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Hou W, Xu H. Incorporating Selenium into Heterocycles and Natural Products─From Chemical Properties to Pharmacological Activities. J Med Chem 2022; 65:4436-4456. [PMID: 35244394 DOI: 10.1021/acs.jmedchem.1c01859] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Selenium (Se)-containing compounds have emerged as potential therapeutic agents for the treatment of a range of diseases. Through tremendous effort, considerable knowledge has been acquired to understand the complex chemical properties and biological activities of selenium, especially after its incorporation into bioactive molecules. From this perspective, we compiled extensive literature evidence to summarize and critically discuss the relationship between the pharmacological activities and chemical properties of selenium compounds and the strategic incorporation of selenium into organic molecules, especially bioactive heterocycles and natural products. We also provide perspectives regarding the challenges in selenium-based medicinal chemistry and future research directions.
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Affiliation(s)
- Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development and Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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2
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Zhao X, Ji J, Wang S, Wang R, Yu Q, Li D. The regulatory pattern of target gene expression by aberrant enhancer methylation in glioblastoma. BMC Bioinformatics 2021; 22:420. [PMID: 34482818 PMCID: PMC8420065 DOI: 10.1186/s12859-021-04345-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) is the most common and aggressive primary malignant brain tumor with grim prognosis. Aberrant DNA methylation is an epigenetic mechanism that promotes GBM carcinogenesis, while the function of DNA methylation at enhancer regions in GBM remains poorly described. Results We integrated multi-omics data to identify differential methylation enhancer region (DMER)-genes and revealed global enhancer hypomethylation in GBM. In addition, a DMER-mediated target genes regulatory network and functional enrichment analysis of target genes that might be regulated by hypomethylation enhancer regions showed that aberrant enhancer regions could contribute to tumorigenesis and progression in GBM. Further, we identified 22 modules in which lncRNAs and mRNAs synergistically competed with each other. Finally, through the construction of drug-target association networks, our study identified potential small-molecule drugs for GBM treatment. Conclusions Our study provides novel insights for understanding the regulation of aberrant enhancer region methylation and developing methylation-based biomarkers for the diagnosis and treatment of GBM. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04345-8.
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Affiliation(s)
- Xiaoxiao Zhao
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing, 100069, People's Republic of China.,Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Jianghuai Ji
- Department of Radiation Physics, Zhejiang Cancer Hospital, Hangzhou, 310022, People's Republic of China.,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, 310022, People's Republic of China
| | - Shijia Wang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing, 100069, People's Republic of China.,Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Rendong Wang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing, 100069, People's Republic of China.,Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Qiuhong Yu
- Department of Hyperbaric Oxygen, Beijing Tiantan Hospital, Capital Medical University, 119 Nansihuan Xi Lu, Fengtai District, Beijing, 100070, People's Republic of China.
| | - Dongguo Li
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing, 100069, People's Republic of China. .,Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing, 100069, People's Republic of China.
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3
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Luo Y, Sun F, Peng X, Dong D, Ou W, Xie Y, Luo Y. Integrated Bioinformatics Analysis to Identify Abnormal Methylated Differentially Expressed Genes for Predicting Prognosis of Human Colon Cancer. Int J Gen Med 2021; 14:4745-4756. [PMID: 34466019 PMCID: PMC8403012 DOI: 10.2147/ijgm.s324483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/06/2021] [Indexed: 12/27/2022] Open
Abstract
Objective To identify the value of key differentially expressed genes (DEGs) regulated by differentially methylated regions (DMRs) in predicting the prognosis of human colon cancer. Materials and Methods RNA sequencing data and DNA methylation data of 455 colon adenocarcinoma (COAD) cases and 41 normal controls were downloaded from The Cancer Genome Atlas (TCGA). Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by the DAVID database. To identify the hub genes regulated by methylation, univariate Cox and multivariate Cox regression analyses were carried out. A nomogram based on the risk score was built to identify the power of the hub genes to predict prognosis in patients with colon cancer. Results A total of 133 DEGs regulated by DMRs were identified through analyzing RNA sequencing data and DNA methylation data from TCGA. GO functional enrichment and KEGG pathway enrichment analysis showed the genes involved in the initiation and progression of colon cancer. Univariate Cox regression analysis and multivariate Cox regression analysis focused on the seven hub genes (CDH4, CR2, KRT85, LGI4, NPAS4, RUVBL1 and SP140) associated with overall survival, the expression of which negatively correlated with their methylation level. The risk score and nomogram model showed that the hub genes served as potential biomarkers for the prognosis prediction of patients with colon cancer. Conclusion Our findings suggest that the DEGs regulated by DMRs are involved in the carcinogenesis and development of colon cancer, and the aberrantly methylated DEGs associated with overall survival of patients may be potential diagnostic and therapeutic targets for colon cancer.
