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Xue X, Wang Z, Wang Y, Zhou X. Disease Diagnosis Based on Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2114-2127. [PMID: 37527510 DOI: 10.1021/acschembio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid modifications include a wide range of epigenetic and epitranscriptomic factors and impact a wide range of nucleic acids due to their profound influence on biological inheritance, growth, and metabolism. The recently developed methods of mapping and characterizing these modifications have promoted their discovery as well as large-scale studies in eukaryotes, especially in humans. Because of these pioneering strategies, nucleic acid modifications have been shown to have a great impact on human disorders such as cancer. Therefore, whether nucleic acid modifications could become a new type of biomarker remains an open question. In this review, we briefly look back at classical nucleic acid modifications and then focus on the progress made in investigating these modifications as diagnostic biomarkers in clinical therapy and present our perspective on their development prospects.
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Affiliation(s)
- Xiaochen Xue
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiying Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Department of Chemistry, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Cross Research Institute of Zhongnan Hospital, Wuhan University, Wuhan 430071, China
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2
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Maekawa T, Miyake T, Tani M, Uemoto S. Diverse antitumor effects of ascorbic acid on cancer cells and the tumor microenvironment. Front Oncol 2022; 12:981547. [PMID: 36203466 PMCID: PMC9531273 DOI: 10.3389/fonc.2022.981547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Ascorbic acid has attracted substantial attention for its potential antitumor effects by acting as an antioxidant in vivo and as a cofactor in diverse enzymatic reactions. However, solid proof of its clinical efficacy against cancer and the mechanism behind its effect have not been established. Moreover, cancer forms cancer-specific microenvironments and interacts with various cells, such as cancer-associated fibroblasts (CAFs), to maintain cancer growth and progression; however, the effect of ascorbic acid on the cancer microenvironment is unclear. This review discusses the effects and mechanisms of ascorbic acid on cancer, including the role of ascorbic acid concentration. In addition, we present future perspectives on the effects of ascorbic acid on cancer cells and the CAF microenvironment. Ascorbic acid has a variety of effects, which contributes to the complexity of these effects. Oral administration of ascorbic acid results in low blood concentrations (<0.2 mM) and acts as a cofactor for antioxidant effects, collagen secretion, and HIFα degradation. In contrast, intravenous treatment achieves large blood concentrations (>1 mM) and has oxidative-promoting actions that exert anticancer effects via reactive oxygen species. Therefore, intravenous administration at high concentrations is required to achieve the desired effects on cancer cells during treatment. Partial data on the effect of ascorbic acid on fibroblasts indicate that it may also modulate collagen secretion in CAFs and impart tumor-suppressive effects. Thus, future studies should verify the effect of ascorbic acid on CAFs. The findings of this review can be used to guide further research and clinical trials.
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Affiliation(s)
- Takeru Maekawa
- Division of Gastrointestinal, Breast, Pediatric, and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Toru Miyake
- Division of Gastrointestinal, Breast, Pediatric, and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
- *Correspondence: Toru Miyake,
| | - Masaji Tani
- Division of Gastrointestinal, Breast, Pediatric, and General Surgery, Department of Surgery, Shiga University of Medical Science, Otsu, Japan
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3
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Yang S, Huang Y, Zhao Q. Epigenetic Alterations and Inflammation as Emerging Use for the Advancement of Treatment in Non-Small Cell Lung Cancer. Front Immunol 2022; 13:878740. [PMID: 35514980 PMCID: PMC9066637 DOI: 10.3389/fimmu.2022.878740] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/21/2022] [Indexed: 12/26/2022] Open
Abstract
Lung cancer remains one of the most common malignancies in the world. Nowadays, the most common lung cancer is non-small cell lung cancer (NSCLC), namely, adenocarcinoma, squamous cell carcinoma, and large cell lung carcinoma. Epigenetic alterations that refer to DNA methylation, histone modifications, and noncoding RNA expression, are now suggested to drive the genesis and development of NSCLC. Additionally, inflammation-related tumorigenesis also plays a vital role in cancer research and efforts have been attempted to reverse such condition. During the occurrence and development of inflammatory diseases, the immune component of inflammation may cause epigenetic changes, but it is not always certain whether the immune component itself or the stimulated host cells cause epigenetic changes. Moreover, the links between epigenetic alterations and cancer-related inflammation and their influences on the human cancer are not clear so far. Therefore, the connection between epigenetic drivers, inflammation, and NSCLC will be summarized. Investigation on such topic is most likely to shed light on the molecular and immunological mechanisms of epigenetic and inflammatory factors and promote the application of epigenetics in the innovative diagnostic and therapeutic strategies for NSCLC.
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Affiliation(s)
- Shuo Yang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shuo Yang, ; Yang Huang, ; Qi Zhao,
| | - Yang Huang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shuo Yang, ; Yang Huang, ; Qi Zhao,
| | - Qi Zhao
- Cancer Centre, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau, Macau SAR, China
- *Correspondence: Shuo Yang, ; Yang Huang, ; Qi Zhao,
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4
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Barrero MJ, Cejas P, Long HW, Ramirez de Molina A. Nutritional Epigenetics in Cancer. Adv Nutr 2022; 13:1748-1761. [PMID: 35421212 PMCID: PMC9526851 DOI: 10.1093/advances/nmac039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/11/2022] [Accepted: 04/09/2022] [Indexed: 01/28/2023] Open
Abstract
Alterations in the epigenome are well known to affect cancer development and progression. Epigenetics is highly influenced by the environment, including diet, which is a source of metabolic substrates that influence the synthesis of cofactors or substrates for chromatin and RNA modifying enzymes. In addition, plants are a common source of bioactives that can directly modify the activity of these enzymes. Here, we review and discuss the impact of diet on epigenetic mechanisms, including chromatin and RNA regulation, and its potential implications for cancer prevention and treatment.
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Affiliation(s)
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,Translational Oncology Laboratory, Hospital La Paz Institute for Health Research, Madrid, Spain
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
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5
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Gerecke C, Egea Rodrigues C, Homann T, Kleuser B. The Role of Ten-Eleven Translocation Proteins in Inflammation. Front Immunol 2022; 13:861351. [PMID: 35386689 PMCID: PMC8977485 DOI: 10.3389/fimmu.2022.861351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Ten-eleven translocation proteins (TET1-3) are dioxygenases that oxidize 5-methyldeoxycytosine, thus taking part in passive and active demethylation. TETs have shown to be involved in immune cell development, affecting from self-renewal of stem cells and lineage commitment to terminal differentiation. In fact, dysfunction of TET proteins have been vastly associated with both myeloid and lymphoid leukemias. Recently, there has been accumulating evidence suggesting that TETs regulate immune cell function during innate and adaptive immune responses, thereby modulating inflammation. In this work, we pursue to review the current and recent evidence on the mechanistic aspects by which TETs regulate immune cell maturation and function. We will also discuss the complex interplay of TET expression and activity by several factors to modulate a multitude of inflammatory processes. Thus, modulating TET enzymes could be a novel pharmacological approach to target inflammation-related diseases and myeloid and lymphoid leukemias, when their activity is dysregulated.
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Affiliation(s)
- Christian Gerecke
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Caue Egea Rodrigues
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Thomas Homann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Burkhard Kleuser
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
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6
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Abstract
5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (A.C.); (S.T.)
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Ciesielski P, Jóźwiak P, Forma E, Krześlak A. TET3- and OGT-Dependent Expression of Genes Involved in Epithelial-Mesenchymal Transition in Endometrial Cancer. Int J Mol Sci 2021; 22:13239. [PMID: 34948036 DOI: 10.3390/ijms222413239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022] Open
Abstract
TET3 is a member of the TET (ten-eleven translocation) proteins family that catalyzes the conversion of the 5-methylcytosine into 5-hydroxymethylcytosine. TET proteins can also affect chromatin modifications and gene expression independently of their enzymatic activity via interactions with other proteins. O-GlcNAc transferase (OGT), the enzyme responsible for modification of proteins via binding of N-acetylglucosamine residues, is one of the proteins whose action may be dependent on TET3. Here, we demonstrated that in endometrial cancer cells both TET3 and OGT affected the expression of genes involved in epithelial to mesenchymal transition (EMT), i.e., FOXC1, TWIST1, and ZEB1. OGT overexpression was caused by an increase in TWIST1 and ZEB1 levels in HEC-1A and Ishikawa cells, which was associated with increased O-GlcNAcylation of histone H2B and trimethylation of H3K4. The TET3 had the opposite effect on gene expressions and histone modifications. OGT and TET3 differently affected FOXC1 expression and the migratory potential of HEC-1A and Ishikawa cells. Analysis of gene expressions in cancer tissue samples from endometrial cancer patients confirmed the association between OGT or TET3 and EMT genes. Our results contribute to the knowledge of the role of the TET3/OGT relationship in the complex mechanism supporting endometrial cancer progression.
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Liu NT, Perng CL, Chou YC, Ko PS, Lin YJ, Lin YC, Chang CC, Wang YC, Shang HS, Chao TK. Loss of ten-eleven translocation 1 (TET1) expression as a diagnostic and prognostic biomarker of endometrial carcinoma. PLoS One 2021; 16:e0259330. [PMID: 34731191 DOI: 10.1371/journal.pone.0259330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
Endometrial carcinoma (EC) is the most common gynecological cancer. However, there is currently no routinely used biomarker for differential diagnosis of malignant and premalignant endometrial lesions. Ten-eleven translocation (TET) proteins, especially TET1, were found to play a significant role in DNA demethylation, via conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC). TET1, 5-mC, and 5-hmC expression profiles in endometrial carcinogenesis are currently unclear. We conducted a hospital-based retrospective review of the immunohistochemical expression of TET1, 5-mC, and 5-hmC in 181 endometrial samples. A “high” TET1 and 5-hmC expression score was observed in all cases of normal endometrium (100.0% and 100.0%, respectively) and in most samples of endometrial hyperplasia without atypia (90.9% and 78.8%, respectively) and atypical hyperplasia (90.6% and 93.8%, respectively), but a “high” score was found in only less than half of the EC samples (48.8% and 46.5%, respectively). The TET1 and 5-hmC expression scores were significantly higher in normal endometrium and premalignant endometrial lesions than in ECs (p < 0.001). A “high” 5-mC expression score was observed more frequently for ECs (81.4%) than for normal endometrium (40.0%), endometrial hyperplasia without atypia (51.5%), and atypical hyperplasia (53.1%) (p < 0.001). We also found that TET1 mRNA expression was lower in ECs compared to normal tissues (p = 0.0037). TET1 immunohistochemistry (IHC) scores were highly proportional to the TET1 mRNA levels and we summarize that the TET1 IHC scoring can be used for biomarker determinations. Most importantly, a higher TET1 score in EC cases was associated with a good overall survival (OS) rate, with a hazard ratio (HR) of 0.31 for death (95% confidence interval: 0.11–0.84). Our findings suggest that TET1, 5-mC, and 5-hmC expression is a potential histopathology biomarker for the differential diagnosis of malignant and premalignant endometrial lesions. TET1 is also a potential prognostic marker for EC.
