - Shijie Xu
- Center for Public Health Research, Medical School of Nanjing University, Nanjing, China
| | - Huanru Wang
- Center for Public Health Research, Medical School of Nanjing University, Nanjing, China
| | - Yu Jin
- Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Zhiwei Wu
- School of Life Sciences, Ningxia University, Yinchuan, China.,Center for Public Health Research, Medical School of Nanjing University, Nanjing, China.,The State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, Nanjing, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
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106
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Stefan-Lifshitz M, Karakose E, Cui L, Ettela A, Yi Z, Zhang W, Tomer Y. Epigenetic modulation of β cells by interferon-α via PNPT1/mir-26a/TET2 triggers autoimmune diabetes. JCI Insight 2019; 4:126663. [PMID: 30721151 DOI: 10.1172/jci.insight.126663] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Type 1 diabetes (T1D) is caused by autoimmune destruction of pancreatic β cells. Mounting evidence supports a central role for β cell alterations in triggering the activation of self-reactive T cells in T1D. However, the early deleterious events that occur in β cells, underpinning islet autoimmunity, are not known. We hypothesized that epigenetic modifications induced in β cells by inflammatory mediators play a key role in initiating the autoimmune response. We analyzed DNA methylation (DNAm) patterns and gene expression in human islets exposed to IFN-α, a cytokine associated with T1D development. We found that IFN-α triggers DNA demethylation and increases expression of genes controlling inflammatory and immune pathways. We then demonstrated that DNA demethylation was caused by upregulation of the exoribonuclease, PNPase old-35 (PNPT1), which caused degradation of miR-26a. This in turn promoted the upregulation of ten-eleven translocation 2 (TET2) enzyme and increased 5-hydroxymethylcytosine levels in human islets and pancreatic β cells. Moreover, we showed that specific IFN-α expression in the β cells of IFNα-INS1CreERT2 transgenic mice led to development of T1D that was preceded by increased islet DNA hydroxymethylation through a PNPT1/TET2-dependent mechanism. Our results suggest a new mechanism through which IFN-α regulates DNAm in β cells, leading to changes in expression of genes in inflammatory and immune pathways that can initiate islet autoimmunity in T1D.
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Affiliation(s)
- Mihaela Stefan-Lifshitz
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Lingguang Cui
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | - Abora Ettela
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | - Zhengzi Yi
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Weijia Zhang
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yaron Tomer
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
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Abstract
The prevalence of insulin resistance (IR) is increasing rapidly worldwide and it is a relevant health problem because it is associated with several diseases, such as type 2 diabetes, cardiovascular disorders and cancer. Understanding the mechanisms involved in IR onset and progression will open new avenues for identifying biomarkers for preventing and treating IR and its co-diseases. Epigenetic mechanisms such as DNA methylation are important factors that mediate the environmental effect in the genome by regulating gene expression and consequently its effect on the phenotype and the development of disease. Taking into account that IR results from a complex interplay between genes and the environment and that epigenetic marks are reversible, disentangling the relationship between IR and epigenetics will provide new tools to improve the management and prevention of IR. Here, we review the current scientific evidence regarding the association between IR and epigenetic markers as mechanisms involved in IR development and potential management.
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Affiliation(s)
- Andrea G Izquierdo
- Epigenomics in Endocrinology and Nutrition group, Instituto de Investigacion Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), C/ Choupana, s/n, 15706, Santiago de Compostela, Spain
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition group, Instituto de Investigacion Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), C/ Choupana, s/n, 15706, Santiago de Compostela, Spain.
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.
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108
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Peer Victimization and Adjustment in Young Adulthood: Introduction to the Special Section. JOURNAL OF ABNORMAL CHILD PSYCHOLOGY 2019; 46:5-9. [PMID: 28936797 DOI: 10.1007/s10802-017-0347-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A substantive number of children and adolescents are bullied by their peers, with serious risks for the victims' emotional, behavioral, physical, and academic adjustment. However, while the immediate and short-term consequences of peer victimization in childhood and adolescence are very well documented, knowledge about the potential long-term consequences for victims' functioning once they reach adulthood is only slowly emerging. Based on prospective, longitudinal data from different countries, the 4 papers in this special section investigate the association between peer victimization suffered in childhood and adolescence and victims' developmental outcomes in late adolescence/early adulthood. This introduction highlights the major findings of each paper and discusses the implications for future research.
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109
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Xie J, Chen J, Wang B, He X, Huang H. Bone mesenchymal stromal cells exhibit functional inhibition but no chromosomal aberrations in chronic myelogenous leukemia. Oncol Lett 2019; 17:999-1007. [PMID: 30655859 PMCID: PMC6312938 DOI: 10.3892/ol.2018.9681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
Abstract
Chronic myelogenous leukemia (CML) is a myeloproliferative neoplasia characterized by the presence of the Philadelphia (Ph) chromosome in hematopoietic cells (HCs). As one of the most important components of the bone marrow microenvironment (BMM), bone mesenchymal stromal cells (BMSCs) are critical in the development of leukemia and essential in the regulation of hematopoiesis. However, little is known regarding the alterations of BMSCs in CML. The current study performed Cell Counting Kit-8 and colony-forming unit fibroblast assays to evaluate the proliferative ability of BMSCs. The percentage of senescent BMSCs was evaluated by a senescence-associated β-galactosidase staining assay. Subsequently, a long-term culture-initiating cell assay was designed to explore the HC-supporting capacity of the BMSCs. Furthermore, cytogenetics were detected by conventional cytogenetic analysis and fluorescence in situ hybridization analysis. The current results revealed that CML-BMSCs exhibited decreased cell proliferation and impaired HC-support capacity, as well as increased susceptibility to senescence. No chromosomal aberrations, including the absence of the Ph chromosome, were noted in all CML-BMSCs. In conclusion, the current study demonstrated functional inhibition of CML-BMSCs; however, no signs of chromosomal aberrations were observed, thereby providing insight into the changes occurring in the CML-BMM.
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Affiliation(s)
- Jieqiong Xie
- Central Laboratory, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jiadi Chen
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Bin Wang
- Central Laboratory, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Xuchun He
- Department of Medical Technology, Fujian Health Career Technical College, Fuzhou, Fujian 350101, P.R. China
| | - Huifang Huang
- Central Laboratory, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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110
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Chen X, Hua W, Huang X, Chen Y, Zhang J, Li G. Regulatory Role of RNA N 6-Methyladenosine Modification in Bone Biology and Osteoporosis. Front Endocrinol (Lausanne) 2019; 10:911. [PMID: 31998240 PMCID: PMC6965011 DOI: 10.3389/fendo.2019.00911] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/13/2019] [Indexed: 12/26/2022] Open
Abstract
Osteoporosis is a metabolic skeletal disorder in which bone mass is depleted and bone structure is destroyed to the degree that bone becomes fragile and prone to fractures. Emerging evidence suggests that N6-methyladenosine (m6A) modification, a novel epitranscriptomic marker, has a significant role in bone development and metabolism. M6A modification not only participates in bone development, but also plays important roles as writers and erasers in the osteoporosis. M6A methyltransferase METTL3 and demethyltransferase FTO involves in the delicate process between adipogenesis differentiation and osteogenic differentiation, which is important for the pathological development of osteoporosis. Conditional knockdown of the METTL3 in bone marrow stem cells (BMSCs) could suppress PI3K-Akt signaling, limit the expression of bone formation-related genes (such as Runx2 and Osterix), restrain the expression of vascular endothelial growth factor (VEGF) and down-regulate the decreased translation efficiency of parathyroid hormone receptor-1 mRNA. Meanwhile, knockdown of the METTL3 significantly promoted the adipogenesis process and janus kinase 1 (JAK1) protein expression via an m6A-dependent way. Specifically, there was a negative correlation between METTL3 expression and porcine BMSCs adipogenesis. The evidence above suggested that the relationship between METTL3 expression and adipogenesis was inverse, and osteogenesis was positive, respectively. Similarly, FTO regulated for BMSCs fate determination during osteoporosis through the GDF11-FTO-PPARγ axis, prompting the shift of MSC lineage commitment to adipocyte and inhibiting bone formation during osteoporosis. In this systematic review, we summarize the most up-to-date evidence of m6A RNA modification in osteoporosis and highlight the potential role of m6A in prevention, treatment, and management of osteoporosis.