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Affiliation(s)
- Yanbo Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People's Republic of China
| | - Fenglin Sun
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People's Republic of China
| | - Xiaowen Peng
- Department of Laboratory Medicine, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, Southern China University of Technology, Guangzhou, Guangdong, 511457, People's Republic of China
| | - Dong Dong
- Department of General Surgery, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 511457, Guangdong, People's Republic of China
| | - Wentao Ou
- Department of General Surgery, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 511457, Guangdong, People's Republic of China
| | - Yongke Xie
- Department of General Surgery, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 511457, Guangdong, People's Republic of China
| | - Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People's Republic of China
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4
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Giacopelli B, Wang M, Cleary A, Wu YZ, Schultz AR, Schmutz M, Blachly JS, Eisfeld AK, Mundy-Bosse B, Vosberg S, Greif PA, Claus R, Bullinger L, Garzon R, Coombes KR, Bloomfield CD, Druker BJ, Tyner JW, Byrd JC, Oakes CC. DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia. Genome Res 2021; 31:747-761. [PMID: 33707228 PMCID: PMC8092005 DOI: 10.1101/gr.269233.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.
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Affiliation(s)
- Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Min Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ada Cleary
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Anna Reister Schultz
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, 86159 Augsburg, Germany
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rainer Claus
- Department of Medicine II, Stem Cell Transplantation Unit, Klinikum Augsburg, Ludwig-Maximilians University Munich, 86156 Munich, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | - Ramiro Garzon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Clara D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
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5
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AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding. Blood 2021; 136:339-352. [PMID: 32232485 DOI: 10.1182/blood.2019002326] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/01/2020] [Indexed: 12/11/2022] Open
Abstract
CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.
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Kimura Y, Iwanaga E, Iwanaga K, Endo S, Inoue Y, Tokunaga K, Nagahata Y, Masuda K, Kawamoto H, Matsuoka M. A regulatory element in the 3'-untranslated region of CEBPA is associated with myeloid/NK/T-cell leukemia. Eur J Haematol 2020; 106:327-339. [PMID: 33197296 DOI: 10.1111/ejh.13551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/01/2022]
Abstract
OBJECTIVES CCAAT/enhancer-binding protein α (CEBPA) is an essential transcription factor for myeloid differentiation. Not only mutation of the CEBPA gene, but also promoter methylation, which results in silencing of CEBPA, contributes to the pathogenesis of acute myeloid leukemia (AML). We sought for another differentially methylated region (DMR) that associates with the CEBPA silencing and disease phenotype. METHODS Using databases, we identified a conserved DMR in the CEBPA 3'-untranslated region (UTR). RESULTS Methylation-specific PCR analysis of 231 AML cases showed that hypermethylation of the 3'-UTR was associated with AML that had a myeloid/NK/T-cell phenotype and downregulated CEBPA. Most of these cases were of an immature phenotype with CD7/CD56 positivity. These cases were significantly associated with lower hemoglobin levels than the others. Furthermore, we discovered that the CEBPA 3'-UTR DMR can enhance transcription from the CEBPA native promoter. In vitro experiments identified IKZF1-binding sites in the 3'-UTR that are responsible for this increased transcription of CEBPA. CONCLUSIONS These results indicate that the CEBPA 3'-UTR DMR is a novel regulatory element of CEBPA related to myeloid/NK/T-cell lineage leukemogenesis. Transcriptional regulation of CEBPA by IKZF1 may provide a clue for understanding the fate determination of myeloid vs. NK/T-lymphoid progenitors.