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Abstract
Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.
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Affiliation(s)
- Yi Dai
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
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10
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Zhao F, Zhang ZW, Zhang J, Zhang S, Zhang H, Zhao C, Chen Y, Luo L, Tong WM, Li C, Niu Y, Liu P. Loss of 5-Hydroxymethylcytosine as an Epigenetic Signature That Correlates With Poor Outcomes in Patients With Medulloblastoma. Front Oncol 2021; 11:603686. [PMID: 33718152 PMCID: PMC7945595 DOI: 10.3389/fonc.2021.603686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
Medulloblastoma, as the most common malignant brain tumor in children, exhibits highly dysregulated DNA methylation. The novel epigenetic marker—5-hydroxymethylcytosine (5hmC) plays essential role in gene regulation during brain development and in brain tumors. However, the biological and clinical implications of 5hmC in medulloblastoma are still unclear. Here, we detected global 5hmC levels in two independent medulloblastoma patient cohorts (discovery cohort: n = 81; validation cohort: n = 171) using ultra-high performance liquid chromatography-tandem mass spectrometry analysis. Immunohistochemistry was used to identify the cell proliferation and expression of Ten-eleven translocation 1 and 2 (TET1/2). The prognostic impacts of covariates on progression-free survival (PFS) and overall survival (OS) were evaluated using multivariate Cox hazards regression models. We observed that global 5hmC levels were decreased in medulloblastomas compared to normal cerebellums (P < 0.001). Multivariate analysis showed that low global 5hmC levels correlated with poor PFS and OS rates (discovery cohort: PFS: P = 0.003, OS: P = 0.002; validation cohort: PFS: P = 0.0002, OS: P = 0.001). Immunohistochemistry showed an inverse correlation between 5hmC score and Ki-67 index (r = -0.747, P < 0.0001). Moreover, 5hmC score in MB samples was associated with nuclear expression of TET1 (r = -0.419, P = 0.003) and TET2 (r = -0.399, P = 0.005) proteins. Our study demonstrates that loss of 5hmC is an epigenetic biomarker in medulloblastomas. Our results indicate that 5hmC could be a candidate prognostic indicator for improving survival prediction of risk stratification in patients with medulloblastoma.
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Affiliation(s)
- Fu Zhao
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhi-Wei Zhang
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Zhang
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Shun Zhang
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Heng Zhang
- Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Chi Zhao
- Department of Neuro-Oncology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Luo
- Department of Pathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Pinan Liu
- Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China.,Department of Neural Reconstruction, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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Oishi N, Vuong HG, Mochizuki K, Kondo T. Loss of 5-Hydroxymethylcytosine is an Epigenetic Hallmark of Thyroid Carcinomas with TERT Promoter Mutations. Endocr Pathol 2020; 31:359-366. [PMID: 33058026 DOI: 10.1007/s12022-020-09652-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic dysregulation is a hallmark of cancer, and aberrant methylation of cytosine residues plays a crucial role in abnormal gene expression in cancer cells. Recent studies demonstrate that 5-hydroxymethylcytosine (5-hmC) generated through 5-methylcytosine (5-mC) oxidation is significantly depleted in various cancers. However, whether 5-hmC levels change during the stepwise progression of thyroid carcinoma and the mechanisms underlying this effect remain unknown. The aims of this study were (i) to assess 5-hmC levels in normal and cancerous thyroid tissues, and (ii) identify clinicopathologic and genetic factors associated with the dysregulated hydroxymethylation of cytosine. Enzyme-linked immunosorbent assay (ELISA) showed that 5-hmC was significantly reduced in TERT promoter-mutated papillary thyroid carcinomas (PTCs) and anaplastic thyroid carcinomas (ATCs), while there was no significant difference in 5-hmC levels between TERT promoter-wild-type PTCs and normal thyroid tissues. Results of semi-quantitative analysis of 5-hmC through immunohistochemistry correlated well with those of ELISA and confirmed the loss of 5-hmC in tumor cells. Immunohistochemistry confirmed lower 5-hmC positivity in TERT promoter-mutated PTCs (n = 10) and ATCs (n = 4) than in normal thyroid tissues (n = 8) and TERT promoter-wild-type PTCs (n = 63). Tumor size (> 1 cm) and advanced stage were associated with decreased global 5-hmC in PTCs, while age, gross extrathyroidal invasion, node metastasis, and BRAF mutation were not. Collectively, these findings demonstrated that loss of 5-hmC is an epigenetic hallmark of thyroid carcinomas with TERT promoter mutation, indicating that TERT promoter-mutated thyroid carcinoma has a distinct molecular profile.
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Affiliation(s)
- Naoki Oishi
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan.
| | - Huy Gia Vuong
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan
| | - Kunio Mochizuki
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan
| | - Tetsuo Kondo
- Faculty of Medicine, Department of Pathology, University of Yamanashi, 1110 Shimokato, 409-3898, Chuo, Yamanashi, Japan
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12
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Avram GE, Marcu A, Moatar A, Samoila C, Podariu A, Seclaman E, Marian C. Changes in global DNA methylation and hydroxymethylation in oral mucosa according to tobacco smoke exposure. J Int Med Res 2020; 48:300060520954677. [PMID: 32938281 PMCID: PMC7503033 DOI: 10.1177/0300060520954677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE This prospective clinical study comparatively investigated the effects of tobacco smoking on global methylation and hydroxymethylation in oral epithelial cells. METHODS Buccal cells from the inside of the cheeks were collected from 47 individuals, including smokers, former smokers, and never smokers. DNA was extracted using dedicated kits. Methylated and hydroxymethylated DNA fractions were measured using assays similar to enzyme-linked immunosorbent assays. The levels of methylation and hydroxymethylation were compared among groups using unpaired two-tailed t-tests or the Mann-Whitney U test; P < 0.05 was considered statistically significant. RESULTS There was no statistically significant difference in the average number of cigarettes between smoker and former smoker groups. Although methylation levels were lower for smokers (3.1%) and former smokers (2.16%), compared with never smokers (4.16%), these differences were not statistically significant. There was a two-fold increase in hydroxymethylation level in never smokers, compared with smokers. CONCLUSIONS Our findings suggest that smoking leads to global reductions in both methylation and hydroxymethylation levels in oral epithelial cells in a manner influenced by the intensity and length of exposure to tobacco smoke.
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Affiliation(s)
- Gabriela-Emilia Avram
- Doctoral School, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania.,Department of Maxillofacial Surgery, Faculty of Dentistry, "Vasile Goldis" Western University of Arad, Arad, Romania
| | - Anca Marcu
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Alexandra Moatar
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Corina Samoila
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Angela Podariu
- Department of Preventive Dentistry, Community and Oral Health, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Edward Seclaman
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
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13
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Abstract
DNA cytosine modifications are important epigenetic marks. To elucidate their roles by a large scale of comparative studies, it is important to quantify the abundance of DNA cytosine modifications accurately. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a golden option. The performance of LC-MS/MS is heavily dependent on the ionization or protonation of target analytes. Initially, we found that two factors, DNA hydrolysate buffer and residual coeluted nucleosides, might greatly suppress the protonation of 5-(hydroxymethyl)-2'-deoxycytidine (5hmdC). Surprisingly, ammonium bicarbonate can eliminate the suppression caused by both factors. Mechanistically, ammonium bicarbonate increases the protonation capacity in the gas phase and facilitates proton transfer to the target nucleosides. Benefiting from these findings, we developed a suppression-free, sensitive, and robust ultrahigh-performance LC-MS/MS assay for massive detection of three DNA cytosine modifications, including 5-methyl-2'-deoxycytidine (5mdC), 5hmdC, and 5-formyl-2'-deoxycytidine (5fdC). In 30 consecutive analyses, the relative standard deviation (RSD) of the 5hmdC and 5fdC peak areas is 2.0% and 3.2%, respectively. In this case, no stable isotope-labeled standard is required for internal calibration. We further performed a comprehensive profiling of DNA cytosine modifications in 26 tissues of age-different C57BL/6N mice. Interestingly, we found that only liver 5hmdC abundance increases with the increasing age of adult mice, suggesting that liver 5hmdC might be a potential indicator of age in adulthood.
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Affiliation(s)
- Jiezhen Mo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiling Lu
- Greater China Market Division, Agilent Technologies, Beijing 100102, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China
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14
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Xu T, Gao H. Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment? Hum Genomics 2020; 14:15. [PMID: 32375881 PMCID: PMC7201531 DOI: 10.1186/s40246-020-00265-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/22/2020] [Indexed: 02/08/2023] Open
Abstract
5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an emerging modification of cytosine bases of recent years. Unlike 5mC, global 5hmC levels vary from tissues that have differential distribution both in mammalian tissues and in the genome. DNA hydroxymethylation is the process that 5mC oxidates into 5hmC with the catalysis of TET (ten-eleven translocation) enzymes. It is an essential option of DNA demethylation, which modulates gene expression by adjusting the DNA methylation level. Various factors can regulate the demethylation of DNA, such as environmental toxins and mental stress. In this review, we summarize the progress in the formation of 5hmC, and obtaining 5hmC in a cell-free DNA sample presents multiple advantages and challenges for the subject. Furthermore, the clinical potential for 5hmC modification in dealing with cancer early diagnosis, prognostic evaluation, and prediction of therapeutic effect is also mentioned.