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Affiliation(s)
- Xuejiao Chen
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Wenfeng Hua
- Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xin Huang
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yuming Chen
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Junguo Zhang
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Guowei Li
- Center for Clinical Epidemiology and Methodology (CCEM), Guangdong Second Provincial General Hospital, Guangzhou, China
- Department of Health Research Methods, Evidence, and Impact (HEI), McMaster University, Hamilton, ON, Canada
- *Correspondence: Guowei Li
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111
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Coppedè F, Seghieri M, Stoccoro A, Santini E, Giannini L, Rossi C, Migliore L, Solini A. DNA methylation of genes regulating appetite and prediction of weight loss after bariatric surgery in obese individuals. J Endocrinol Invest 2019; 42:37-44. [PMID: 29603098 DOI: 10.1007/s40618-018-0881-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/25/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Epigenetic traits are influenced by clinical variables; interaction between DNA methylation (DNAmeth) and bariatric surgery-induced weight loss has been scarcely explored. We investigated whether DNAmeth of genes encoding for molecules/hormones regulating appetite, food intake or obesity could predict successful weight outcome following Roux-en-Y gastric bypass (RYGB). METHODS Forty-five obese individuals with no known comorbidities were stratified accordingly to weight decrease one-year after RYGB (excess weight loss, EWL ≥ 50%: good responders, GR; EWL < 50%: worse responders, WR). DNAmeth of leptin (LEP), ghrelin (GHRL), ghrelin receptor (GHSR) and insulin-growth factor-2 (IGF2) was assessed before intervention. Single nucleotide polymorphisms of genes affecting DNAmeth, DNMT3A and DNMT3B, were also determined. RESULTS At baseline, type 2 diabetes was diagnosed by OGTT in 13 patients. Post-operatively, GR (n = 23) and WR (n = 22) achieved an EWL of 67.7 ± 9.6 vs 38.2 ± 9.0%, respectively. Baseline DNAmeth did not differ between GR and WR for any tested genes, even when the analysis was restricted to subjects with no diabetes. A relationship between GHRL and LEP methylation profiles emerged (r = 0.47, p = 0.001). Searching for correlation between DNAmeth of the studied genes with demographic characteristics and baseline biochemical parameters of the studied population, we observed a correlation between IGF2 methylation and folate (r = 0.44, p = 0.003). Rs11683424 for DNMT3A and rs2424913 for DNMT3B did not correlate with DNAmeth of the studied genes. CONCLUSIONS In severely obese subjects, the degree of DNAmeth of some genes affecting obesity and related conditions does not work as predictor of successful response to RYGB.
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Affiliation(s)
- F Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - M Seghieri
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - A Stoccoro
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - E Santini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Giannini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - C Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Migliore
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A Solini
- Department of Surgical, Medical, Molecular and Critical Area Pathology, University of Pisa, Via Roma 67, 56126, Pisa, Italy.
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112
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Chen N, Zhao G, Yan X, Lv Z, Yin H, Zhang S, Song W, Li X, Li L, Du Z, Jia L, Zhou L, Li W, Hoffman AR, Hu JF, Cui J. A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1. Genome Biol 2018; 19:218. [PMID: 30537986 PMCID: PMC6290540 DOI: 10.1186/s13059-018-1594-y] [Citation(s) in RCA: 287] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/23/2018] [Indexed: 01/10/2023] Open
Abstract
Background Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. However, little is known about the mechanisms underlying the activation of this proto-oncogene in tumors. Results Immunohistochemical staining showed that FLI1 is aberrantly overexpressed in advanced stage and metastatic breast cancers. Using a CRISPR Cas9-guided immunoprecipitation assay, we identify a circular RNA in the FLI1 promoter chromatin complex, consisting of FLI1 exons 4-2-3, referred to as FECR1.Overexpression of FECR1 enhances invasiveness of MDA-MB231 breast cancer cells. Notably, FECR1 utilizes a positive feedback mechanism to activate FLI1 by inducing DNA hypomethylation in CpG islands of the promoter. FECR1 binds to the FLI1 promoter in cis and recruits TET1, a demethylase that is actively involved in DNA demethylation. FECR1 also binds to and downregulates in trans DNMT1, a methyltransferase that is essential for the maintenance of DNA methylation. Conclusions These data suggest that FECR1 circular RNA acts as an upstream regulator to control breast cancer tumor growth by coordinating the regulation of DNA methylating and demethylating enzymes. Thus, FLI1 drives tumor metastasis not only through the canonical oncoprotein pathway, but also by using epigenetic mechanisms mediated by its exonic circular RNA. Electronic supplementary material The online version of this article (10.1186/s13059-018-1594-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naifei Chen
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Gang Zhao
- Department of Breast Cancer Surgery, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Xu Yan
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Zheng Lv
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Hongmei Yin
- Department of General Internal Medicine, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Shilin Zhang
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Wei Song
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Xueli Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Lingyu Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Zhonghua Du
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Lin Jia
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Lei Zhou
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Wei Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Andrew R Hoffman
- Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China. .,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA.
| | - Jiuwei Cui
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.
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Shafabakhsh R, Aghadavod E, Ghayour‐Mobarhan M, Ferns G, Asemi Z. Role of histone modification and DNA methylation in signaling pathways involved in diabetic retinopathy. J Cell Physiol 2018; 234:7839-7846. [DOI: 10.1002/jcp.27844] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
| | - Esmat Aghadavod
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
| | - Majid Ghayour‐Mobarhan
- Metabolic Syndrome Research Center School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Gordon Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton UK
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
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114
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. The influence of CpG (5'-d(CpG)-3' dinucleotides) methylation on ultrasonic DNA fragmentation. J Biomol Struct Dyn 2018; 37:3877-3886. [PMID: 30351231 DOI: 10.1080/07391102.2018.1533888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
DNA methylation is an important way of gene regulation. The variety of methods for DNA methylation analysis based on chemical modification or enzyme digestion has been proposed. However, DNA is able to undergo transformations under physical power. Here, we report that the cytosine methylation in CpG dinucleotides determines the difference in fragmentation rate of methylated and unmethylated DNA under sonication. We found that at the beginning of sonication, methylated DNAs are degraded faster than unmethylated one, and the difference in fragmentation degree can be evaluated with high reliability by quantitative polymerase chain reaction (qPCR). The optimal parameters that provide the greatest difference in amount of amplifiable DNA targets corresponding to fragmentation degree are the following: moderate amplicon size (about 150-250 bp), medium CpG sparseness (one CpG dinucleotide per ∼12-14 nucleotides of the chain), and short sonication time (less than 5 min). Along with CpG, the CpA and CpT contents of amplified regions should be taken into account for proper DNA fragmentation by ultrasound as well. The obtained data could be used for elaboration of a method for comparative methylation testing, when there is no need to detect methylation of certain CpG dinucleotides. This method will be simple (can be used by any technician familiar with PCR), low cost (no need to use an expensive reagents), and fast (only brief DNA sonication and conventional qPCR are carried out). Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravil R Garafutdinov
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
| | - Aizilya A Galimova
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
| | - Assol R Sakhabutdinova
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
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115
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Zhang Y, Charlton J, Karnik R, Beerman I, Smith ZD, Gu H, Boyle P, Mi X, Clement K, Pop R, Gnirke A, Rossi DJ, Meissner A. Targets and genomic constraints of ectopic Dnmt3b expression. eLife 2018; 7:e40757. [PMID: 30468428 PMCID: PMC6251628 DOI: 10.7554/elife.40757] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
DNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer types, yet little is known about its ectopic genomic targets. Here, we used an inducible transgenic mouse model to delineate rules for abnormal DNMT3B targeting, as well as the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpG islands to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually non-overlapping at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation. Our genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a distributive activity of ectopically expressed Dnmt3b that leads to discordant CpG island hypermethylation and provides new insights for interpreting the cancer methylome.
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Affiliation(s)
- Yingying Zhang
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Rahul Karnik
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Isabel Beerman
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of PediatricsHarvard Medical SchoolMassachusettsUnited States
- Program in Cellular and Molecular Medicine, Division of Hematology/OncologyBoston Children's HospitalMassachusettsUnited States
| | - Zachary D Smith
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Hongcang Gu
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Patrick Boyle
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Xiaoli Mi
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Kendell Clement
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Ramona Pop
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Andreas Gnirke
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of PediatricsHarvard Medical SchoolMassachusettsUnited States
- Program in Cellular and Molecular Medicine, Division of Hematology/OncologyBoston Children's HospitalMassachusettsUnited States
| | - Alexander Meissner
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
- Broad Institute of MIT and HarvardMassachusettsUnited States
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116
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Emperle M, Dukatz M, Kunert S, Holzer K, Rajavelu A, Jurkowska RZ, Jeltsch A. The DNMT3A R882H mutation does not cause dominant negative effects in purified mixed DNMT3A/R882H complexes. Sci Rep 2018; 8:13242. [PMID: 30185810 PMCID: PMC6125428 DOI: 10.1038/s41598-018-31635-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/23/2018] [Indexed: 12/17/2022] Open
Abstract
The DNA methyltransferase DNMT3A R882H mutation is observed in 25% of all AML patients. DNMT3A is active as tetramer and the R882H mutation is located in one of the subunit/subunit interfaces. Previous work has reported that formation of mixed wildtype/R882H complexes leads to a strong loss of catalytic activity observed in in vitro DNA methylation assays (Russler-Germain et al., 2014, Cancer Cell 25:442–454). To investigate this effect further, we have prepared mixed wildtype/R882H DNMT3A complexes by incubation of individually purified subunits of the DNMT3A catalytic domain and full-length DNMT3A2. In addition, we have used a double affinity tag approach and specifically purified mixed catalytic domain complexes formed after co-expression of R882H and wildtype subunits in E. coli cells. Afterwards, we determined the catalytic activity of the mixed complexes and compared it to that of purified complexes only consisting of one subunit type. In both settings, the expected catalytic activities of mixed R882H/wildtype complexes were observed demonstrating an absence of a dominant negative effect of the R882H mutation in purified DNMT3A enzymes. This result suggests that heterocomplex formation of DNMT3A and R882H is unlikely to cause dominant negative effects in human cells as well. The limitations of this conclusion and its implications are discussed.