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Affiliation(s)
- Yukiko Kimura
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Eisaku Iwanaga
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Kouta Iwanaga
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Shinya Endo
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Yoshitaka Inoue
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Kenji Tokunaga
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan
| | - Yousuke Nagahata
- Laboratory of Immunology, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto, Japan
| | - Kyoko Masuda
- Laboratory of Immunology, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto, Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University, Kumamoto, Japan.,Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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7
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Deshpande SS, Nemani H, Arumugam G, Ravichandran A, Balasinor NH. High-fat diet-induced and genetically inherited obesity differentially alters DNA methylation profile in the germline of adult male rats. Clin Epigenetics 2020; 12:179. [PMID: 33213487 PMCID: PMC7678167 DOI: 10.1186/s13148-020-00974-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Paternal obesity has been associated with reduced live birth rates. It could lead to inheritance of metabolic disturbances to the offspring through epigenetic mechanisms. However, obesity is a multifactorial disorder with genetic or environmental causes. Earlier we had demonstrated differential effects of high-fat diet-induced obesity (DIO) and genetically inherited obesity (GIO) on metabolic, hormonal profile, male fertility, and spermatogenesis using two rat models. The present study aimed to understand the effect of DIO and GIO on DNA methylation in male germline, and its subsequent effects on the resorbed (post-implantation embryo loss) and normal embryos. First, we assessed the DNA methylation enzymatic machinery in the testis by Real-Time PCR, followed global DNA methylation levels in spermatozoa and testicular cells by ELISA and flow cytometry, respectively. Further, we performed Methylation Sequencing in spermatozoa for both the groups. Sequencing data in spermatozoa from both the groups were validated using Pyrosequencing. Expression of the differentially methylated genes was assessed in the resorbed and normal embryos sired by the DIO group using Real-Time PCR for functional validation. RESULTS We noted a significant decrease in Dnmt transcript and global DNA methylation levels in the DIO group and an increase in the GIO group. Sequencing analysis showed 16,966 and 9113 differentially methylated regions in the spermatozoa of the DIO and GIO groups, respectively. Upon pathway analysis, we observed genes enriched in pathways involved in embryo growth and development namely Wnt, Hedgehog, TGF-beta, and Notch in spermatozoa for both the groups, the methylation status of which partially correlated with the gene expression pattern in resorbed and normal embryos sired by the DIO group. CONCLUSION Our study reports the mechanism by which diet-induced and genetically inherited obesity causes differential effects on the DNA methylation in the male germline that could be due to a difference in the white adipose tissue accumulation. These differences could either lead to embryo loss or transmit obesity-related traits to the offspring in adult life.
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Affiliation(s)
- Sharvari S. Deshpande
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai 400012 India
| | - Harishankar Nemani
- National Institute of Nutrition Animal Facility, ICMR-National Institute of Nutrition, Jamai-Osmania PO, Hyderabad 500 007 India
| | - Gandhimathi Arumugam
- Genome Informatics Department, Genotypic Technologies Pvt. Ltd., #2/13, Balaji Complex, Poojari Layout, 80 Feet Road, R.M.V. 2nd stage, Bengaluru, India
| | - Avinash Ravichandran
- Genome Informatics Department, Genotypic Technologies Pvt. Ltd., #2/13, Balaji Complex, Poojari Layout, 80 Feet Road, R.M.V. 2nd stage, Bengaluru, India
| | - Nafisa H. Balasinor
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai 400012 India
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8
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Casalino L, Verde P. Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis. Genes (Basel) 2020; 11:E922. [PMID: 32806509 PMCID: PMC7463745 DOI: 10.3390/genes11080922] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Among the major mechanisms involved in tumorigenesis, DNA methylation is an important epigenetic modification impacting both genomic stability and gene expression. Methylation of promoter-proximal CpG islands (CGIs) and transcriptional silencing of tumor suppressors represent the best characterized epigenetic changes in neoplastic cells. The global cancer-associated effects of DNA hypomethylation influence chromatin architecture and reactivation of repetitive elements. Moreover, recent analyses of cancer cell methylomes highlight the role of the DNA hypomethylation of super-enhancer regions critically controlling the expression of key oncogenic players. We will first summarize some basic aspects of DNA methylation