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Affiliation(s)
- Tianmin Xu
- The Second HospitaI of Jilin University, Changchun, Jilin, China.
| | - Haoyue Gao
- The Second HospitaI of Jilin University, Changchun, Jilin, China
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15
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Zhang Y, Zheng D, Fang Q, Zhong M. Aberrant hydroxymethylation of ANGPTL4 is associated with selective intrauterine growth restriction in monochorionic twin pregnancies. Epigenetics 2020; 15:887-899. [PMID: 32114885 DOI: 10.1080/15592294.2020.1737355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective intrauterine growth restriction (sIUGR) is a severe complication in monochorionic (MC) twin pregnancies, and it carries increased risks of poor prognosis. Current data suggest that vascular anastomoses and unequal placental sharing may be the key contributor to discordant foetal growth. While MC twins derive from a single zygote and have almost identical genetic information, the precise mechanisms remain unknown. DNA hydroxymethylation is a newly discovered epigenetic feature associated with gene regulation and modification. Here, we investigate discordant hydroxymethylation patterns between two placental shares of sIUGR and analyse the potential role of aberrant hydroxymethylation of angiopoietin-like 4 (ANGPTL4) in placental dysplasia. Hydroxymethylation DNA immunoprecipitation (hMeDIP)-chip and mRNA sequencing were performed to identify hydroxymethylation-associated genes. Real-time qPCR, western blotting, and immunohistochemistry were used to confirm ANGPTL4 expression. The mechanisms regulating ANGPTL4 were investigated by cell migration assay, invasion assay, viability assay, and apoptotic ratio assays, western blotting and hMeDIP-qPCR. Decreased ANGPTL4 was detected in the smaller placental shares of sIUGR. ANGPTL4 knockdown suppressed trophoblast invasiveness and migration, which possibly occurred through hypoxia inducible factor 1α (HIF-1α) and HIF-1 signalling pathway. Hypoxia leads to aberrant expression of ANGPTL4 and HIF-1α, positively correlated with their aberrant hydroxymethylation levels in promoter regions. Aberrant hydroxymethylation of ANGPTL4 may contribute to placental impairment by the HIF-1 signalling pathway in smaller placental shares of sIUGR.
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Affiliation(s)
- Yi Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Dezhong Zheng
- Department of Cardiology, The Third Affiliated Hospital of Southern Medical University, Southern Medical University , Guangzhou, China.,Department of Cardiology, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Qun Fang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University , Guangzhou, China
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University , Guangzhou, China
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16
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Stöhr D, Jeltsch A, Rehm M. TRAIL receptor signaling: From the basics of canonical signal transduction toward its entanglement with ER stress and the unfolded protein response. Int Rev Cell Mol Biol 2020; 351:57-99. [PMID: 32247582 DOI: 10.1016/bs.ircmb.2020.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cytokine tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the large TNF superfamily that can trigger apoptosis in transformed or infected cells by binding and activating two receptors, TRAIL receptor 1 (TRAILR1) and TRAIL receptor 2 (TRAILR2). Compared to other death ligands of the same family, TRAIL induces apoptosis preferentially in malignant cells while sparing normal tissue and has therefore been extensively investigated for its suitability as an anti-cancer agent. Recently, it was noticed that TRAIL receptor signaling is also linked to endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). The role of TRAIL receptors in regulating cellular apoptosis susceptibility therefore is broader than previously thought. Here, we provide an overview of TRAIL-induced signaling, covering the core signal transduction during extrinsic apoptosis as well as its link to alternative outcomes, such as necroptosis or NF-κB activation. We discuss how environmental factors, transcriptional regulators, and genetic or epigenetic alterations regulate TRAIL receptors and thus alter cellular TRAIL susceptibility. Finally, we provide insight into the role of TRAIL receptors in signaling scenarios that engage the unfolded protein response and discuss how these findings might be translated into new combination therapies for cancer treatment.
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Affiliation(s)
- Daniela Stöhr
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany; University of Stuttgart, Stuttgart Research Center Systems Biology, Stuttgart, Germany.
| | - Albert Jeltsch
- Department of Biochemistry, University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
| | - Markus Rehm
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany; University of Stuttgart, Stuttgart Research Center Systems Biology, Stuttgart, Germany; University of Stuttgart, Stuttgart Centre for Simulation Science, Stuttgart, Germany
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17
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Wu T, Zhang ZW, Li S, Wang B, Yang Z, Li P, Zhang J, Tong WM, Li C, Zhao F, Niu Y, Liu P. Characterization of global 5-hydroxymethylcytosine in pediatric posterior fossa ependymoma. Clin Epigenetics 2020; 12:19. [PMID: 31992357 PMCID: PMC6988368 DOI: 10.1186/s13148-020-0809-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/06/2020] [Indexed: 12/16/2022] Open
Abstract
Background 5-Hydroxymethylcytosine (5hmC) is a novel epigenetic mark and may be involved in the mechanisms of tumorigenesis and malignant transformation. However, the role of 5hmC in ependymoma, the third most common brain tumor in children, remains unclear. The aim of this study sought to identify the characterization of 5hmC levels in pediatric posterior fossa ependymoma and to evaluate whether 5hmC levels could be a potential factor to predict clinical outcomes. Results Our results showed that 5hmC levels were globally decreased in posterior fossa ependymoma compared with normal cerebellum tissues (P < 0.001). Group A posterior fossa ependymomas had higher 5hmC levels than group B tumors (P = 0.007). Moreover, 5hmC levels positively correlated with Ki-67 index in posterior fossa ependymoma (r = 0.428, P = 0.003). Multivariate Cox hazards model revealed that patients with high 5hmC levels (> 0.102%) had worse PFS and OS than patients with lower 5hmC levels (< 0.102%) (PFS: HR = 3.014; 95% CI, 1.040–8.738; P = 0.042; OS: HR = 2.788; 95% CI, 0.974–7.982; P = 0.047). Conclusions Our findings suggest that loss of 5hmC is an epigenetic hallmark for pediatric posterior fossa ependymoma. 5hmC levels may represent a potential biomarker to predict prognosis in children with posterior fossa ependymoma.
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Affiliation(s)
- Tao Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Zhi-Wei Zhang
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Science, School of Basic Medicine Peking Union Medical College; Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Shiwei Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Bo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Zhijun Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Peng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Jing Zhang
- Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Science, School of Basic Medicine Peking Union Medical College; Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Fu Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China.,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Science, School of Basic Medicine Peking Union Medical College; Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
| | - Pinan Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119# South 4th Ring Road, Fengtai District, Beijing, 100070, China. .,Department of Neural reconstruction, Beijing Neurosurgical Institute, Capital Medical University, No. 119, South 4th Ring Road, Fengtai District, Beijing, 100070, China.
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18
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Wilkins OM, Johnson KC, Houseman EA, King JE, Marsit CJ, Christensen BC. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019; 15:398-418. [PMID: 31842685 PMCID: PMC7153548 DOI: 10.1080/15592294.2019.1695332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
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Affiliation(s)
- Owen M Wilkins
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - E Andres Houseman
- Department of Biostatistics, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Jessica E King
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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19
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Affiliation(s)
- Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry and Sauvage Center for Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
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20
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Gambichler T, Schmitt K, Rüddel I, Dreibigacker M, Stockfleth E, Becker JC. Decreased 5-hydroxymethylcytosine immunoreactivity in primary Merkel cell carcinoma is a strong predictor for disease-specific death. Br J Dermatol 2019; 181:389-390. [PMID: 30703276 DOI: 10.1111/bjd.17705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- T Gambichler
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - K Schmitt
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - I Rüddel
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - M Dreibigacker
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - E Stockfleth
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - J C Becker
- Translational Skin Cancer Research, DKTK Partner Site Essen/Düsseldorf, German Cancer Consortium, Dermatology, University Duisburg-Essen, Essen, Germany
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21
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Li M, Tang Y, Li Q, Xiao M, Yang Y, Wang Y. Mono-ADP-ribosylation of H3R117 traps 5mC hydroxylase TET1 to impair demethylation of tumor suppressor gene TFPI2. Oncogene 2019; 38:3488-503. [PMID: 30651599 DOI: 10.1038/s41388-018-0671-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 11/12/2018] [Accepted: 12/14/2018] [Indexed: 02/06/2023]
Abstract
Recently, nuclear poly-ADP-ribosylation had aroused research interest in epigenetics, but little attempt to explore functions of mono-ADP-ribosylation of histone, the major formation of histone ADP-ribosylated modification. We have previously reported a novel mono-ADP-ribosylation of H3R117, which promoted proliferation of LoVo cells. Here we showed that mono-ADP-ribosylated H3R117 of LoVo cells depressed demethylation of tumor suppressor TFPI2 promoter by suppressing TET1 expression and adjusting H3K9me3 enrichment of TFPI2 promoter to attenuate affinity of TET1, besides, since high H3K27me3 level was associated with hypermethylation, mono-ADP-ribosylated-H3R117-depended-H3K27me3 of TFPI2 promoter may contribute to hypermethylation of TFPI2. However, H3R117A mutation increased poly-ADP-ribosylated modification of TET1 promoter not TFPI2 promoter, which resulted in boosting transcription and expression of TET1 by altering DNA methylated modification, chromatin accessibility, and histone-methylated modification of TET1 promoter, while knockout TET1 of H3R117A LoVo cells directly led to hypermethylation of TFPI2 promoter and depression of TFPI2 secretion as well as enhanced proliferation, suggested that TET1 played a key role in demethylation of TFPI2, production of TFPI2, and cell proliferation. Bioinformatics analyses reveal prevalent hypermethylation of TFPI2 was an early event in tumorigenesis of colorectal caner, and expression of TET1 and TFPI2 was positive correlation in colorectal cancer and normal tissue. These data suggested that mono-ADP-ribosylation of H3R117 upregulated methylation of TFPI2 by impact TET1, since hypermethyaltion of TFPI2 was an early event in tumorigenesis, selectively target mono-ADP-ribosylation of H3R117 deficiency could be a feasible way to block tumorigenesis of colorectal cancer.