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Affiliation(s)
- Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stefan Kunert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Katharina Holzer
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,Rajiv Gandhi Center for Biotechnology (RGCB), Trivandrum, 695014, Kerala, India
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120, Heidelberg, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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117
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Atdjian C, Iannazzo L, Braud E, Ethève-Quelquejeu M. Synthesis of SAM-Adenosine Conjugates for the Study of m 6
A-RNA Methyltransferases. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
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118
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Norvil AB, Petell CJ, Alabdi L, Wu L, Rossie S, Gowher H. Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry 2018; 57:4312-4324. [PMID: 27768276 PMCID: PMC5992102 DOI: 10.1021/acs.biochem.6b00964] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catalytic domains of the de novo DNA methyltransferases Dnmt3a-C and Dnmt3b-C are highly homologous. However, their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to the case for processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule; however, it is unclear whether Dnmt3b-C methylates DNA by a cooperative or processive mechanism. The importance of the tetramer structure and cooperative mechanism is emphasized by the observation that the R882H mutation in the dimer interface of DNMT3A is highly prevalent in acute myeloid leukemia and leads to a substantial loss of its activity. Under conditions that distinguish between cooperativity and processivity, we show that in contrast to that of Dnmt3a-C, the activity of Dnmt3b-C is not cooperative and confirm the processivity of Dnmt3b-C and the full length Dnmt3b enzyme. Whereas the R878H mutation (mouse homologue of R882H) led to the loss of cooperativity of Dnmt3a-C, the activity and processivity of the analogous Dnmt3b-C R829H variant were comparable to those of the wild-type enzyme. Additionally, buffer acidification that attenuates the dimer interface interactions of Dnmt3a-C had no effect on Dnmt3b-C activity. Taken together, these results demonstrate an important mechanistic difference between Dnmt3b and Dnmt3a and suggest that interactions at the dimer interface may play a limited role in regulating Dnmt3b-C activity. These new insights have potential implications for the distinct biological roles of Dnmt3a and Dnmt3b.
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Affiliation(s)
- Allison B. Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher J. Petell
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lama Alabdi
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lanchen Wu
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sandra Rossie
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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119
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May S, Owen H, Phesse TJ, Greenow KR, Jones G, Blackwood A, Cook PC, Towers C, Gallimore AM, Williams GT, Stürzl M, Britzen‐Laurent N, Sansom OJ, MacDonald AS, Bird AP, Clarke AR, Parry L. Mbd2 enables tumourigenesis within the intestine while preventing tumour-promoting inflammation. J Pathol 2018; 245:270-282. [PMID: 29603746 PMCID: PMC6032908 DOI: 10.1002/path.5074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 01/14/2023]
Abstract
Epigenetic regulation plays a key role in the link between inflammation and cancer. Here we examine Mbd2, which mediates epigenetic transcriptional silencing by binding to methylated DNA. In separate studies the Mbd2-/- mouse has been shown (1) to be resistant to intestinal tumourigenesis and (2) to have an enhanced inflammatory/immune response, observations that are inconsistent with the links between inflammation and cancer. To clarify its role in tumourigenesis and inflammation, we used constitutive and conditional models of Mbd2 deletion to explore its epithelial and non-epithelial roles in the intestine. Using a conditional model, we found that suppression of intestinal tumourigenesis is due primarily to the absence of Mbd2 within the epithelia. Next, we demonstrated, using the DSS colitis model, that non-epithelial roles of Mbd2 are key in preventing the transition from acute to tumour-promoting chronic inflammation. Combining models revealed that prior to inflammation the altered Mbd2-/- immune response plays a role in intestinal tumour suppression. However, following inflammation the intestine converts from tumour suppressive to tumour promoting. To summarise, in the intestine the normal function of Mbd2 is exploited by cancer cells to enable tumourigenesis, while in the immune system it plays a key role in preventing tumour-enabling inflammation. Which role is dominant depends on the inflammation status of the intestine. As environmental interactions within the intestine can alter DNA methylation patterns, we propose that Mbd2 plays a key role in determining whether these interactions are anti- or pro-tumourigenic and this makes it a useful new epigenetic model for inflammation-associated carcinogenesis. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Stephanie May
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Heather Owen
- Wellcome Trust Centre for Cell BiologyUniversity of Edinburgh, Michael Swann BuildingEdinburghUK
| | - Toby J Phesse
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Kirsty R Greenow
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Gareth‐Rhys Jones
- Manchester Collaborative Centre for Inflammation ResearchManchesterUK
| | - Adam Blackwood
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Peter C Cook
- Manchester Collaborative Centre for Inflammation ResearchManchesterUK
| | - Christopher Towers
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Awen M Gallimore
- Cardiff Institute of Infection and Immunity, Henry Wellcome BuildingCardiffUK
| | - Geraint T Williams
- Institute of Cancer and GeneticsCardiff University School of MedicineCardiffUK
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of SurgeryFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg and Universitätsklinikum ErlangenErlangenGermany
| | - Nathalie Britzen‐Laurent
- Division of Molecular and Experimental Surgery, Department of SurgeryFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg and Universitätsklinikum ErlangenErlangenGermany
| | | | | | - Adrian P Bird
- Wellcome Trust Centre for Cell BiologyUniversity of Edinburgh, Michael Swann BuildingEdinburghUK
| | - Alan R Clarke
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Lee Parry
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
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120
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Svahn F, Paulsson JO, Stenman A, Fotouhi O, Mu N, Murtha TD, Korah R, Carling T, Bäckdahl M, Wang N, Juhlin CC, Larsson C. TERT promoter hypermethylation is associated with poor prognosis in adrenocortical carcinoma. Int J Mol Med 2018; 42:1675-1683. [PMID: 29956721 DOI: 10.3892/ijmm.2018.3735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/11/2018] [Indexed: 11/05/2022] Open
Abstract
Telomere maintenance, most commonly achieved by telomerase activation through induction of the telomerase reverse transcriptase (TERT) gene, is required for cell immortalization, a hallmark of cancer. Adrenocortical carcinoma (ACC) is an endocrine tumor for which TERT promoter mutations and telomerase activation have been reported. The present study assessed alterations of the TERT gene locus and telomere length in relation to clinical characteristics in ACC. In total, 38 cases of ACC with known TERT promoter mutational status were included. TERT promoter methylation densities were assessed by pyrosequencing, and TERT copy numbers and telomere length were determined by quantitative polymerase chain reaction analysis, followed by comparison of the mRNA expression of TERT and clinical parameters. The ACC tissue samples showed increased TERT copy numbers, compared with normal adrenal tissue (NAT) samples (P=0.001). Mutually exclusive TERT copy number gains or promoter mutation were present in 70% of the ACC samples. The ACC tissues exhibited higher levels of CpG promoter methylation of all eight CpG sites investigated within the ‑578 to ‑541 bp (Region A), compared with the NATs (P=0.001). High methylation density at this region was associated with metastatic disease and/or relapse, poor survival rates and higher European Network for the Study of Adrenal Tumor stage (P<0.05). The mRNA expression of TERT was inversely correlated with methylation density at ‑162 to ‑100 bp (Region B). Correlation was observed between relative telomere length and the gene expression of TERT. It was concluded that epigenetic alterations of the TERT promoter are frequent and associated with advanced disease and poorer clinical outcome in ACC.
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Affiliation(s)
- Fredrika Svahn
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Johan O Paulsson
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Omid Fotouhi
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Ninni Mu
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Timothy D Murtha
- Department of Surgery, Yale School of Medicine, Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT 06520, USA
| | - Reju Korah
- Department of Surgery, Yale School of Medicine, Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT 06520, USA
| | - Tobias Carling
- Department of Surgery, Yale School of Medicine, Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT 06520, USA
| | - Martin Bäckdahl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, SE‑17176 Stockholm, Sweden
| | - Na Wang
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - C Christofer Juhlin
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
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121
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Deobagkar D. Epigenetics with special reference to the human X chromosome inactivation and the enigma of Drosophila DNA methylation. J Genet 2018. [DOI: 10.1007/s12041-018-0937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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122
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Zanger UM, Klein K, Kugler N, Petrikat T, Ryu CS. Epigenetics and MicroRNAs in Pharmacogenetics. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:33-64. [PMID: 29801581 DOI: 10.1016/bs.apha.2018.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Germline pharmacogenetics has so far mainly studied common variants in "pharmacogenes," i.e., genes encoding drug metabolizing enzymes and transporters (DMET genes), certain auxiliary and regulatory genes, and drug target genes. Despite remarkable progress in understanding genetically determined differences in pharmacokinetics and pharmacodynamics of drugs, currently known common variants even in important pharmacogenes explain genetic variability only partially. This suggests "missing heritability" that may in part be due to rare variants in the classical pharmacogenes, but current evidence suggests that largely unexplored resources with potential for pharmacogenetics exist, both within already known pharmacogenes and in entirely new areas. In particular, recent studies suggest that epigenetic processes and noncoding RNAs, including mostly microRNAs (miRNAs), represent important and largely unexplored layers of DMET gene regulation that may fill some of the gaps in understanding interindividual variability and lead to new biomarkers. In this chapter we summarize recent advances in the understanding of genetic variability in epigenetic and miRNA-mediated processes with focus on their significance for DMET regulation and pharmacokinetic or pharmacological endpoints.
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Affiliation(s)
- Ulrich M Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany; University Hospital Tübingen, Tübingen, Germany.