in tumorigenesis, along with the role of dysregulated DNA methyltransferases and TET (Ten-Eleven Translocation)-family methylcytosine dioxygenases. We will then examine the potential contribution of epimutations to causality and heritability of cancer. By reviewing some representative genes subjected to hypermethylation-mediated silencing, we will survey their oncosuppressor functions and roles as biomarkers in various types of cancer. Epithelial-to-mesenchymal transition (EMT) and the gain of stem-like properties are critically involved in cancer cell dissemination, metastasis, and therapeutic resistance. However, the driver vs passenger roles of epigenetic changes, such as DNA methylation in EMT, are still poorly understood. Therefore, we will focus our attention on several aspects of DNA methylation in control of EMT and metastasis suppressors, including both protein-coding and noncoding genes.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
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9
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Zhang C, Zhao N, Zhang X, Xiao J, Li J, Lv D, Zhou W, Li Y, Xu J, Li X. SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis. Brief Bioinform 2020; 22:5890509. [PMID: 32778890 DOI: 10.1093/bib/bbaa162] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/04/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a tool to comprehensively assess the impact of DMFEs on prognosis. Therefore, we developed SurvivalMeth (http://bio-bigdata.hrbmu.edu.cn/survivalmeth) to explore the prognosis-related DMFEs, which documented many kinds of DMFEs, including 309,465 CpG island-related elements, 104,748 transcript-related elements, 77,634 repeat elements, as well as cell-type specific 1,689,653 super enhancers (SE) and 1,304,902 CTCF binding regions for analysis. SurvivalMeth is a convenient tool which collected DNA methylation profiles of 36 cancers and allowed users to query their genes of interest in different datasets for prognosis. Furthermore, SurvivalMeth not only integrated different combinations, including single DMFE, multiple DMFEs, SEs and clinical data, to perform survival analysis on preupload data but also allowed for uploading customized DNA methylation profile of DMFEs from various diseases to analyze. SurvivalMeth provided a comprehensive resource and automated analysis for prognostic DMFEs, including DMFE methylation level, correlation analysis, clinical analysis, differential analysis, DMFE annotation, survival-related detailed result and visualization of survival analysis. In summary, we believe that SurvivalMeth will facilitate prognostic research of DMFEs in diverse cancers.
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Affiliation(s)
- Chunlong Zhang
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Ning Zhao
- School of Life Sciences and Technology at Harbin Institute of Technology
| | - Xue Zhang
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Jun Xiao
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Junyi Li
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Dezhong Lv
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Yongsheng Li
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Juan Xu
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xia Li
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
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10
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Liu Y, Han Y, Zhou L, Pan X, Sun X, Liu Y, Liang M, Qin J, Lu Y, Liu P. A comprehensive evaluation of computational tools to identify differential methylation regions using RRBS data. Genomics 2020; 112:4567-4576. [PMID: 32712292 DOI: 10.1016/j.ygeno.2020.07.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 01/01/2023]
Abstract
DNA methylation plays a vital role in transcription regulation. Reduced representation bisulfite sequencing (RRBS) is becoming common for analyzing genome-wide methylation profiles at the single nucleotide level. A major goal of RRBS studies is to detect differentially methylated regions (DMRs) between different biological conditions. The previous tools to predict DMRs lack consistency. Here, we simulated RRBS datasets with significant attributes of real sequencing data under a wide range of scenarios, and systematically evaluated seven DMR detection tools in terms of type I error rate, precision/recall (PR), and area under ROC curve (AUC) using different methylation levels, sequencing coverage depth, length of DMRs, read length, and sample sizes. DMRfinder, methylSig, and methylKit were our preferred tools for RRBS data analysis, in terms of their AUC and PR curves. Our comparison highlights the different applicability of DMR detection tools and provides information to guide researchers towards the advancement of sequence-based DMR analysis.
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Affiliation(s)
- Yi Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yi Han
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Liyuan Zhou
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiwei Sun
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jiale Qin
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China.
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China.