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22
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Abstract
The use of intravenous vitamin C (IVC) for cancer therapy has long been an area of intense controversy. Despite this, high dose IVC has been administered for decades by complementary health care practitioners and physicians, with little evidence base resulting in inconsistent clinical practice. In this review we pose a series of questions of relevance to both researchers and clinicians, and also patients themselves, in order to identify current gaps in our knowledge. These questions include: Do oncology patients have compromised vitamin C status? Is intravenous the optimal route of vitamin C administration? Is IVC safe? Does IVC interfere with chemotherapy or radiotherapy? Does IVC decrease the toxic side effects of chemotherapy and improve quality of life? What are the relevant mechanisms of action of IVC? What are the optimal doses, frequency, and duration of IVC therapy? Researchers have made massive strides over the last 20 years and have addressed many of these important aspects, such as the best route for administration, safety, interactions with chemotherapy, quality of life, and potential mechanisms of action. However, we still do not know the answers to a number of fundamental questions around best clinical practice, such as how much, how often and for how long to administer IVC to oncology patients. These questions point the way forward for both basic research and future clinical trials.
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Affiliation(s)
- Anitra C Carr
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John Cook
- New Brighton Health Care, Christchurch, New Zealand
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23
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Shahal T, Koren O, Shefer G, Stern N, Ebenstein Y. Hypersensitive quantification of global 5-hydroxymethylcytosine by chemoenzymatic tagging. Anal Chim Acta 2018; 1038:87-96. [PMID: 30278911 DOI: 10.1016/j.aca.2018.08.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 02/07/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is an epigenetic DNA modification. Tissue-specific reduction in global 5hmC levels has been associated with various types of cancer. One of the challenges associated with detecting 5hmC levels is its extremely low content, especially in blood. The gold-standard for reliable global 5hmC quantitation is liquid chromatography-tandem mass spectroscopy (LC-MS/MS) operating in a multiple reaction monitoring (MRM) mode. Difficulties associated with 5hmC detection by LC-MS/MS include its low abundance, low ionization efficiency and possible ion suppression from co-eluted compounds. Hence, detecting 5hmC levels in blood samples for diagnosis of leukemia and other blood malignancies presents a unique challenge. To overcome these difficulties we introduce a simple chemoenzymatic method for specifically tagging 5hmC, resulting in an eight-fold increase in detection sensitivity. We demonstrate that we could quantitatively detect 5hmC levels in various human tissues, including blood samples from healthy individuals and leukemia patients, using the most basic quadrupole mass-analyzer instrument and only 200 ng of DNA. The limit of detection (LOD) of our technique is 0.001% 5hmC from 300 ng DNA, sufficient for future mass-spectroscopy based diagnostics of diseases associated with low 5hmC levels such as leukemia.
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Affiliation(s)
- Tamar Shahal
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Omri Koren
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gabi Shefer
- Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Naftali Stern
- Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel.
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24
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Shishodia S, Zhang D, El-Sagheer AH, Brown T, Claridge TDW, Schofield CJ, Hopkinson RJ. NMR analyses on N-hydroxymethylated nucleobases - implications for formaldehyde toxicity and nucleic acid demethylases. Org Biomol Chem 2018; 16:4021-4032. [PMID: 29767200 PMCID: PMC5977384 DOI: 10.1039/c8ob00734a] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Formaldehyde is produced in cells by enzyme-catalysed demethylation reactions, including those occurring on N-methylated nucleic acids. Formaldehyde reacts with nucleobases to form N-hydroxymethylated adducts that may contribute to its toxicity/carcinogenicity when added exogenously, but the chemistry of these reactions has been incompletely defined. We report NMR studies on the reactions of formaldehyde with canonical/modified nucleobases. The results reveal that hydroxymethyl hemiaminals on endocyclic nitrogens, as observed with thymidine and uridine monophosphates, are faster to form than equivalent hemiaminals on exocyclic nitrogens; however, the exocyclic adducts, as formed with adenine, guanine and cytosine, are more stable in solution. Nucleic acid demethylase (FTO)-catalysed hydroxylation of (6-methyl)adenosine results in (6-hydroxymethyl)adenosine as the major observed product; by contrast no evidence for a stable 3-hydroxymethyl adduct was accrued with FTO-catalysed oxidation of (3-methyl)thymidine. Collectively, our results imply N-hydroxymethyled adducts of nucleic acid bases, formed either by reactions with formaldehyde or via demethylase catalysis, have substantially different stabilities, with some being sufficiently stable to have functional roles in disease or the regulation of nucleic acid/nucleobase activity.
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Affiliation(s)
- S. Shishodia
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - D. Zhang
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - A. H. El-Sagheer
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
- Chemistry Branch, Department of Science and Mathematics
, Faculty of Petroleum and Mining Engineering
, Suez University
,
43721 Suez
, Egypt
| | - T. Brown
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - T. D. W. Claridge
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - C. J. Schofield
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - R. J. Hopkinson
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
- Leicester Institute of Structural and Chemical Biology and Department of Chemistry
, University of Leicester
,
Henry Wellcome Building
, Lancaster Road
, Leicester
, LE1 7RH
, UK
.
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25
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Feng C, Dong J, Chang W, Cui M, Xu T. The Progress of Methylation Regulation in Gene Expression of Cervical Cancer. Int J Genomics 2018; 2018:8260652. [PMID: 29850477 DOI: 10.1155/2018/8260652] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/02/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer is one of the most common gynecological tumors in females, which is closely related to high-rate HPV infection. Methylation alteration is a type of epigenetic decoration that regulates the expression of genes without changing the DNA sequence, and it is essential for the progression of cervical cancer in pathogenesis while reflecting the prognosis and therapeutic sensitivity in clinical practice. Hydroxymethylation has been discovered in recent years, thus making 5-hmC, the more stable marker, attract more attention in the field of methylation research. As markers of methylation, 5-hmC and 5-mC together with 5-foC and 5-caC draw the outline of the reversible cycle, and 6-mA takes part in the methylation of RNA, especially mRNA. Furthermore, methylation modification participates in ncRNA regulation and histone decoration. In this review, we focus on recent advances in the understanding of methylation regulation in the process of cervical cancer, as well as HPV and CIN, to identify the significant impact on the prospect of overcoming cervical cancer.
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26
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Müller SM, Finke H, Ebert F, Kopp JF, Schumacher F, Kleuser B, Francesconi KA, Raber G, Schwerdtle T. Arsenic-containing hydrocarbons: effects on gene expression, epigenetics, and biotransformation in HepG2 cells. Arch Toxicol 2018; 92:1751-65. [PMID: 29602950 DOI: 10.1007/s00204-018-2194-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 01/29/2023]
Abstract
Arsenic-containing hydrocarbons (AsHCs), a subgroup of arsenolipids found in fish and algae, elicit substantial toxic effects in various human cell lines and have a considerable impact on cellular energy levels. The underlying mode of action, however, is still unknown. The present study analyzes the effects of two AsHCs (AsHC 332 and AsHC 360) on the expression of 44 genes covering DNA repair, stress response, cell death, autophagy, and epigenetics via RT-qPCR in human liver (HepG2) cells. Both AsHCs affected the gene expression, but to different extents. After treatment with AsHC 360, flap structure-specific endonuclease 1 (FEN1) as well as xeroderma pigmentosum group A complementing protein (XPA) and (cytosine-5)-methyltransferase 3A (DNMT3A) showed time- and concentration-dependent alterations in gene expression, thereby indicating an impact on genomic stability. In the subsequent analysis of epigenetic markers, within 72 h, neither AsHC 332 nor AsHC 360 showed an impact on the global DNA methylation level, whereas incubation with AsHC 360 increased the global DNA hydroxymethylation level. Analysis of cell extracts and cell media by HPLC-mass spectrometry revealed that both AsHCs were considerably biotransformed. The identified metabolites include not only the respective thioxo-analogs of the two AsHCs, but also several arsenic-containing fatty acids and fatty alcohols, contributing to our knowledge of biotransformation mechanisms of arsenolipids.
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Ahn JS, Kim HJ, Kim YK, Lee SS, Ahn SY, Jung SH, Yang DH, Lee JJ, Park HJ, Choi SH, Jung CW, Jang JH, Kim HJ, Moon JH, Sohn SK, Won JH, Kim SH, Michael S, Minden MD, Kim DD. 5-Hydroxymethylcytosine correlates with epigenetic regulatory mutations, but may not have prognostic value in predicting survival in normal karyotype acute myeloid leukemia. Oncotarget 2017; 8:8305-14. [PMID: 28039446 DOI: 10.18632/oncotarget.14171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/24/2016] [Indexed: 12/18/2022] Open
Abstract
Stem cells display remarkably high levels of 5-hydroxymethylcytosine (5hmC). Both TET2 and IDH1/2 mutations can impair the production of 5hmC, thus decreasing 5hmC levels. TET2 or IDH1/2 mutations are commonly observed in acute myeloid leukemia (AML). However, the implications of 5hmC on survival in normal karyotype AML patients have not been fully evaluated. The 5hmC levels were analyzed in 375 patients using ELISA. The levels of 5hmC in DNA samples were converted to a log scale for the analysis and correlations with TET2 and/or IDH1/2 mutations were evaluated. The median 5hmC level was 0.065% (range 0.001–0.999). Mutation rates were 13.1% for TET2mut, 6.7% for IDH1mut, and 13.9% for IDH2mut. The prevalence of TET2 and/or IDH1/2 was 33.1% (124/375). TET2 and IDH1/2 mutated patients had significantly lower levels of log(5hmC) compared with patients without TET2 or IDH1/2 mutations (p<0.001). With a median follow-up of 55.5 months (range, 0.7–179.8), there was no significant difference in overall survival, event-free survival, and relapse risk according to TET2mut or IDH1/2mut (all, p>0.05). To identify its prognostic value, we sub-classified the levels of 5hmC into tertiles for 5hmC values. However, there was no significant association between the categories of 5hmC levels and survival or relapse risk (all p>0.05). Patients with TET2 or IDH1/2 mutations had lower levels of 5hmC. The 5hmC levels may not be predictive of survival in patients with normal karyotype AML.