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Nicole Kugler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Tamara Petrikat
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Chang S Ryu
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
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123
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Guan B, Xing Y, Xiong G, Cao Z, Fang D, Li Y, Zhan Y, Peng D, Liu L, Li X, Zhou L. Predictive value of gene methylation for second recurrence following surgical treatment of first bladder recurrence of a primary upper-tract urothelial carcinoma. Oncol Lett 2018; 15:9397-9405. [PMID: 29805663 DOI: 10.3892/ol.2018.8498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
The clinical relevance of aberrant DNA promoter methylation is being increasingly recognized in urothelial carcinoma. The present study was conducted to explore the methylation status of patients with upper-tract urothelial carcinoma (UTUC) who experienced bladder recurrence, and to evaluate the predictive value of gene methylation for second bladder recurrence and tumor progression. A total of 85 patients with primary UTUC, who experienced bladder recurrence after radical nephroureterectomy, were enrolled between January 2001 and December 2013. Using methylation-sensitive polymerase chain reaction, the promoter methylation statuses of 10 genes were analyzed in the bladder tumor specimens. Among the patient group, 32 patients experienced second bladder recurrence, and bladder progression was detected in 16. With the exception of BRCA1, the methylation rate of the majority of genes tended to gradually increase to varying extents with the number of recurrences; a smaller proportion of primary tumors exhibited gene methylation when compared with the first recurrent tumors and second recurrent tumors. Univariate and multivariate Cox regression analyses revealed that unmethylated GDF15 [hazard ratio (HR)=0.36; 95% confidence interval (CI), 0.14-0.92] and methylated VIM (HR=2.91; 95% CI, 1.11-7.61) in the first recurrent bladder tumor, as well as male gender (HR=2.28; 95% CI, 1.06-4.87), first recurrence interval <8 months (HR=2.34; 95% CI, 1.15-4.78) and primary UTUC tumor size ≥5 cm (HR=3.48; 95% CI, 1.43-8.45) were independent risk factors for a second bladder recurrence after surgery for the first bladder recurrence; the Harrell's concordance index (c-index) for the related nomogram was 0.71 (95% CI: 0.61-0.81). Furthermore, methylated CDH1 (HR=2.91; 95% CI, 1.08-7.77) and VIM (HR=4.91; 95% CI, 1.11-21.7) in the first recurrent bladder tumor, male gender (HR=3.6; 95% CI, 1.1-11.73), and primary tumor stage T2-T4 (HR=4.57; 95% CI, 1.22-17.13), multifocality (HR=3.64; 95% CI, 1.19-11.16) and size ≥5 cm (HR=3.1; 95% CI, 1.91-10.54) for the primary UTUC were considered to be predictors of tumor progression; the c-index for the nomogram was 0.88 (95% CI, 0.69-0.92). The present findings demonstrated that promoter methylation of cancer-related genes was frequently observed in patients with urothelial carcinoma, and that the gene methylation rate of certain genes tended to gradually increase with the number of bladder recurrences. This may be used as a predictive factor for a second bladder recurrence and tumor progression after the surgical treatment of the first bladder recurrence.
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Affiliation(s)
- Bao Guan
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Yunchao Xing
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Gengyan Xiong
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Zhenpeng Cao
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Dong Fang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Yifan Li
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Yonghao Zhan
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Ding Peng
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Libo Liu
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, P.R. China
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Zhu Y, Lu H, Zhang D, Li M, Sun X, Wan L, Yu D, Tian Y, Jin H, Lin A, Gao F, Lai M. Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer. Clin Epigenetics 2018; 10:30. [PMID: 29507648 PMCID: PMC5833094 DOI: 10.1186/s13148-018-0458-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/14/2018] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification, associated with gene expression. 5-Methylcytosine and 5-hydroxymethylcytosine are two epigenetic hallmarks that maintain the equilibrium of epigenetic reprogramming. Disequilibrium in genomic methylation leads to carcinogenesis. The purpose of this study was to elucidate the epigenetic mechanisms of DNA methylation and hydroxymethylation in the carcinogenesis of colorectal cancer. Methods Genome-wide patterns of DNA methylation and hydroxymethylation in six paired colorectal tumor tissues and corresponding normal tissues were determined using immunoprecipitation and sequencing. Transcriptional expression was determined by RNA sequencing (RNA-Seq). Groupwise differential methylation regions (DMR), differential hydroxymethylation regions (DhMR), and differentially expressed gene (DEG) regions were identified. Epigenetic biomarkers were screened by integrating DMR, DhMR, and DEGs and confirmed using functional analysis. Results We identified a genome-wide distinct hydroxymethylation pattern that could be used as an epigenetic biomarker for clearly differentiating colorectal tumor tissues from normal tissues. We identified 59,249 DMRs, 187,172 DhMRs, and 948 DEGs by comparing between tumors and normal tissues. After cross-matching genes containing DMRs or DhMRs with DEGs, we screened seven genes that were aberrantly regulated by DNA methylation in tumors. Furthermore, hypermethylation of the HADHB gene was persistently found to be correlated with downregulation of its transcription in colorectal cancer (CRC). These findings were confirmed in other patients of colorectal cancer. Tumor functional analysis indicated that HADHB reduced cancer cell migration and invasiveness. These findings suggested its possible role as a tumor suppressor gene (TSG). Conclusion This study reveals the global patterns of methylation and hydroxymethylation in CRC. Several CRC-associated genes were screened with multi-omic analysis. Aberrant methylation and hydroxymethylation were found to be in the carcinogenesis of CRC. Electronic supplementary material The online version of this article (10.1186/s13148-018-0458-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yimin Zhu
- 1Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, Hangzhou, 310058 China
| | - Hanlin Lu
- 2BGI-Shenzhen, Shenzhen, 518083 China.,3Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Dandan Zhang
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Meiyan Li
- 2BGI-Shenzhen, Shenzhen, 518083 China
| | - Xiaohui Sun
- 1Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, Hangzhou, 310058 China
| | - Ledong Wan
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Dan Yu
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Yiping Tian
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Hongchuan Jin
- 5Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Runrun Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Aifen Lin
- Human Tissue Bank/Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang 317000 China
| | - Fei Gao
- 2BGI-Shenzhen, Shenzhen, 518083 China.,3Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Maode Lai
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China.,7Department of Pathology, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Zhejiang, Hangzhou 310058 China
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125
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Stalman SE, Solanky N, Ishida M, Alemán-Charlet C, Abu-Amero S, Alders M, Alvizi L, Baird W, Demetriou C, Henneman P, James C, Knegt LC, Leon LJ, Mannens MMAM, Mul AN, Nibbering NA, Peskett E, Rezwan FI, Ris-Stalpers C, van der Post JAM, Kamp GA, Plötz FB, Wit JM, Stanier P, Moore GE, Hennekam RC. Genetic Analyses in Small-for-Gestational-Age Newborns. J Clin Endocrinol Metab 2018; 103:917-925. [PMID: 29342293 DOI: 10.1210/jc.2017-01843] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
Abstract
CONTEXT Small for gestational age (SGA) can be the result of fetal growth restriction, which is associated with perinatal morbidity and mortality. Mechanisms that control prenatal growth are poorly understood. OBJECTIVE The aim of the current study was to gain more insight into prenatal growth failure and determine an effective diagnostic approach in SGA newborns. We hypothesized that one or more copy number variations (CNVs) and disturbed methylation and sequence variants may be present in genes associated with fetal growth. DESIGN A prospective cohort study of subjects with a low birth weight for gestational age. SETTING The study was conducted at an academic pediatric research institute. PATIENTS A total of 21 SGA newborns with a mean birth weight below the first centile and a control cohort of 24 appropriate-for-gestational-age newborns were studied. INTERVENTIONS Array comparative genomic hybridization, genome-wide methylation studies, and exome sequencing were performed. MAIN OUTCOME MEASURES The numbers of CNVs, methylation disturbances, and sequence variants. RESULTS The genetic analyses demonstrated three CNVs, one systematically disturbed methylation pattern, and one sequence variant explaining SGA. Additional methylation disturbances and sequence variants were present in 20 patients. In 19 patients, multiple abnormalities were found. CONCLUSION Our results confirm the influence of a large number of mechanisms explaining dysregulation of fetal growth. We concluded that CNVs, methylation disturbances, and sequence variants all contribute to prenatal growth failure. These genetic workups can be an effective diagnostic approach in SGA newborns.
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Affiliation(s)
- Susanne E Stalman
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Nita Solanky
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Miho Ishida
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Cristina Alemán-Charlet
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Sayeda Abu-Amero
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Lucas Alvizi
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - William Baird
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Charalambos Demetriou
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Peter Henneman
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Chela James
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Lia C Knegt
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Lydia J Leon
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Adi N Mul
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole A Nibbering
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Emma Peskett
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Faisal I Rezwan
- Department of Human Development and Health, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Carrie Ris-Stalpers
- Department of Gynecology and Obstetrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Joris A M van der Post
- Department of Gynecology and Obstetrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerdine A Kamp
- Department of Pediatrics, Tergooi Hospitals, Blaricum, The Netherlands
| | - Frans B Plötz
- Department of Pediatrics, Tergooi Hospitals, Blaricum, The Netherlands
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Philip Stanier
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Gudrun E Moore
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, United Kingdom
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
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Association between Retinoic acid receptor-β hypermethylation and NSCLC risk: a meta-analysis and literature review. Oncotarget 2018; 8:5814-5822. [PMID: 28008143 PMCID: PMC5351591 DOI: 10.18632/oncotarget.14023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/12/2016] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence indicates that Retinoic acid receptor-β (RARβ) is a tumor suppressor in many types of tumor. However, whether or not RARβ is a risk factor and is correlated to clinicopathological characteristics of non-small cell lung cancer (NSCLC) remains unclear. In this report, we performed a meta-analysis to determine the effects of RARβ hypermethylation on the incidence of NSCLC and clinicopathological characteristics in human NSCLC patients. Final valuation and analysis of 1780 cancer patients from 16 eligible studies was performed. RARβ hypermethylation was found to be significantly higher in NSCLC than in normal lung tissue, the pooled OR from 7 studies including 646 NSCLC and 580 normal lung tissues, OR = 6.05, 95% CI = 3.56-10.25, p<0.00001. RARβ hypermethylation was significantly higher in adenocarcinoma (AC) compared to squamous cell carcinoma (SCC), pooled OR is 0.68 (95% CI = 0.52-0.89, p = 0.005). RARβ hypermethylation was also found to occur significantly higher in smoker (n = 232) than non-smoker (n = 213) (OR = 2.46, 95% CI = 1.54-3.93, p = 0.0002). Our results indicate that RARβ hypermethylation correlates well with an increased risk in NSCLC patients. RARβ geneinactivation caused by RARβ methylation contributes the NSCLC tumorigenesis and may serve as a potential risk factor, diagnostic marker and drug target of NSCLC.