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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11
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Cheung K, Barter MJ, Falk J, Proctor CJ, Reynard LN, Young DA. Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity. FASEB J 2020; 34:5317-5331. [PMID: 32058623 PMCID: PMC7187454 DOI: 10.1096/fj.201902061rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next‐generation sequencing (ChIP‐seq) was used to assess a range of N‐terminal posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP‐seq and cis‐regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis‐related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de‐methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell‐types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell‐types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross‐talk between different epigenetic mechanisms during chondrocyte differentiation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Julia Falk
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Carole J Proctor
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
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12
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Identification of Two DNMT3A Mutations Compromising Protein Stability and Methylation Capacity in Acute Myeloid Leukemia. JOURNAL OF ONCOLOGY 2019; 2019:5985923. [PMID: 31827512 PMCID: PMC6881567 DOI: 10.1155/2019/5985923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022]
Abstract
Somatic mutations of DNMT3A occur in about 20% of acute myeloid leukemia (AML) patients. They mostly consist in heterozygous missense mutations targeting a hotspot site at R882 codon, which exhibit a dominant negative effect and are associated with high myeloblast count, advanced age, and poor prognosis. Other types of mutations such as truncations, insertions, or single-nucleotide deletion also affect the DNMT3A gene, though with lower frequency. The present study aimed to characterize two DNMT3A gene mutations identified by next-generation sequencing (NGS), through analysis of protein stability and DNA methylation status at CpG islands. The first mutation was a single-nucleotide variant of DNMT3A at exon 20 causing a premature STOP codon (c.2385G > A; p.Trp795 ∗ ; NM_022552.4). The DNMT3A mutation load increased from 4.5% to 38.2% during guadecitabine treatment, with a dominant negative effect on CpG methylation and on protein expression. The second mutation was a novel insertion of 35 nucleotides in exon 22 of DNMT3A (NM_022552.4) that introduced a STOP codon too, after the amino acid Glu863 caused by a frameshift insertion (c.2586_2587insTCATGAATGAGAAAGAGGACATCTTATGGTGCACT; p. Thr862_Glu863fsins). The mutation, which was associated with reduced DNMT3A expression and CpG methylation, persisted at relapse with minor changes in the methylation profile and at protein level. Our data highlight the need to better understand the consequences of DNMT3A mutations other than R882 substitutions in the leukemogenic process in order to tailor patient treatments, thus avoiding therapeutic resistance and disease relapse.
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13
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Gambacorta V, Gnani D, Vago L, Di Micco R. Epigenetic Therapies for Acute Myeloid Leukemia and Their Immune-Related Effects. Front Cell Dev Biol 2019; 7:207. [PMID: 31681756 PMCID: PMC6797914 DOI: 10.3389/fcell.2019.00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Over the past decades, our molecular understanding of acute myeloid leukemia (AML) pathogenesis dramatically increased, thanks also to the advent of next-generation sequencing (NGS) technologies. Many of these findings, however, have not yet translated into new prognostic markers or rationales for treatments. We now know that AML is a highly heterogeneous disease characterized by a very low mutational burden. Interestingly, the few mutations identified mainly reside in epigenetic regulators, which shape and define leukemic cell identity. In the light of these discoveries and given the increasing number of drugs targeting epigenetic regulators in clinical development and testing, great interest is emerging for the use of small molecules targeting leukemia epigenome. Together with their effects on leukemia cell-intrinsic properties, such as proliferation and survival, epigenetic drugs may affect the way leukemic cells communicate with the surrounding components of the tumor and immune microenvironment. Here, we review current knowledge on alterations in the AML epigenetic landscape and discuss the promises of epigenetic therapies for AML treatment. Finally, we summarize emerging molecular studies elucidating how epigenetic rewiring in cancer cells may as well exert immune-modulatory functions, boost the immune system, and potentially contribute to better patient outcomes.
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Affiliation(s)
- Valentina Gambacorta
- Unit of Senescence in Stem Cell Aging, Differentiation and Cancer, San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy.,Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Milano-Bicocca University, Milan, Italy
| | - Daniela Gnani
- Unit of Senescence in Stem Cell Aging, Differentiation and Cancer, San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Di Micco
- Unit of Senescence in Stem Cell Aging, Differentiation and Cancer, San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
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14
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Ordoñez R, Martínez-Calle N, Agirre X, Prosper F. DNA Methylation of Enhancer Elements in Myeloid Neoplasms: Think Outside the Promoters? Cancers (Basel) 2019; 11:cancers11101424. [PMID: 31554341 PMCID: PMC6827153 DOI: 10.3390/cancers11101424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/15/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
Gene regulation through DNA methylation is a well described phenomenon that has a prominent role in physiological and pathological cell-states. This epigenetic modification is usually grouped in regions denominated CpG islands, which frequently co-localize with gene promoters, silencing the transcription of those genes. Recent genome-wide DNA methylation studies have challenged this paradigm, demonstrating that DNA methylation of regulatory regions outside promoters is able to influence cell-type specific gene expression programs under physiologic or pathologic conditions. Coupling genome-wide DNA methylation assays with histone mark annotation has allowed for the identification of specific epigenomic changes that affect enhancer regulatory regions, revealing an additional layer of complexity to the epigenetic regulation of gene expression. In this review, we summarize the novel evidence for the molecular and biological regulation of DNA methylation in enhancer regions and the dynamism of these changes contributing to the fine-tuning of gene expression. We also analyze the contribution of enhancer DNA methylation on the expression of relevant genes in acute myeloid leukemia and chronic myeloproliferative neoplasms. The characterization of the aberrant enhancer DNA methylation provides not only a novel pathogenic mechanism for different tumors but also highlights novel potential therapeutic targets for myeloid derived neoplasms.