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Goetzman ES, Prochownik EV. The Role for Myc in Coordinating Glycolysis, Oxidative Phosphorylation, Glutaminolysis, and Fatty Acid Metabolism in Normal and Neoplastic Tissues. Front Endocrinol (Lausanne) 2018; 9:129. [PMID: 29706933 PMCID: PMC5907532 DOI: 10.3389/fendo.2018.00129] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 12/24/2022] Open
Abstract
That cancer cells show patterns of metabolism different from normal cells has been known for over 50 years. Yet, it is only in the past decade or so that an appreciation of the benefits of these changes has begun to emerge. Altered cancer cell metabolism was initially attributed to defective mitochondria. However, we now realize that most cancers do not have mitochondrial mutations and that normal cells can transiently adopt cancer-like metabolism during periods of rapid proliferation. Indeed, an encompassing, albeit somewhat simplified, conceptual framework to explain both normal and cancer cell metabolism rests on several simple premises. First, the metabolic pathways used by cancer cells and their normal counterparts are the same. Second, normal quiescent cells use their metabolic pathways and the energy they generate largely to maintain cellular health and organelle turnover and, in some cases, to provide secreted products necessary for the survival of the intact organism. By contrast, undifferentiated cancer cells minimize the latter functions and devote their energy to producing the anabolic substrates necessary to maintain high rates of unremitting cellular proliferation. Third, as a result of the uncontrolled proliferation of cancer cells, a larger fraction of the metabolic intermediates normally used by quiescent cells purely as a source of energy are instead channeled into competing proliferation-focused and energy-consuming anabolic pathways. Fourth, cancer cell clones with the most plastic and rapidly adaptable metabolism will eventually outcompete their less well-adapted brethren during tumor progression and evolution. This attribute becomes increasingly important as tumors grow and as their individual cells compete in a constantly changing and inimical environment marked by nutrient, oxygen, and growth factor deficits. Here, we review some of the metabolic pathways whose importance has gained center stage for tumor growth, particularly those under the control of the c-Myc (Myc) oncoprotein. We discuss how these pathways differ functionally between quiescent and proliferating normal cells, how they are kidnapped and corrupted during the course of transformation, and consider potential therapeutic strategies that take advantage of common features of neoplastic and metabolic disorders.
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Affiliation(s)
- Eric S. Goetzman
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, United States
| | - Edward V. Prochownik
- Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, United States
- Department of Microbiology and Molecular Genetics, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, United States
- *Correspondence: Edward V. Prochownik,
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Rajkumar T, Mani S; Vittal Rangan Arvinden, Arunagiri Kuha Deva Magendhra Rao. Regulation and Functional Significance of 5-Hydroxymethylcytosine in Cancer. Epigenomes 2017; 1:19. [DOI: 10.3390/epigenomes1030019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Epigenetic modes of gene regulation are important for physiological conditions and its aberrant changes can lead to disease like cancer. 5-hydroxymethylcytosine (5hmC) is an oxidized form of 5-methylcytosine (5mC) catalyzed by Ten Eleven Translocation (TET) enzymes. 5hmC is considered to be a demethylation intermediate and is emerging as a stable and functional base modification. The global loss of 5hmC level is commonly observed in cancers and tumorigenic germline mutations in IDH, SDH and FH are found to be inhibiting TET activity. Although a global loss of 5hmC is characteristic in cancers, locus-specific 5hmC gain implicates selective gene expression control. The definitive role of 5hmC as a tumor suppressing or promoting modification can be deduced by identifying locus-specific 5hmC modification in different types of cancer. Determining the genes carrying 5hmC modifications and its selective variation will open up new therapeutic targets. This review outlines the role of global and locus-specific changes of 5hmC in cancers and the possible mechanisms underlying such changes. We have described major cellular factors that influence 5hmC levels and highlighted the significance of 5hmC in tumor micro environmental condition like hypoxia.
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Zhou Z, Zhang H, Liu Y, Zhang Z, Du G, Li H, Yu X, Huang Y. Loss of TET1 facilitates DLD1 colon cancer cell migration via H3K27me3‐mediated down‐regulation of E‐cadherin. J Cell Physiol 2017; 233:1359-1369. [DOI: 10.1002/jcp.26012] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/15/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Zhen Zhou
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Hong‐Sheng Zhang
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Yang Liu
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Zhong‐Guo Zhang
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Guang‐Yuan Du
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Hu Li
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Xiao‐Ying Yu
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
| | - Ying‐Hui Huang
- College of Life Science and BioengineeringBeijing University of TechnologyChaoyangBeijingChina
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Parfett CL, Desaulniers D. A Tox21 Approach to Altered Epigenetic Landscapes: Assessing Epigenetic Toxicity Pathways Leading to Altered Gene Expression and Oncogenic Transformation In Vitro. Int J Mol Sci 2017; 18:E1179. [PMID: 28587163 DOI: 10.3390/ijms18061179] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 02/07/2023] Open
Abstract
An emerging vision for toxicity testing in the 21st century foresees in vitro assays assuming the leading role in testing for chemical hazards, including testing for carcinogenicity. Toxicity will be determined by monitoring key steps in functionally validated molecular pathways, using tests designed to reveal chemically-induced perturbations that lead to adverse phenotypic endpoints in cultured human cells. Risk assessments would subsequently be derived from the causal in vitro endpoints and concentration vs. effect data extrapolated to human in vivo concentrations. Much direct experimental evidence now shows that disruption of epigenetic processes by chemicals is a carcinogenic mode of action that leads to altered gene functions playing causal roles in cancer initiation and progression. In assessing chemical safety, it would therefore be advantageous to consider an emerging class of carcinogens, the epigenotoxicants, with the ability to change chromatin and/or DNA marks by direct or indirect effects on the activities of enzymes (writers, erasers/editors, remodelers and readers) that convey the epigenetic information. Evidence is reviewed supporting a strategy for in vitro hazard identification of carcinogens that induce toxicity through disturbance of functional epigenetic pathways in human somatic cells, leading to inactivated tumour suppressor genes and carcinogenesis. In the context of human cell transformation models, these in vitro pathway measurements ensure high biological relevance to the apical endpoint of cancer. Four causal mechanisms participating in pathways to persistent epigenetic gene silencing were considered: covalent histone modification, nucleosome remodeling, non-coding RNA interaction and DNA methylation. Within these four interacting mechanisms, 25 epigenetic toxicity pathway components (SET1, MLL1, KDM5, G9A, SUV39H1, SETDB1, EZH2, JMJD3, CBX7, CBX8, BMI, SUZ12, HP1, MPP8, DNMT1, DNMT3A, DNMT3B, TET1, MeCP2, SETDB2, BAZ2A, UHRF1, CTCF, HOTAIR and ANRIL) were found to have experimental evidence showing that functional perturbations played “driver” roles in human cellular transformation. Measurement of epigenotoxicants presents challenges for short-term carcinogenicity testing, especially in the high-throughput modes emphasized in the Tox21 chemicals testing approach. There is need to develop and validate in vitro tests to detect both, locus-specific, and genome-wide, epigenetic alterations with causal links to oncogenic cellular phenotypes. Some recent examples of cell-based high throughput chemical screening assays are presented that have been applied or have shown potential for application to epigenetic endpoints.
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Zhong S, Li Z, Jiang T, Li X, Wang H. Immunofluorescence Imaging Strategy for Evaluation of the Accessibility of DNA 5-Hydroxymethylcytosine in Chromatins. Anal Chem 2017; 89:5702-5706. [DOI: 10.1021/acs.analchem.7b01428] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shangwei Zhong
- School
of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Li
- State
Key Laboratory of Environmental Chemistry and Ecotoxicoogy, Research Center for Eco-Environmental Sciences, Beijing 100085, China
| | - Ting Jiang
- School
of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjun Li
- School
of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicoogy, Research Center for Eco-Environmental Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Wang D, Huang JH, Zeng QH, Gu C, Ding S, Lu JY, Chen J, Yang SB. Increased 5-hydroxymethylcytosine and Ten-eleven Translocation Protein Expression in Ultraviolet B-irradiated HaCaT Cells. Chin Med J (Engl) 2017; 130:594-599. [PMID: 28229992 PMCID: PMC5339934 DOI: 10.4103/0366-6999.200539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine (5mC) is catalyzed to 5- hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) family proteins. Recent studies have revealed that aberrant TETs expression or 5hmC level may play important roles in the occurrence and development of various pathological and physiological processes including cancer and aging. This study aimed to explore the relation between aberrant DNA hydroxymethylation with skin photoaging and to investigate the levels of TETs, 5mC, and 5hmC expression 24 h after 40 mJ/cm2 and 80 mJ/cm2 doses of ultraviolet B (UVB) irradiation to HaCaT cells. Methods: To explore whether aberrant DNA hydroxymethylation is also related to skin photoaging, 40 mJ/cm2 and 80 mJ/cm2 doses of UVB were chosen to treat keratinocytes (HaCaT cells). After 24 h of UVB irradiation, 5mC and 5hmC levels were determined by immunohistochemistry (IHC) and immunofluorescence (IF), and at the same time, the expression levels of matrix metalloproteinase 1 (MMP-1) and TETs were assessed by reverse transcription-polymerase chain reaction or Western blot analysis. Results: After 40 mJ/cm2 and 80 mJ/cm2 doses of UVB exposure, both IHC and IF results showed that 5hmC levels increased significantly, while the 5mC levels did not exhibit significant changes in HaCaT cells, compared with HaCat cells without UVB exposure. Moreover, compared with HaCat cells without UVB exposure, the levels of TET1, TET2, and TET3 mRNA and protein expression were significantly upregulated (mRNA: P = 0.0022 and 0.0043 for TET1; all P < 0.0001 for TET2; all P = 0.0006 for TET3; protein: P = 0.0012 and 0.0006 for TET1; all P = 0.0022 for TET2; and all P = 0.0002 for TET3), and the levels of MMP-1 mRNA expression increased dose dependently in 40 mJ/cm2 and 80 mJ/cm2 UVB-irradiated groups. Conclusion: UVB radiation could cause increased 5hmC and TET expression, which might become a novel biomarker in UVB-related skin aging.