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127
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Ji S, Ding X, Ji J, Wu H, Sun R, Li X, Zhang L, Tian Y. Cranial irradiation inhibits hippocampal neurogenesis via DNMT1 and DNMT3A. Oncol Lett 2018; 15:2899-2904. [PMID: 29435016 PMCID: PMC5778827 DOI: 10.3892/ol.2017.7643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 11/16/2017] [Indexed: 02/07/2023] Open
Abstract
Impairment of neurogenesis in the hippocampus following whole-brain irradiation is the most important mechanism of radiation-induced cognitive dysfunction. However, the underlying mechanism remains obscure, meaning an ideal therapeutic target has not been identified. Evidence indicates that DNA methylation in neurons regulates synaptic plasticity and neuronal network activity. In the present study, the expression of DNA methyltransferases (DNMTs) in the hippocampus was analyzed to investigate their potential function in radiation-induced neurogenesis impairment. Sprague-Dawley rats were used throughout the present study, apportioned to the following groups: Control, radiation only, zebularine (a DNMT inhibitor) only, and radiation and zebularine together. Immunofluorescence staining revealed that radiation inhibited cellular proliferation and dendritic growth within new neurons of the hippocampus. In addition, western blot analysis demonstrated lower expression levels of DNMT1 and DNMT3A protein following radiation treatment compared with that in the non-irradiated control. Furthermore, compared with the radiation-only group, the radiation and zebularine group had significantly lower cell proliferative abilities, dendritic growth, and DNMT1 and DNMT3A protein levels. The results of the present study indicated that DNMT1 and DNMT3A may be involved in the pathogenesis of whole-brain radiation-induced neurogenesis impairment.
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Affiliation(s)
- Shengjun Ji
- Cancer Center, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, P.R. China
| | - Xin Ding
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Jiang Ji
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Haohao Wu
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Rui Sun
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Xiaoyang Li
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Liyuan Zhang
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Ye Tian
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
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128
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Chen HL, Li ZM, Liu JF, Han B, Wu ZX, Mao YQ, Sun KY, Wang LS. Polymorphism of the DNA methyltransferase 1 gene is associated with the susceptibility to essential hypertension in male. Clin Exp Hypertens 2018; 40:695-701. [PMID: 29400588 DOI: 10.1080/10641963.2018.1425420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Essential hypertension is a leading global public health issue, billions of people suffered from it every year. Recently, multiple evidence suggests that DNA methylation play an important role in regulating blood pressure. Here, we tested the risk for essential hypertension conferred by single nucleotide polymorphisms (SNPs) within DNA methyltransferase 1 (DNMT1). Three loci (rs2228611, rs2228612, and rs16999593) were selected to be analyzed in 3410 cases and 1307 normal controls in southern Chinese aged 60 or above. No significant association with essential hypertension was observed for rs2228612 and rs16999593. A higher risk of essential hypertension was found in the minor A allele of rs2228611 in the codominant and recessive model (P < 0.05). After stratified by sex, this association was found in male but not female. Furthermore, this difference was abolished after BMI adjustment in the whole population and reduced in male. In addition, the mutation rate of rs2228611 was higher in the obesity group compared with the normal weight group of male. Intriguingly, rs2228611 was also a risk factor of essential hypertension in normal weight male. These findings indicated that rs2228611 might contribute to male hypertension via BMI-dependent mechanisms in obesity male and BMI-independent mechanisms in normal weight male.
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Affiliation(s)
- Hui-Ling Chen
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
| | - Zhan-Ming Li
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
| | - Jin-Feng Liu
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
| | - Bing Han
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
| | - Zhao-Xia Wu
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
| | - Yu-Qin Mao
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
| | - Ke-Yu Sun
- b Emergency Department, Minhang Hospital , Fudan University , Shanghai , P.R. China
| | - Li-Shun Wang
- a Institute of Fudan-Minhang Academic Health System, Minhang Hospital , Fudan University , Shanghai , P.R.China
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Wang LH, Huang J, Wu CR, Huang LY, Cui J, Xing ZZ, Zhao CY. Downregulation of miR‑29b targets DNMT3b to suppress cellular apoptosis and enhance proliferation in pancreatic cancer. Mol Med Rep 2018; 17:2113-2120. [PMID: 29207141 PMCID: PMC5783451 DOI: 10.3892/mmr.2017.8145] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 05/19/2017] [Indexed: 12/16/2022] Open
Abstract
As one of the most aggressive types of tumor, pancreatic cancer is a principal cause of tumor‑associated mortality. Negative associations between microRNA‑29 (miR‑29) and DNA methyltransferases (DNMT) 3a and 3b have been demonstrated to be associated with the carcinogenesis of a number of types of cancer; however, this has not been completely elucidated in pancreatic cancer. In the present study, pancreatic cancer tissues (n=15) and corresponding paracancerous tissues (n=15) were obtained and the results of reverse transcription‑quantitative polymerase chain reaction analysis indicated decreased expression of miR‑29b and enhanced mRNA expression of DNMT3b in pancreatic cancer tissues, compared with the corresponding paracancerous tissues. Increased protein expression of DNMT3b was demonstrated by western blotting and immunohistochemistry. In addition, the negative association between miR‑29b and DNMT3b was noted in pancreatic cancer tissues, and luciferase reporter assays confirmed that miR‑29b was able to directly target DNMT3b in vitro. Notably, miR‑29b overexpression was able to decrease cell viability and to promote the apoptosis by targeting DNMT3b, and the knockdown of DNMT3b exhibited consistent results in vitro and in vivo. The results of the present study suggested that miR‑29b, as a tumor suppressor, may be a novel target for the development of treatments for pancreatic cancer.
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Affiliation(s)
- Li-Hua Wang
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Ju Huang
- Department of Queen Mary University, Medical College of Nanchang University, Nanchang, Jiangxi 330038, P.R. China
| | - Cheng-Rong Wu
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Liu-Ye Huang
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Jun Cui
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Zhi-Zhi Xing
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Chun-Yu Zhao
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
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130
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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131
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Roulois D, Deshayes S, Guilly MN, Nader JS, Liddell C, Robard M, Hulin P, Ouacher A, Le Martelot V, Fonteneau JF, Grégoire M, Blanquart C, Pouliquen DL. Characterization of preneoplastic and neoplastic rat mesothelial cell lines: the involvement of TETs, DNMTs, and 5-hydroxymethylcytosine. Oncotarget 2017; 7:34664-87. [PMID: 27129173 PMCID: PMC5085183 DOI: 10.18632/oncotarget.8970] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 04/10/2016] [Indexed: 12/12/2022] Open
Abstract
Malignant mesothelioma (MM) is one of the worst cancers in terms of clinical outcome, urging the need to establish and characterize new preclinical tools for investigation of the tumorigenic process, improvement of early diagnosis and evaluation of new therapeutic strategies. For these purposes, we characterized a collection of 27 cell lines established from F344 rats, after 136 to 415 days of induction with crocidolite asbestos administered intraperitoneally. Four mesotheliomas were distinguished from 23 preneoplastic mesothelial cell lines (PN) according to their propensity to generate tumors after orthotopic transplantation into syngeneic rats, their growth pattern, and the expression profile of three genes. PN cell lines were further discriminated into groups / subgroups according to morphology in culture and the expression profiles of 14 additional genes. This approach was completed by analysis of positive and negative immunohistochemical MM markers in the four tumors, of karyotype alterations in the most aggressive MM cell line in comparison with a PN epithelioid cell line, and of human normal mesothelial and mesothelioma cells and a tissue array. Our results showed that both the rat and human MM cell lines shared in common a dramatic decrease in the relative expression of Cdkn2a and of epigenetic regulators, in comparison with PN and normal human mesothelial cells, respectively. In particular, we identified the involvement of the relative expression of the Ten-Eleven Translocation (TET) family of dioxygenases and Dnmt3a in relation to the 5-hydroxymethylcytosine level in malignant transformation and the acquisition of metastatic potential.