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Affiliation(s)
- Raquel Ordoñez
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Nicolás Martínez-Calle
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain.
- Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Avenida Pío XII-36, 31008 Pamplona, Spain.
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15
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Loh XY, Sun QY, Ding LW, Mayakonda A, Venkatachalam N, Yeo MS, Silva TC, Xiao JF, Doan NB, Said JW, Ran XB, Zhou SQ, Dakle P, Shyamsunder P, Koh APF, Huang RYJ, Berman BP, Tan SY, Yang H, Lin DC, Koeffler HP. RNA-Binding Protein ZFP36L1 Suppresses Hypoxia and Cell-Cycle Signaling. Cancer Res 2019; 80:219-233. [PMID: 31551365 DOI: 10.1158/0008-5472.can-18-2796] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/28/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022]
Abstract
ZFP36L1 is a tandem zinc-finger RNA-binding protein that recognizes conserved adenylate-uridylate-rich elements (ARE) located in 3'untranslated regions (UTR) to mediate mRNA decay. We hypothesized that ZFP36L1 is a negative regulator of a posttranscriptional hub involved in mRNA half-life regulation of cancer-related transcripts. Analysis of in silico data revealed that ZFP36L1 was significantly mutated, epigenetically silenced, and downregulated in a variety of cancers. Forced expression of ZFP36L1 in cancer cells markedly reduced cell proliferation in vitro and in vivo, whereas silencing of ZFP36L1 enhanced tumor cell growth. To identify direct downstream targets of ZFP36L1, systematic screening using RNA pull-down of wild-type and mutant ZFP36L1 as well as whole transcriptome sequencing of bladder cancer cells {plus minus} tet-on ZFP36L1 was performed. A network of 1,410 genes was identified as potential direct targets of ZFP36L1. These targets included a number of key oncogenic transcripts such as HIF1A, CCND1, and E2F1. ZFP36L1 specifically bound to the 3'UTRs of these targets for mRNA degradation, thus suppressing their expression. Dual luciferase reporter assays and RNA electrophoretic mobility shift assays showed that wild-type, but not zinc-finger mutant ZFP36L1, bound to HIF1A 3'UTR and mediated HIF1A mRNA degradation, leading to reduced expression of HIF1A and its downstream targets. Collectively, our findings reveal an indispensable role of ZFP36L1 as a posttranscriptional safeguard against aberrant hypoxic signaling and abnormal cell-cycle progression. SIGNIFICANCE: RNA-binding protein ZFP36L1 functions as a tumor suppressor by regulating the mRNA stability of a number of mRNAs involved in hypoxia and cell-cycle signaling.
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Affiliation(s)
- Xin-Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Mei-Shi Yeo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tiago C Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ngan B Doan
- Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Jonathan W Said
- Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center, Los Angeles, California
| | - Xue-Bin Ran
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Si-Qin Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Angele Pei-Fern Koh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ruby Yun-Ju Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.,National University Cancer Institute of Singapore, National University Hospital, Singapore
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16
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Yin X, Huang S, Xu A, Fan F, Chen L, Sun C, Hu Y. Identification of distinctive long noncoding RNA competitive interactions and a six-methylated-gene prognostic signature in acute myeloid leukemia with -5/del(5q) or -7/del(7q). J Cell Biochem 2019; 121:1563-1574. [PMID: 31535409 DOI: 10.1002/jcb.29391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 08/28/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) with -5/del(5q) or -7/del(7q) has special clinical and biological characteristics, but its molecular mechanisms and risk stratification remain unknown. METHODS The RNA sequencing and DNA methylation of 23 patients with -5/del(5q) or -7/del(7q) and 128 patients with other subtypes of acute myeloid leukemia were obtained from The Cancer Genome Atlas (TCGA). The regulatory mechanisms of competitive endogenous RNA (ceRNA) network and DNA methylation on gene expression were explored. To find robust and specific risk stratification for this AML subtype, a prognostic model was established and evaluated through four independent data sets. RESULTS We identified 966 differentially expressed long noncoding RNA, 2274 differentially expressed genes, and 47 differentially expressed microRNAs, and constructed a ceRNA network. After the integrated analysis of differentially methylated and expressed genes, 19 genes showed the opposite trend between the methylation variation and gene expression. An six-methylated-gene prognostic signature which highly correlated with overall survival was established, and the performance was validated by leave-one-out cross validation method and permutation test. Furthermore, the excellent prognostic value of this model was supported by an independent cohort, while specificity of this model was validated by three independent data sets, suggesting it as a predictive classifier with high efficiency for distinguishing those with -5/del(5q) or -7/del(7q) from other AML subtypes. CONCLUSIONS The ceRNA network may provide new ideas for the diagnosis and treatment for patients with -5/del(5q) or -7/del(7q).The six-methylated-gene prognostic signature was a robust, specific, and clinically practical risk stratification for the outcome of patients with AML having -5/del(5q) or -7/del(7q).