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Affiliation(s)
- Dan Wang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jin-Hua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Qing-Hai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Can Gu
- Department of Community Nursing, Xiangya School of Nursing, Central South University, Changsha, Hunan 410013, China
| | - Shu Ding
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jian-Yun Lu
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Sheng-Bo Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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Tyagi M, Reddy D, Gupta S. Genomic characterization and dynamic methylation of promoter facilitates transcriptional regulation of H2A variants, H2A.1 and H2A.2 in various pathophysiological states of hepatocyte. Int J Biochem Cell Biol 2017; 85:15-24. [PMID: 28163185 DOI: 10.1016/j.biocel.2017.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 12/31/2022]
Abstract
Differential expression of homomorphous variants of H2A family of histone H2A.1 and H2A.2 have been associated with hepatocellular carcinoma and maintenance of undifferentiated state of hepatocyte. However, not much is known about the transcriptional regulation of these H2A variants. The current study revealed the presence of 43bp 5'-regulatory region upstream of translation start site and a 26bp 3' stem loop conserved region for both the H2A.1 and H2A.2 variants. However, alignment of both H2A.1 and H2A.2 5'-untranslated region (UTR) sequences revealed no significant degree of homology between them despite the coding exon being very similar amongst the variants. Further, transient transfection coupled with dual luciferase assay of cloned 5' upstream sequences of H2A.1 and H2A.2 of length 1.2 (-1056 to +144) and 1.379kb (-1160 to +219) from experimentally identified 5'UTR in rat liver cell line (CL38) confirmed their promoter activity. Moreover, in silico analysis revealed a presence of multiple CpG sites interspersed in the cloned promoter of H2A.1 and a CpG island near TSS for H2A.2, suggesting that histone variants transcription might be regulated epigenetically. Indeed, treatment with DNMT and HDAC inhibitors increased the expression of H2A.2 with no significant change in H2A.1 levels. Further, methyl DNA immunoprecipitation coupled with quantitative analysis of DNA methylation using real-time PCR revealed hypo-methylation and hyper-methylation of H2A.1 and H2A.2 respectively in embryonic and HCC compared to control adult liver tissue. Collectively, the data suggests that differential DNA methylation on histone promoters is a dynamic player regulating their expression status in different pathophysiological stages of liver.
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Affiliation(s)
- Monica Tyagi
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410210 MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085, India.
| | - Divya Reddy
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410210 MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085, India.
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410210 MH, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085, India.
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Tammen SA, Park JE, Shin PK, Friso S, Chung J, Choi SW. Iron Supplementation Reverses the Reduction of Hydroxymethylcytosine in Hepatic DNA Associated With Chronic Alcohol Consumption in Rats. J Cancer Prev 2016; 21:264-270. [PMID: 28053961 PMCID: PMC5207611 DOI: 10.15430/jcp.2016.21.4.264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/10/2016] [Accepted: 11/13/2016] [Indexed: 11/05/2022] Open
Abstract
Background Alcohol is known to affect two epigenetic phenomena, DNA methylation and DNA hydroxymethylation, and iron is a cofactor of ten-eleven translocation (TET) enzymes that catalyze the conversion from methylcytosine to hydroxymethylcytosine. In the present study we aimed to determine the effects of alcohol on DNA hydroxymethylation and further effects of iron on alcohol associated epigenetic changes. Methods Twenty-four male Sprague-Dawley rats were fed either Lieber-DeCarli alcohol diet (36% calories from ethanol) or Lieber-DeCarli control diet along with or without iron supplementation (0.6% carbonyl iron) for 8 weeks. Hepatic non-heme iron concentrations were measured by colorimetric assays. Protein levels of hepatic ferritin and transferrin receptor were determined by Western blotting. Methylcytosine, hydroxymethylcytosine and unmodified cytosine in DNA were simultaneously measured by liquid chromatography/mass spectrometry method. Results Iron supplementation significantly increased hepatic non-heme iron contents (P < 0.05) but alcohol alone did not. However, both alcohol and iron significantly increased hepatic ferritin levels and decreased hepatic transferrin receptor levels (P < 0.05). Alcohol reduced hepatic DNA hydroxymethylation (0.21% ± 0.04% vs. 0.33% ± 0.04%, P = 0.01) compared to control, while iron supplementation to alcohol diet did not change DNA hydroxymethylation. There was no significant difference in methylcytosine levels, while unmodified cytosine levels were significantly increased in alcohol-fed groups compared to control (95.61% ± 0.08% vs. 95.26% ± 0.12%, P = 0.03), suggesting that alcohol further increases the conversion from hydroxymethylcytosine to unmodified cytosine. Conclusions Chronic alcohol consumption alters global DNA hydroxymethylation in the liver but iron supplementation reverses the epigenetic effect of alcohol.
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Affiliation(s)
- Stephanie A Tammen
- Friedman School of Nutrition Science and Policy Tufts University, Boston, MA, USA
| | - Jung Eun Park
- Department of Food and Nutrition, College of Human Ecology, Kyung Hee University, Seoul, Korea
| | - Phil Kyung Shin
- Department of Food and Nutrition, College of Human Ecology, Kyung Hee University, Seoul, Korea; Chaum Life Center, CHA University School of Medicine, Seoul, Korea
| | | | - Jayong Chung
- Department of Food and Nutrition, College of Human Ecology, Kyung Hee University, Seoul, Korea
| | - Sang-Woon Choi
- Friedman School of Nutrition Science and Policy Tufts University, Boston, MA, USA; Chaum Life Center, CHA University School of Medicine, Seoul, Korea
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Singhal SK, Usmani N, Michiels S, Metzger-Filho O, Saini KS, Kovalchuk O, Parliament M. Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data. Oncotarget 2016; 7:3002-17. [PMID: 26657508 PMCID: PMC4823086 DOI: 10.18632/oncotarget.6503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/16/2015] [Indexed: 02/06/2023] Open
Abstract
Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation. Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing. Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer. Changes in DNA methylation profoundly affect global gene expression patterns. What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed. Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement. Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and high-level analyses of DNA methylation data. Low-level analysis refers to pre-processing of methylation data (i.e. normalization, transformation and filtering), whereas high-level analysis is focused on illustrating the application of the widely used class comparison, class prediction and class discovery methods to DNA methylation data. Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region.
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Affiliation(s)
- Sandeep K Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
| | - Stefan Michiels
- Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Villejuif, France.,INSERM U1018, CESP, Université Paris-Sud, Villejuif, France
| | - Otto Metzger-Filho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada.,Canada Cancer and Aging Research Laboratories Ltd., Lethbridge, Canada
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
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Wang Y, Guan H. The Role of DNA Methylation in Lens Development and Cataract Formation. Cell Mol Neurobiol 2017; 37:979-84. [DOI: 10.1007/s10571-016-0447-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
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Liu D, Zhao C, Wang H. Glucosylation Mediated Rolling Circle Amplification Combined with a qPCR Assay for the Detection of 5-Hydroxymethylcytosine. ANAL SCI 2016; 32:963-8. [PMID: 27682401 DOI: 10.2116/analsci.32.963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The detection of 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic mark, is essential to its functional study. Here, an efficient and simple two-step-amplification method to detect 5hmC mediated by glucosylation is reported, which combines rolling circle amplification (RCA) and a quantitative polymerase chain reaction (qPCR). In the first step RCA, the glucosylated 5hmC (5ghmC), but not 5hmC, 5-methylcytosine (5mC) or cytosine (C) bases, could directly and specifically inhibit the activity of phi29 DNA polymerase, resulting in less RCA product compared to that using C-/5mC-/5hmC-containing templates. Then, the second step qPCR is adopted to test and verify the difference of the product quantity of 5ghmC-related RCA. The results show that the delta cycle threshold, ΔCt, obtained by subtracting the cycle threshold value (Ct) of C-related qPCR from that of each qPCR, of 5ghmC-related qPCR reaches 1.59 ± 0.03, significantly different from that of C-/5mC-/5hmC-related qPCR (-0.00 ± 0.09, 0.06 ± 0.08 and -0.02 ± 0.03, respectively). Meanwhile, a linear relationship is observed between the 5ghmC levels and the ΔCt values. This suggests that the strategy has a potential application for 5hmC detection and quantification.
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Affiliation(s)
- Di Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
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Park JL, Kim HJ, Seo EH, Kwon OH, Lim B, Kim M, Kim SY, Song KS, Kang GH, Kim HJ, Choi BY, Kim YS. Decrease of 5hmC in gastric cancers is associated with TET1 silencing due to with DNA methylation and bivalent histone marks at TET1 CpG island 3'-shore. Oncotarget 2016; 6:37647-62. [PMID: 26462176 PMCID: PMC4741955 DOI: 10.18632/oncotarget.6069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 09/26/2015] [Indexed: 12/14/2022] Open
Abstract
Recent evidence has shown that the level of 5-hydroxymethylcytosine (5hmC) in chromosomal DNA is aberrantly decreased in a variety of cancers, but whether this decrease is a cause or a consequence of tumorigenesis is unclear. Here we show that, in gastric cancers, the 5hmC decrease correlates with a decrease in ten-eleven translocation 1 (TET1) expression, which is strongly associated with metastasis and poor survival in patients with gastric cancer. In gastric cancer cells, TET1-targeted siRNA induced a decrease in 5hmC, whereas TET1 overexpression induced an increase in 5hmC and reduced cell proliferation, thus correlating decreased 5hmC with gastric carcinogenesis. We also report the epigenetic signatures responsible for regulating TET1 transcription. Methyl-CpG Binding Domain Sequencing and Reduced Representation Bisulfite Sequencing identified unique CpG methylation signatures at the CpG island 3′-shore region located 1.3 kb from the transcription start site of TET1 in gastric tumor cells but not in normal mucosa. The luciferase activity of constructs with a methylated 3′-shore sequence was greatly decreased compared with that of an unmethylated sequence in transformed gastric cancer cells. In gastric cancer cells, dense CpG methylation in the 3′-shore was strongly associated with TET1 silencing and bivalent histone marks. Thus, a decrease in 5hmC may be a cause of gastric tumorigenesis owing to a decrease in TET1 expression through DNA methylation coupled with bivalent marks in the 3′-shore of TET1.