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Affiliation(s)
- David Roulois
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Sophie Deshayes
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | - Joëlle S Nader
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Charly Liddell
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Myriam Robard
- INSERM, Université d'Angers, Université de Nantes, Nantes, France.,Cellular and Tissular Imaging Core Facility (MicroPICell), Nantes, France
| | - Philippe Hulin
- INSERM, Université d'Angers, Université de Nantes, Nantes, France.,Cellular and Tissular Imaging Core Facility (MicroPICell), Nantes, France
| | - Amal Ouacher
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Vanessa Le Martelot
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Jean-François Fonteneau
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Marc Grégoire
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Christophe Blanquart
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Daniel L Pouliquen
- CRCNA, Université d'Angers, Université de Nantes, Nantes, France.,INSERM, Université d'Angers, Université de Nantes, Nantes, France.,CNRS, Université d'Angers, Université de Nantes, Nantes, France
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132
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Pei YF, Tao R, Li JF, Su LP, Yu BQ, Wu XY, Yan M, Gu QL, Zhu ZG, Liu BY. TET1 inhibits gastric cancer growth and metastasis by PTEN demethylation and re-expression. Oncotarget 2017; 7:31322-35. [PMID: 27121319 PMCID: PMC5058759 DOI: 10.18632/oncotarget.8900] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/31/2016] [Indexed: 12/29/2022] Open
Abstract
Ten-Eleven Translocation 1 (TET1) is a member of ten eleven translocation enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC). TET1 can promote CpG islands demethylation in specific genes and often absent in various cancers. Herein, we found that TET1 expression and 5-hmC content were low in gastric tumors compared to its adjacent non-tumor tissues. Cell proliferation, migration and invasion were enhanced upon TET1 knockdown in gastric cancer cells in vitro. This phenomenon was confirmed by an animal xeongraft model. We also found that TET1 directly binds to the promoter region of PTEN and activates its transcription through demethylation of CpG islands. TET1 knockdown activated AKT and FAK pathways, which were suppressed by PTEN. The activation of AKT and FAK facilitated tumor migration, invasion and accelerated cell growth. In conclusion, we found a novel mechanism that TET1 suppresses tumor cell growth, migration and invasion through demethylation of CpG island in PTEN promoter by increasing 5-hmC content. The re-expressed PTEN subsequently down regulates AKT and FAK activity.
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Affiliation(s)
- Yao-Fei Pei
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Ran Tao
- Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Province People's Hospital, Hangzhou 310014, PR China
| | - Jian-Fang Li
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Li-Ping Su
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Bei-Qin Yu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Xiong-Yan Wu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Min Yan
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Qin-Long Gu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Zheng-Gang Zhu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Bing-Ya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
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133
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Kovalchuk A, Rodriguez-Juarez R, Ilnytskyy Y, Byeon B, Shpyleva S, Melnyk S, Pogribny I, Kolb B, Kovalchuk O. Sex-specific effects of cytotoxic chemotherapy agents cyclophosphamide and mitomycin C on gene expression, oxidative DNA damage, and epigenetic alterations in the prefrontal cortex and hippocampus - an aging connection. Aging (Albany NY) 2017; 8:697-711. [PMID: 27032448 PMCID: PMC4925823 DOI: 10.18632/aging.100920] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/30/2016] [Indexed: 01/21/2023]
Abstract
Recent research shows that chemotherapy agents can be more toxic to healthy brain cells than to the target cancer cells. They cause a range of side effects, including memory loss and cognitive dysfunction that can persist long after the completion of treatment. This condition is known as chemo brain. The molecular and cellular mechanisms of chemo brain remain obscure. Here, we analyzed the effects of two cytotoxic chemotherapy drugs—cyclophosphamide (CPP) and mitomycin C (MMC) - on transcriptomic and epigenetic changes in the murine prefrontal cortex (PFC) and hippocampal regions. We for the first time showed that CPP and MMC treatments led to profound sex- and brain region-specific alterations in gene expression profiles. Gene expression changes were most prominent in the PFC tissues of female mice 3 weeks after MMC treatment, and the gene expression response was much greater for MCC than CPP exposure. MMC exposure resulted in oxidative DNA damage, evidenced by accumulation of 8-oxo-2′-deoxyguanosine (8-oxodG) and a decrease in the level of 8-oxodG repair protein OGG1 in the PFC of female animals 3 weeks after treatment. MMC treatment decreased global DNA methylation and increased DNA hydroxymethylation in the PFC tissues of female mice. The majority of the changes induced by chemotherapy in the PFC tissues of female mice resembled those that occur during the brain's aging processes. Therefore, our study suggests a link between chemotherapy-induced chemo brain and brain aging, and provides an important roadmap for future analysis.
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Affiliation(s)
- Anna Kovalchuk
- Department of Neuroscience, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Rocio Rodriguez-Juarez
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Boseon Byeon
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Svitlana Shpyleva
- Division of Biochemical Toxicology, Food and Drug Administration National Center for Toxicological Research, Jefferson, AR 72079, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Stepan Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Igor Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Bryan Kolb
- Department of Neuroscience, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.,Alberta Epigenetics Network, Calgary, AB, T2L 2A6, Canada.,Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.,Alberta Epigenetics Network, Calgary, AB, T2L 2A6, Canada
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134
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Fernandes GFS, Silva GDB, Pavan AR, Chiba DE, Chin CM, Dos Santos JL. Epigenetic Regulatory Mechanisms Induced by Resveratrol. Nutrients 2017; 9:nu9111201. [PMID: 29104258 PMCID: PMC5707673 DOI: 10.3390/nu9111201] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/05/2017] [Accepted: 09/18/2017] [Indexed: 12/11/2022] Open
Abstract
Resveratrol (RVT) is one of the main natural compounds studied worldwide due to its potential therapeutic use in the treatment of many diseases, including cancer, diabetes, cardiovascular diseases, neurodegenerative diseases and metabolic disorders. Nevertheless, the mechanism of action of RVT in all of these conditions is not completely understood, as it can modify not only biochemical pathways but also epigenetic mechanisms. In this paper, we analyze the biological activities exhibited by RVT with a focus on the epigenetic mechanisms, especially those related to DNA methyltransferase (DNMT), histone deacetylase (HDAC) and lysine-specific demethylase-1 (LSD1).
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Affiliation(s)
- Guilherme Felipe Santos Fernandes
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
- Institute of Chemistry, São Paulo State University (UNESP), 14800060 Araraquara, Brazil.
| | | | - Aline Renata Pavan
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
| | - Diego Eidy Chiba
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
| | - Chung Man Chin
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
| | - Jean Leandro Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), 14800903 Araraquara, Brazil.
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135
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Lai CY, Huang CC, Tsai CH, Wang JY, Kerr CL, Chen YY, Cai YW, Wong RH. The DNA Methyltransferase 3B -149 Genetic Polymorphism Modulates Lung Cancer Risk from Smoking. Asian Pac J Cancer Prev 2017; 18:2717-2723. [PMID: 29072397 PMCID: PMC5747395 DOI: 10.22034/apjcp.2017.18.10.2717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: Smoking can cause increase of DNA methylation and hypermethylation of tumor suppressor genes, this possible contributing to subsequent lung cancer development. DNA methyltransferase 3B (DNMT3B) is crucial in regulation of DNA methylation and it has been proposed that green tea might lower cancer risk through inhibiting its activity. Here, we designed a case-control study to investigate whether the DNMT3B -149 genetic polymorphism could modulate lung cancer risk due to smoking. Possible interactions of smoking and green tea consumption with this DNMT3B genetic polymorphism were also assessed. Materials and Methods: A total of 190 lung cancer patients and 380 healthy controls were recruited. Questionnaires were administered to obtain data on sociodemographic and lifestyle variables, as well as family history of lung cancer. Genotypes for DNMT3B -149 were identified by polymerase chain reaction. Results: Smoking, green tea consumption, exposure to cooking fumes, family history of lung cancer, and the DNMT3B -149 genotype (odds ratio (OR)=2.65; 95% confidence interval (CI) 1.15-6.10) were all significantly associated with the development of lung cancer. Smokers carrying the DNMT3B -149 TT genotype were at elevated risk compared to non-smokers carrying DNMT3B -149 (OR=7.69; 95% CI 2.55-23.14). Interaction of smoking with DNMT3B -149 genotypes was significant regarding lung cancer risk. However, interaction between green tea drinking and DNMT3B -149 genotypes was not. Conclusions: The DNMT3B -149 TT genotype might increase the smoking-associated lung cancer risk.
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Affiliation(s)
- Chung Yu Lai
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- ,Department of Surgery, Cheng-Ching General Hospital, Taichung, Taiwan
- ,Center for General Education, Chung Shan Medical University,Taichung, Taiwan.
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136
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Cheng Z, Zheng L, Almeida FA. Epigenetic reprogramming in metabolic disorders: nutritional factors and beyond. J Nutr Biochem 2017; 54:1-10. [PMID: 29154162 DOI: 10.1016/j.jnutbio.2017.10.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/13/2022]
Abstract
Environmental factors (e.g., malnutrition and physical inactivity) contribute largely to metabolic disorders including obesity, type 2 diabetes, cardiometabolic disease and nonalcoholic fatty liver diseases. The abnormalities in metabolic activity and pathways have been increasingly associated with altered DNA methylation, histone modification and noncoding RNAs, whereas lifestyle interventions targeting diet and physical activity can reverse the epigenetic and metabolic changes. Here we review recent evidence primarily from human studies that links DNA methylation reprogramming to metabolic derangements or improvements, with a focus on cross-tissue (e.g., the liver, skeletal muscle, pancreas, adipose tissue and blood samples) epigenetic markers, mechanistic mediators of the epigenetic reprogramming, and the potential of using epigenetic traits to predict disease risk and intervention response. The challenges in epigenetic studies addressing the mechanisms of metabolic diseases and future directions are also discussed and prospected.