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Affiliation(s)
- Jong-Lyul Park
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Hee-Jin Kim
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Eun-Hye Seo
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Oh-Hyung Kwon
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea
| | - Byungho Lim
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea
| | - Mirang Kim
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Seon-Young Kim
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Kyu-Sang Song
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Ja Kim
- Departments of Preventive Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Bo Youl Choi
- Departments of Preventive Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Yong Sung Kim
- Epigenome Research Center, Genome Institute, KRIBB, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
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Li M, Gao F, Xia Y, Tang Y, Zhao W, Jin C, Luo H, Wang J, Li Q, Wang Y. Filtrating colorectal cancer associated genes by integrated analyses of global DNA methylation and hydroxymethylation in cancer and normal tissue. Sci Rep 2016; 6:31826. [PMID: 27546520 DOI: 10.1038/srep31826] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023] Open
Abstract
Recently, 5-hydroxymethylcytosine patterning across the tumor genome was considered as a hallmark of cancer development and progression. However, locus-specific difference of hydroxymethylation between colorectal cancer and normal tissue is unknown. In this study, we performed a newly developed method, HMST-seq, to profile 726 aberrant methylated loci and 689 aberrant hydroxymethylated loci synchronously in genome wide of colorectal cancers, majority of which presented higher methylation or lower hydroxymethylationin than in normal group. Besides, abnormal hydroxymethylated modification was more frequently occur at proximal regions close to TSSs and TSSs regions than abnormal methylation. Subsequently, we screened four genes (ALOX15, GHRHR, TFPI2 and TKTL1) with aberrant methylation and aberrant hydroxymethylation at some genome position by functional enrichment analysis as candidate genes associated with colorectal cancer. Our results may allow us to select differentially epigenetically modified target genes implicated in colorectal cancer tumorigenesis.
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Ciccarone F, Valentini E, Zampieri M, Caiafa P. 5mC-hydroxylase activity is influenced by the PARylation of TET1 enzyme. Oncotarget 2016; 6:24333-47. [PMID: 26136340 PMCID: PMC4695189 DOI: 10.18632/oncotarget.4476] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/30/2015] [Indexed: 12/15/2022] Open
Abstract
5-hydroxymethylcytosine is a new epigenetic modification deriving from the oxidation of 5-methylcytosine by the TET hydroxylase enzymes. DNA hydroxymethylation drives DNA demethylation events and is involved in the control of gene expression. Deregulation of TET enzymes causes developmental defects and is associated with pathological conditions such as cancer. Little information thus far is available on the regulation of TET activity by post-translational modifications. Here we show that TET1 protein is able to interact with PARP-1/ARTD1 enzyme and is target of both noncovalent and covalent PARylation. In particular, we have demonstrated that the noncovalent binding of ADP-ribose polymers with TET1 catalytic domain decreases TET1 hydroxylase activity while the covalent PARylation stimulates TET1 enzyme. In addition, TET1 activates PARP-1/ARTD1 independently of DNA breaks. Collectively, our results highlight a complex interplay between PARylation and TET1 which may be helpful in coordinating the multiple biological roles played by 5-hydroxymethylcytosine and TET proteins.
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Affiliation(s)
- Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
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Toraño EG, Bayón GF, Del Real Á, Sierra MI, García MG, Carella A, Belmonte T, Urdinguio RG, Cubillo I, García-Castro J, Delgado-Calle J, Pérez-Campo FM, Riancho JA, Fraga MF, Fernández AF. Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells. J Transl Med 2016; 14:207. [PMID: 27393146 PMCID: PMC4938941 DOI: 10.1186/s12967-016-0966-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/01/2016] [Indexed: 12/20/2022] Open
Abstract
Background Age-associated changes in genomic DNA methylation have been primarily attributed to 5-methylcytosine (5mC). However, the recent discovery of 5-hydroxymethylcytosine (5hmC) suggests that this epigenetic mark might also play a role in the process. Methods Here, we analyzed the genome-wide profile of 5hmc in mesenchymal stem cells (MSCs) obtained from bone-marrow donors, aged 2–89 years. Results We identified 10,685 frequently hydroxymethylated CpG sites in MSCs that were, as in other cell types, significantly associated with low density CpG regions, introns, the histone posttranslational modification H3k4me1 and enhancers. Study of the age-associated changes to 5hmC identified 785 hyper- and 846 hypo-hydroxymethylated CpG sites in the MSCs obtained from older individuals. Conclusions DNA hyper-hydroxymethylation in the advanced-age group was associated with loss of 5mC, which suggests that, at specific CpG sites, this epigenetic modification might play a role in DNA methylation changes during lifetime. Since bone-marrow MSCs have many clinical applications, and the fact that the epigenomic alterations in this cell type associated with aging identified in this study could have associated functional effects, the age of donors should be taken into account in clinical settings. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0966-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Estela G Toraño
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Gustavo F Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Álvaro Del Real
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Marta I Sierra
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - María G García
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Antonella Carella
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Thalia Belmonte
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Isabel Cubillo
- Unidad de Biotecnología Celular, Área de Genética Humana, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier García-Castro
- Unidad de Biotecnología Celular, Área de Genética Humana, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Delgado-Calle
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Flor M Pérez-Campo
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - José A Riancho
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo-Principado de Asturias, El Entrego, Spain.
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain.
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Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M. Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression. Nucleic Acids Res 2016; 44:6756-69. [PMID: 27131363 PMCID: PMC5001587 DOI: 10.1093/nar/gkw316] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 04/13/2016] [Indexed: 01/31/2023] Open
Abstract
To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.
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Affiliation(s)
- Maxim Ivanov
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia Institute of Mathematics and Statistics, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Volker Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Isabel Barragan
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Von Eulers väg 8 IV, 17177 Stockholm, Sweden
| | - Philip Ewels
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Max Käller
- Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Tomas Axelsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory, Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, 17121 Stockholm, Sweden
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
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Abstract
Recent advances have uncovered a previously unknown function of vitamin C in epigenetic regulation. Vitamin C exists predominantly as an ascorbate anion under physiological pH conditions. Ascorbate was discovered as a cofactor for methylcytosine dioxygenases that are responsible for DNA demethylation, and also as a likely cofactor for some JmjC domain-containing histone demethylases that catalyze histone demethylation. Variation in ascorbate bioavailability thus can influence the demethylation of both DNA and histone, further leading to different phenotypic presentations. Ascorbate deficiency can be presented systematically, spatially and temporally in different tissues at the different stages of development and aging. Here, we review how ascorbate deficiency could potentially be involved in embryonic and postnatal development, and plays a role in various diseases such as neurodegeneration and cancer through epigenetic dysregulation.
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Affiliation(s)
- Vladimir Camarena
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Rm. 608, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - Gaofeng Wang
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Rm. 608, 1501 NW 10th Ave, Miami, FL, 33136, USA.
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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Zhang R, Lin H. 5-hydroxymethylcytosine: A new marker for early detection of digestive system tumors? Shijie Huaren Xiaohua Zazhi 2016; 24:1213-1219. [DOI: 10.11569/wcjd.v24.i8.1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
5-methylcytosine (5-mc) has been recognized as an important epigenetic modification in mammalian genomic DNA. Studies have revealed that TET (ten-eleven translocation) protein family could catalyze the conversion of 5-mc into 5-hydroxyme-thylcytosine (5-hmc), which is now widely recognized as the sixth base in the genome. Recent reports showed that the level of 5-hmc was decreased in digestive system tumors, indicating that 5-hmc may be a useful epigenetic biomarker for the early diagnosis of gastrointestinal tumors. To better understand the roles of TET and 5-hmc, this article will elucidate the function of TET protein and the connections between 5-hmc and digestive system tumors.