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Affiliation(s)
- Zhiyong Cheng
- Department of Human Nutrition, Foods, and Exercise, Fralin Translational Obesity Research Center, College of Agriculture and Life Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Louise Zheng
- Department of Human Nutrition, Foods, and Exercise, Fralin Translational Obesity Research Center, College of Agriculture and Life Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Fabio A Almeida
- Department of Health Promotion, Social & Behavioral Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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137
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Angioimmunoblastic T cell lymphoma: novel molecular insights by mutation profiling. Oncotarget 2017; 8:17763-17770. [PMID: 28148900 PMCID: PMC5392284 DOI: 10.18632/oncotarget.14846] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 01/19/2017] [Indexed: 01/02/2023] Open
Abstract
Angioimmunoblastic T cell lymphoma (AITL) originates from follicular helper T-cells and is characterised by a polymorphic infiltrate with the neoplastic T-cells forming small clusters around the follicle and high endothelial venules. Despite the recent advances in its phenotypic characterisation, the genetics and molecular mechanisms underlying AITL are not fully understood. In the present study, we performed whole exome sequencing in 9 cases of AITL from Taiwan (n = 6) and U.K. (n = 3). We confirmed frequent mutations in TET2 (9/9), DNMT3A (3/9), IDH2 (3/9), RHOA (3/9) and PLCG1 (2/9) as recently reported by others. More importantly, we identified mutations in TNFRSF21 (1/9), CCND3 (1/9) and SAMSN1 (1/9), which are not yet seen or strongly implicated in the pathogenesis of AITL. Among the pathogenic mutations identified in AITL, mutations in DNA methylation regulators TET2 and DNMT3A occur early in hematopoietic stem cells as shown by previous studies, and these genetic events enhance the self-renewal of hematopoietic stem cells, but are unlikely to have any major impact on T-cell differentiation. Mutations in RHOA, PLCG1 and TNFRSF21 (DR6), which encode proteins critical for T-cell biology, most likely promote T-cell differentiation and malignant transformation, consequently generating the malignant phenotype. Our findings extend the molecular insights into the multistage development of AITL.
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138
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McGee SL, Walder KR. Exercise and the Skeletal Muscle Epigenome. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029876. [PMID: 28320830 DOI: 10.1101/cshperspect.a029876] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An acute bout of exercise is sufficient to induce changes in skeletal muscle gene expression that are ultimately responsible for the adaptive responses to exercise. Although much research has described the intracellular signaling responses to exercise that are linked to transcriptional regulation, the epigenetic mechanisms involved are only just emerging. This review will provide an overview of epigenetic mechanisms and what is known in the context of exercise. Additionally, we will explore potential interactions between metabolism during exercise and epigenetic regulation, which serves as a framework for potential areas for future research. Finally, we will consider emerging opportunities to pharmacologically manipulate epigenetic regulators and mechanisms to induce aspects of the skeletal muscle exercise adaptive response for therapeutic intervention in various disease states.
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Affiliation(s)
- Sean L McGee
- Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3216, Australia
| | - Ken R Walder
- Metabolic Research Unit, School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3216, Australia
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139
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Xu YM, Yu FY, Lau ATY. Discovering Epimodifications of the Genome, Transcriptome, Proteome, and Metabolome: the Quest for Conquering the Uncharted Epi(c) Territories. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40495-017-0103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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140
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Chen H, Cai W, Chu ESH, Tang J, Wong CC, Wong SH, Sun W, Liang Q, Fang J, Sun Z, Yu J. Hepatic cyclooxygenase-2 overexpression induced spontaneous hepatocellular carcinoma formation in mice. Oncogene 2017; 36:4415-4426. [PMID: 28346420 PMCID: PMC5543258 DOI: 10.1038/onc.2017.73] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 12/12/2022]
Abstract
Cyclooxygenase (COX)-2 is upregulated in hepatocellular carcinoma (HCC). However, the direct causative effect of COX-2 in spontaneous HCC formation remains unknown. We thus investigate the role and molecular pathogenesis of COX-2 in HCC by using liver-specific COX-2 transgenic (TG) mice. We found spontaneous HCC formation with elevated inflammatory infiltrates and neovessels in male TG mice (3/21, 14.3%), but not in any of male WT mice (0/19). Reduced representation bisulfite sequencing (RRBS) and gene expression microarrays were performed in the HCC tumor and non-HCC liver tissues to investigate the molecular mechanisms of COX-2-driven HCC. By RRBS, DNA promoter hypermethylation was identified in HCC from TG mice. Induction of promoter hypermethylation was associated with reduced tet methylcytosine dioxygenase 1 (TET1) expression by COX-2. TET1 could catalyze the conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5hmC) and prevents DNA hypermethylation. In keeping with this, loss of 5hmC was demonstrated in COX-2-induced HCC. Consistently, COX-2 overexpression in human HCC cell lines could reduce both TET1 expression and 5hmc levels. Integrative analyses of DNA methylation and gene expression profiles further identified significantly downregulated genes including LTBP1, ADCY5 and PRKCZ by promoter methylation in COX-2-induced HCC. Reduced expression of LTBP1, ADCY5 and PRKCZ by promoter hypermethylation was further validated in human HCCs. Bio-functional investigation revealed that LTBP1 inhibited cell proliferation in HCC cell lines, suggesting its potential role as a tumor suppressor in HCC. Gene expression microarrays revealed that signaling cascades (AKT (protein kinase B), STK33 (Serine/Threonine kinase 33) and MTOR (mechanistic target of rapamycin) pathways) were enriched in COX-2-induced HCC. In conclusion, this study demonstrated for the first time that enhanced COX-2 expression in hepatocytes is sufficient to induce HCC through inducing promoter hypermethylation by reducing TET1, silencing tumor-suppressive genes and activating key oncogenic pathways. Inhibition of COX-2 represents a mechanism-based target for HCC prevention.
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Affiliation(s)
- H Chen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - W Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - E S H Chu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - J Tang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - C-C Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - S H Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - W Sun
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Q Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - J Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Z Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - J Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
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141
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Fu RJ, He W, Wang XB, Li L, Zhao HB, Liu XY, Pang Z, Chen GQ, Huang L, Zhao KW. DNMT1-maintained hypermethylation of Krüppel-like factor 5 involves in the progression of clear cell renal cell carcinoma. Cell Death Dis 2017; 8:e2952. [PMID: 28749461 PMCID: PMC5550868 DOI: 10.1038/cddis.2017.323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/27/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the major subtype of renal cell carcinoma (RCC) that is resistant to conventional radiation and chemotherapy. It is a challenge to explore effective therapeutic targets and drugs for this kind of cancer. Transcription factor Krüppel-like factor 5 (KLF5) exerts diverse functions in various tumor types. By analyzing cohorts of the Cancer Genome Atlas (TCGA) data sets, we find that KLF5 expression is suppressed in ccRCC patients and higher level of KLF5 expression is associated with better prognostic outcome. Our further investigations demonstrate that KLF5 genomic loci are hypermethylated at proximal exon 4 and suppression of DNA methyltransferase 1 (DNMT1) expression by ShRNAs or a methylation inhibitor 5-Aza-CdR can recover KLF5 expression. Meanwhile, there is a negative correlation between expressions of KLF5 and DNMT1 in ccRCC tissues. Ectopic KLF5 expression inhibits ccRCC cell proliferation and migration/invasion in vitro and decreases xenograft growth and metastasis in vivo. Moreover, 5-Aza-CdR, a chemotherapy drug as DNMTs' inhibitor that can induce KLF5 expression, suppresses ccRCC cell growth, while knockdown of KLF5 abolishes 5-Aza-CdR-induced growth inhibition. Collectively, our data demonstrate that KLF5 inhibits ccRCC growth as a tumor suppressor and highlight the potential of 5-Aza-CdR to release KLF5 expression as a therapeutic modality for the treatment of ccRCC.
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Affiliation(s)
- Rong-Jie Fu
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS) &Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Wei He
- Department of Pathology, Ren-Ji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Bo Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Lei Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Huan-Bin Zhao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Xiao-Ye Liu
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS) &Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Zhi Pang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Guo-Qiang Chen
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS) &Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China.,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Lei Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Ke-Wen Zhao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
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142
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Li Y, Liu X, Guo X, Liu X, Luo J. DNA methyltransferase 1 mediated aberrant methylation and silencing of SHP-1 gene in chronic myelogenous leukemia cells. Leuk Res 2017; 58:9-13. [DOI: 10.1016/j.leukres.2017.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 11/16/2022]
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143
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Effects of Folic Acid on DNMT1, GAP43, and VEGFR1 in Intrauterine Growth Restriction Filial Rats. Reprod Sci 2017. [DOI: 10.1177/1933719117715128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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144
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Samtani R, Sharma N, Garg D. Effects of Endocrine-Disrupting Chemicals and Epigenetic Modifications in Ovarian Cancer: A Review. Reprod Sci 2017; 25:7-18. [PMID: 28602118 DOI: 10.1177/1933719117711261] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ovarian cancer (OC) is a relatively fatal female reproductive malignancy. Since the underlying causes are uncertain, it brings us to believe that both genetic and external factors contribute toward development of this lethal disorder. Exposure to endocrine-disrupting chemicals (EDCs) in the form of occupational usage of pesticides, fungicides, herbicides, plasticizers, cosmetics, and so on is potentially carcinogenic and their ability to cause epigenetic modifications has led us to hypothesize that they may play a catalytic role in OC progression. In response to synthetic chemicals, animal models have demonstrated disturbances in the development of ovaries and steroid hormonal levels but in humans, more research is required. The present review is an attempt to address the impact of EDCs on the hormonal system and gene methylation levels that may lead to malfunctioning of the ovaries which may consequently develop in the form of cancer. It can be concluded that endocrine disruptors do have a potential carcinogenicity and their high proportions in human body may cause epigenetic modifications, prompting ovarian surface epithelium to grow in an abnormal manner.
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Affiliation(s)
- Ratika Samtani
- 1 Amity Institute of Anthropology, Amity University, Noida, Uttar Pradesh, India
| | - Noopur Sharma
- 1 Amity Institute of Anthropology, Amity University, Noida, Uttar Pradesh, India
| | - Deepali Garg
- 2 Dr Deepali Path Labs & Cancer Diagnostic Centre, Bathinda, Punjab, India
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145
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Atkins RM, Fawcett TJ, Gilbert R, Hoff AM, Connolly R, Brown DW, Llewellyn AJ, Jaroszeski MJ. Impedance spectroscopy as an indicator for successful in vivo electric field mediated gene delivery in a murine model. Bioelectrochemistry 2017; 115:33-40. [DOI: 10.1016/j.bioelechem.2017.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 12/19/2022]
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146
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Bartosch C, Lopes JM, Jerónimo C. Epigenetics in endometrial carcinogenesis - part 1: DNA methylation. Epigenomics 2017; 9:737-755. [PMID: 28470096 DOI: 10.2217/epi-2016-0166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Carcinogenesis is a multistep multifactorial process that involves the accumulation of genetic and epigenetic alterations. In the past two decades, there has been an exponential growth of knowledge establishing the importance of epigenetic changes in cancer. Our work focused on reviewing the main role of epigenetics in the pathogenesis of endometrial carcinoma, highlighting the reported results concerning each epigenetic mechanistic layer. The present review is the first part of this work, in which we examined the contribution of DNA methylation alterations for endometrial carcinogenesis.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - José Manuel Lopes
- Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Department of Pathology, Centro Hospitalar São João (CHSJ), Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology & Immunology, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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147
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Gallo A, Landi R, Rubino V, Di Cerbo A, Giovazzino A, Palatucci AT, Centenaro S, Guidetti G, Canello S, Cortese L, Ruggiero G, Alessandrini A, Terrazzano G. Oxytetracycline induces DNA damage and epigenetic changes: a possible risk for human and animal health? PeerJ 2017; 5:e3236. [PMID: 28462039 PMCID: PMC5410137 DOI: 10.7717/peerj.3236] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/27/2017] [Indexed: 01/26/2023] Open
Abstract
Background Oxytetracycline (OTC), which is largely employed in zootechnical and veterinary practices to ensure wellness of farmed animals, is partially absorbed within the gastrointestinal tract depositing in several tissues. Therefore, the potential OTC toxicity is relevant when considering the putative risk derived by the entry and accumulation of such drug in human and pet food chain supply. Despite scientific literature highlights several OTC-dependent toxic effects on human and animal health, the molecular mechanisms of such toxicity are still poorly understood. Methods Here, we evaluated DNA damages and epigenetic alterations by quantitative reverse transcription polymerase chain reaction, quantitative polymerase chain reaction, chromatin immuno-precipitation and Western blot analysis. Results We observed that human peripheral blood mononuclear cells (PBMCs) expressed DNA damage features (activation of ATM and p53, phosphorylation of H2AX and modifications of histone H3 methylation of lysine K4 in the chromatin) after the in vitro exposure to OTC. These changes are linked to a robust inflammatory response indicated by an increased expression of Interferon (IFN)-γ and type 1 superoxide dismutase (SOD1). Discussion Our data reveal an unexpected biological in vitro activity of OTC able to modify DNA and chromatin in cultured human PBMC. In this regard, OTC presence in foods of animal origin could represent a potential risk for both the human and animal health.
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Affiliation(s)
- Adriana Gallo
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples, Italy
| | - Rosaria Landi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Valentina Rubino
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessandro Di Cerbo
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy
| | - Angela Giovazzino
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Sara Centenaro
- Division of Research and Development, Sanypet SpA, Padova, Italy
| | | | - Sergio Canello
- Division of Research and Development, Sanypet SpA, Padova, Italy
| | - Laura Cortese
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Giuseppina Ruggiero
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Andrea Alessandrini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy.,National Research Council (CNR), Nanoscience Istitute, Modena, Italy
| | - Giuseppe Terrazzano
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Department of Science, University of Basilicata, Potenza, Italy
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148
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Wang S, He Z, Li D, Zhang B, Li M, Li W, Zhu W, Xing X, Zeng X, Wang Q, Dong G, Xiao Y, Chen W, Chen L. Aberrant methylation of RUNX3 is present in Aflatoxin B 1-induced transformation of the L02R cell line. Toxicology 2017; 385:1-9. [PMID: 28458013 DOI: 10.1016/j.tox.2017.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/22/2017] [Accepted: 04/23/2017] [Indexed: 12/13/2022]
Abstract
Chronic exposure to aflatoxin B1 (AFB1) is linked to the development of hepatocellular carcinoma (HCC). To identify differentially methylated genes involved in AFB1-induced cell transformation, we analyzed DNA methylation patterns in immortal human hepatocyte L02 cells expressing an oncogenic H-Ras allele (L02R cells) and AFB1-transformed L02R (L02RT-AFB1) cells by performing genome-wide methylation profiling. We treated L02R cells with 0.3μM AFB1 weekly and observed a transformed phenotype at the 17th week post-treatment. The transformed cells (L02RT-AFB1) could grow in an anchorage independent fashion and form tumors in immunodeficient mice. qRT-PCR was performed to examine whether gene methylation led to a reduction in gene expression of methylated candidate genes. As a result, the expression of the following seven genes including JUNB, RUNX3, NAV1, CXCR4, RARRES1, INTS1, and POLL was down-regulated in transformed L02RT-AFB1 cells. The reduction of gene expression of these genes could be reversed by treatment of 5-azadeoxycytidine. The methylated CpG sites of RUNX3 genes were verified using bisulfite sequencing PCR (BSP) assay. Furthermore, a dynamic change in RUNX3 methylation was observed over the course of AFB1-induced cell transformation, which was corresponded to the alteration of gene expression and the extent of DNA damage. In vitro study showed that methylation of RUNX3 tended to abate in L02R cells treated with AFB1 for a short-term period of time. Notably, hypermethylation of RUNX3 appeared in 70% (14/20) of human hepatocellular carcinomas. Moreover, LINE-1 hypomethylation and dynamic changes of DNMTs, TETs and MeCP2 expression were also observed during AFB1-induced transformation. Taken together, these observations suggest that aberrant methylation of RUNX3 and LINE-1 might be involved in AFB1-induced carcinogenesis.
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Affiliation(s)
- Shan Wang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhini He
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bo Zhang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Miao Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wenxue Li
- Departmant of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Wei Zhu
- Departmant of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Xiumei Xing
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaowen Zeng
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Guanghui Dong
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yongmei Xiao
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wen Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liping Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China.
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149
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Klotho preservation via histone deacetylase inhibition attenuates chronic kidney disease-associated bone injury in mice. Sci Rep 2017; 7:46195. [PMID: 28387374 PMCID: PMC5384196 DOI: 10.1038/srep46195] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/10/2017] [Indexed: 01/01/2023] Open
Abstract
Bone loss and increased fracture are the devastating outcomes of chronic kidney disease-mineral and bone disorder (CKD-MBD) resulting from Klotho deficit-related mineral disturbance and hyperparathyroidism. Because Klotho down-regulation after renal injury is presumably affected by aberrant histone deacetylase (HDAC) activities, here we assess whether HDAC inhibition prevents Klotho loss and attenuates the CKD-associated bone complication in a mouse model of CKD-MBD. Mice fed adenine-containing diet developed the expected renal damage, a substantial Klotho loss and the deregulated key factors causally affecting bone remodeling, which were accompanied by a marked reduction of bone mineral density. Intriguingly, administration of a potent HDAC inhibitor trichostatin A (TSA) impressively alleviated the Klotho deficit and the observed alterations of serum, kidney and bone. TSA prevented Klotho loss by increasing the promoter-associated histone acetylation, therefore increasing Klotho transcription. More importantly the mice lacking Klotho by siRNA interference largely abolished the TSA protections against the serum and renal abnormalities, and the deranged bone micro-architectures. Thus, our study identified Klotho loss as a key event linking HDAC deregulation to the renal and bone injuries in CKD-MBD mice and demonstrated the therapeutic potentials of endogenous Klotho restoration by HDAC inhibition in treating CKD and the associated extrarenal complications.
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150
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Mitochondrial DNA Hypomethylation Is a Biomarker Associated with Induced Senescence in Human Fetal Heart Mesenchymal Stem Cells. Stem Cells Int 2017; 2017:1764549. [PMID: 28484495 PMCID: PMC5397648 DOI: 10.1155/2017/1764549] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/05/2017] [Accepted: 01/16/2017] [Indexed: 02/07/2023] Open
Abstract
Background. Fetal heart can regenerate to restore its normal anatomy and function in response to injury, but this regenerative capacity is lost within the first week of postnatal life. Although the specific molecular mechanisms remain to be defined, it is presumed that aging of cardiac stem or progenitor cells may contribute to the loss of regenerative potential. Methods. To study this aging-related dysfunction, we cultured mesenchymal stem cells (MSCs) from human fetal heart tissues. Senescence was induced by exposing cells to chronic oxidative stress/low serum. Mitochondrial DNA methylation was examined during the period of senescence. Results. Senescent MSCs exhibited flattened and enlarged morphology and were positive for the senescence-associated beta-galactosidase (SA-β-Gal). By scanning the entire mitochondrial genome, we found that four CpG islands were hypomethylated in close association with senescence in MSCs. The mitochondrial COX1 gene, which encodes the main subunit of the cytochrome c oxidase complex and contains the differentially methylated CpG island 4, was upregulated in MSCs in parallel with the onset of senescence. Knockdown of DNA methyltransferases (DNMT1, DNMT3a, and DNMT3B) also upregulated COX1 expression and induced cellular senescence in MSCs. Conclusions. This study demonstrates that mitochondrial CpG hypomethylation may serve as a critical biomarker associated with cellular senescence induced by chronic oxidative stress.
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