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Barazeghi E, Gill AJ, Sidhu S, Norlén O, Dina R, Palazzo FF, Hellman P, Stålberg P, Westin G. 5-Hydroxymethylcytosine discriminates between parathyroid adenoma and carcinoma. Clin Epigenetics 2016; 8:31. [PMID: 26973719 PMCID: PMC4789293 DOI: 10.1186/s13148-016-0197-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/02/2016] [Indexed: 12/14/2022] Open
Abstract
Background Primary hyperparathyroidism is characterized by enlarged parathyroid glands due to an adenoma (80–85 %) or multiglandular disease (~15 %) causing hypersecretion of parathyroid hormone (PTH) and generally hypercalcemia. Parathyroid cancer is rare (<1–5 %). The epigenetic mark 5-hydroxymethylcytosine (5hmC) is reduced in various cancers, and this may involve reduced expression of the ten-eleven translocation 1 (TET1) enzyme. Here, we have performed novel experiments to determine the 5hmC level and TET1 protein expression in 43 parathyroid adenomas (PAs) and 17 parathyroid carcinomas (PCs) from patients who had local invasion or metastases and to address a potential growth regulatory role of TET1. Results The global 5hmC level was determined by a semi-quantitative DNA immune-dot blot assay in a smaller number of tumors. The global 5hmC level was reduced in nine PCs and 15 PAs compared to four normal tissue samples (p < 0.05), and it was most severely reduced in the PCs. By immunohistochemistry, all 17 PCs stained negatively for 5hmC and TET1 showed negative or variably heterogeneous staining for the majority. All 43 PAs displayed positive 5hmC staining, and a similar aberrant staining pattern of 5hmC and TET1 was seen in about half of the PAs. Western blotting analysis of two PCs and nine PAs showed variable TET1 protein expression levels. A significantly higher tumor weight was associated to PAs displaying a more severe aberrant staining pattern of 5hmC and TET1. Overexpression of TET1 in a colony forming assay inhibited parathyroid tumor cell growth. Conclusions 5hmC can discriminate between PAs and PCs. Whether 5hmC represents a novel marker for malignancy warrants further analysis in additional parathyroid tumor cohorts. The results support a growth regulatory role of TET1 in parathyroid tissue. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0197-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elham Barazeghi
- Department of Surgical Sciences, Endocrine Unit, Uppsala University, Uppsala, SE-751 85 Sweden
| | - Anthony J Gill
- Department of Anatomical Pathology, Royal North Shore Hospital, Pacific Highway, St Leonards, NSW 2065 Australia ; University of Sydney, Sydney, NSW 2006 Australia
| | - Stan Sidhu
- University of Sydney, Sydney, NSW 2006 Australia ; Department of Surgery, Royal North Shore Hospital, Pacific Highway, St Leonards, NSW 2065 Australia
| | - Olov Norlén
- Department of Surgical Sciences, Endocrine Unit, Uppsala University, Uppsala, SE-751 85 Sweden ; University of Sydney, Sydney, NSW 2006 Australia ; Department of Surgery, Royal North Shore Hospital, Pacific Highway, St Leonards, NSW 2065 Australia
| | - Roberto Dina
- Department of Histopathology, Hammersmith Hospital, Imperial College, London, UK
| | - F Fausto Palazzo
- Endocrine Surgery, Hammersmith Hospital, Imperial College, London, UK
| | - Per Hellman
- Department of Surgical Sciences, Endocrine Unit, Uppsala University, Uppsala, SE-751 85 Sweden
| | - Peter Stålberg
- Department of Surgical Sciences, Endocrine Unit, Uppsala University, Uppsala, SE-751 85 Sweden
| | - Gunnar Westin
- Department of Surgical Sciences, Endocrine Unit, Uppsala University, Uppsala, SE-751 85 Sweden
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Abstract
Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Wei X, Zhang S, Cao D, Zhao M, Zhang Q, Zhao J, Yang T, Pei M, Wang L, Li Y, Yang X. Aberrant Hypermethylation of SALL3 with HPV Involvement Contributes to the Carcinogenesis of Cervical Cancer. PLoS One 2015; 10:e0145700. [PMID: 26697877 PMCID: PMC4689451 DOI: 10.1371/journal.pone.0145700] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/06/2015] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE This study aimed to investigate the methylation status of the promoter region of spalt-like transcription factor 3 (SALL3) and the expression of SALL3 in cervical cancer to explore the function of this gene in cervical cancer carcinogenesis. METHODS The methylation status of SALL3 was detected by methylation-specific PCR, and SALL3 gene expression was assessed by real-time quantitative PCR in the cervical cancer cell lines, SiHa, HeLa and C33A, as well as in cervical cancer tissue samples (n = 23), matched pericarcinomatous tissue samples (n = 23) and normal cervix tissue samples (n = 17). MTT was used to measure the cell viability and proliferation capacity of SiHa and HeLa cells. RESULTS The SALL3 promoter was completely methylated in SiHa cells, unmethylated in C33A cells and partially methylated in HeLa cells. After treatment of SiHa and HeLa cells with 5 μM and 10 μM of 5-Azacytidine (5-Aza), respectively, the methylation level of the SALL3 promoter decreased and observed increase in the degree of unmethylation in a dose-dependent manner. Moreover, the relative expression of SALL3 mRNA increased as the concentration of 5-Aza increased in SiHa (p<0.05) and HeLa (p<0.05) cells. This above-mentioned increase in SALL3 mRNA in SiHa cells was more remarkable than that observed in HeLa cells. Cell proliferation capacity also decreased after administration of 5-Aza to SiHa and HeLa cells (p<0.05). Methylation of the SALL3 promoter was observed in 15 of 23 (65.21%) cervical cancer tissue samples, 15 of 23 (65.21%) matched pericarcinomatous tissue samples and 5 of 17 (29.41%) normal cervical tissue samples (p<0.05). SALL3 mRNA expression was significantly lower in cervical cancer and pericarcinomatous tissues compared with normal cervical tissues (p<0.05). In all cervix tissue samples, HPV infection was positively associated with hypermethylation of the promoter region of SALL3 (p<0.05, r = 0.408), and the expression of SALL3 mRNA in HPV-positive tissues was lower than that in HPV-negative tissues (p<0.05). CONCLUSION The aberrant hypermethylation of SALL3 together with HPV involvement inactivated its function as a tumor suppressor and contributed to carcinogenesis in cervical cancer.
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Affiliation(s)
- Xing Wei
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Shaohua Zhang
- Department of Gynecology and Obstetrics, The Affiliated Hospital of Xi’an Medical College, Xi’an 710077, China
| | - Di Cao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Minyi Zhao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Qian Zhang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Juan Zhao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Ting Yang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Meili Pei
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Li Wang
- Center of Maternal and Child Health Care, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Yang Li
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
| | - Xiaofeng Yang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Medical School, Xi’an Jiaotong University, 277 West Yanta Road, Xi’an 710061, China
- * E-mail:
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Huisman C, van der Wijst MGP, Schokker M, Blancafort P, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Re-expression of Selected Epigenetically Silenced Candidate Tumor Suppressor Genes in Cervical Cancer by TET2-directed Demethylation. Mol Ther 2015; 24:536-47. [PMID: 26686387 DOI: 10.1038/mt.2015.226] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/11/2015] [Indexed: 12/18/2022] Open
Abstract
DNA hypermethylation is extensively explored as therapeutic target for gene expression modulation in cancer. Here, we re-activated hypermethylated candidate tumor suppressor genes (TSGs) (C13ORF18, CCNA1, TFPI2, and Maspin) by TET2-induced demethylation in cervical cancer cell lines. To redirect TET2 to hypermethylated TSGs, we engineered zinc finger proteins (ZFPs), which were first fused to the transcriptional activator VP64 to validate effective gene re-expression and confirm TSG function. ChIP-Seq not only revealed enriched binding of ZFPs to their intended sequence, but also considerable off-target binding, especially at promoter regions. Nevertheless, results obtained by targeted re-expression using ZFP-VP64 constructs were in line with cDNA overexpression; both revealed strong growth inhibition for C13ORF18 and TFPI2, but not for CCNA1 and Maspin. To explore effectivity of locus-targeted demethylation, ZFP-TET2 fusions were constructed which efficiently demethylated genes with subsequent gene re-activation. Moreover, targeting TET2 to TFPI2 and C13ORF18, but not CCNA1, significantly decreased cell growth, viability, and colony formation in cervical cancer cells compared to a catalytically inactive mutant of TET2. These data underline that effective re-activation of hypermethylated genes can be achieved through targeted DNA demethylation by TET2, which can assist in realizing sustained re-expression of genes of interest.
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Affiliation(s)
- Christian Huisman
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands.,Current address: Department of Pediatrics, Oregon Health and Science University, Portland, Oregon, USA
| | - Monique G P van der Wijst
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Matthijs Schokker
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Martijn M Terpstra
- Department of Genetics, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecological Oncology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - G Bea A Wisman
- Department of Gynecological Oncology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
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Strand SH, Hoyer S, Lynnerup AS, Haldrup C, Storebjerg TM, Borre M, Orntoft TF, Sorensen KD. High levels of 5-hydroxymethylcytosine (5hmC) is an adverse predictor of biochemical recurrence after prostatectomy in ERG-negative prostate cancer. Clin Epigenetics 2015; 7:111. [PMID: 26478752 PMCID: PMC4608326 DOI: 10.1186/s13148-015-0146-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
Background Prostate cancer (PC) can be stratified into distinct molecular subtypes based on TMPRSS2-ERG gene fusion status, but its potential prognostic value remains controversial. Likewise, routine clinicopathological features cannot clearly distinguish aggressive from indolent tumors at the time of diagnosis; thus, new prognostic biomarkers are urgently needed. The DNA methylation variant 5-hydroxymethylcytosine (5hmC, an oxidized derivative of 5-methylcytosine) has recently emerged as a new diagnostic and/or prognostic biomarker candidate for several human malignancies. However, this remains to be systematically investigated for PC. In this study, we determined 5hmC levels in 311 PC (stratified by ERG status) and 228 adjacent non-malignant (NM) prostate tissue specimens by immunohistochemical analysis of a tissue microarray, representing a large radical prostatectomy (RP) cohort with long clinical follow-up. We investigated possible correlations between 5hmC and routine clinicopathological variables and assessed the prognostic potential of 5hmC by Kaplan-Meier and uni- and multivariate Cox regression analyses in ERG+ (n = 178) vs. ERG− (n = 133) PCs using biochemical recurrence (BCR) as endpoint. Results We observed a borderline significant (p = 0.06) reduction in 5hmC levels in PC compared to NM tissue samples, which was explained by a highly significant (p < 0.001) loss of 5hmC in ERG− PCs. ERG status was not predictive of BCR in this cohort (p = 0.73), and no significant association was found between BCR and 5hmC levels in ERG+ PCs (p = 0.98). In contrast, high 5hmC immunoreactivity was a significant adverse predictor of BCR after RP in ERG− PCs, independent of Gleason score, pathological tumor stage, surgical margin status, and pre-operative prostate-specific antigen (PSA) level (hazard ratio (HR) (95 % confidence interval (CI)): 1.62 (1.15–2.28), p = 0.006). Conclusions This is the first study to demonstrate a prognostic potential for 5hmC in PC. Our findings highlight the importance of ERG stratification in PC biomarker studies and suggest that epigenetic mechanisms involving 5hmC are important for the development and/or progression of ERG− PC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0146-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Soren Hoyer
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Anne-Sofie Lynnerup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ; Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark ; Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tine Maj Storebjerg
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ; Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark ; Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben F Orntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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