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Affiliation(s)
- Xuejiao Yin
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sui Huang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aoshuang Xu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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17
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Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman R, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature 2019; 569:576-580. [PMID: 31092926 PMCID: PMC6533116 DOI: 10.1038/s41586-019-1198-z] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/12/2019] [Indexed: 11/22/2022]
Abstract
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer1. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy2,3. The CLL epigenome is also an important disease-defining feature4,5, and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations6. However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously. Here, to measure the epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced-representation bisulfite sequencing to B cells from healthy donors and patients with CLL. We observed that the common clonal origin of CLL results in a consistently increased epimutation rate, with low variability in the cell-to-cell epimutation rate. By contrast, variable epimutation rates across healthy B cells reflect diverse evolutionary ages across the trajectory of B cell differentiation, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed us to reconstruct lineages at high-resolution with single-cell data, and to apply this directly to patient samples. The CLL lineage tree shape revealed earlier branching and longer branch lengths than in normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. Integration of single-cell bisulfite sequencing analysis with single-cell transcriptomes and genotyping confirmed that genetic subclones mapped to distinct clades, as inferred solely on the basis of epimutation information. Finally, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells that were preferentially expelled from the lymph node after treatment, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts the lineage history of CLL and its evolution with therapy.
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Affiliation(s)
- Federico Gaiti
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ryan Matthew Brand
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Steven Kothen-Hill
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Rafael Schulman
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | | | - Davide Risso
- Weill Cornell Medicine, New York, NY, 10021, USA,Department of Statistical Sciences, University of Padova, Padova, 35121, Italy
| | - Kyu-Tae Kim
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kevin Y. Huang
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | | | | | - Nathaniel D. Omans
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Evan Biederstedt
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lili Wang
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA,Beckman Research Institute, City of Hope, Monrovia, CA, 91016, USA
| | | | | | - Martin J. Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine J. Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Dan A. Landau
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA,Corresponding author: Dan A. Landau, MD, PhD, Weill Cornell Medicine, Belfer Research Building, 413 East 69th Street, New York, NY 10021,
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18
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Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat Commun 2019; 10:1874. [PMID: 31015400 PMCID: PMC6478836 DOI: 10.1038/s41467-019-09645-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/22/2019] [Indexed: 12/31/2022] Open
Abstract
Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. Here, to comprehensively study the epigenetic dimension of cancer evolution, we integrate DNAme analysis with histone modification mapping and single cell analyses of RNA expression and DNAme in 22 primary CLL and 13 healthy donor B lymphocyte samples. Our data reveal corrupted coherence across different layers of the CLL epigenome. This manifests in decreased mutual information across epigenetic modifications and gene expression attributed to cell-to-cell heterogeneity. Disrupted epigenetic-transcriptional coordination in CLL is also reflected in the dysregulation of the transcriptional output as a function of the combinatorial chromatin states, including incomplete Polycomb-mediated gene silencing. Notably, we observe unexpected co-mapping of typically mutually exclusive activating and repressing histone modifications, suggestive of intra-tumoral epigenetic diversity. Thus, CLL epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging cellular identities. In chronic lymphocytic leukemia (CLL), evolution is driven by transcriptional and epigenetic heterogeneity. Here, the authors integrate epigenomic analyses to show how intra-tumoral epigenetic diversity results in divergent chromatin states in CLL cells, increasing cell-to-cell transcriptional heterogeneity.
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19
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Martínez-Calle N, Pascual M, Ordoñez R, Enériz ESJ, Kulis M, Miranda E, Guruceaga E, Segura V, Larráyoz MJ, Bellosillo B, Calasanz MJ, Besses C, Rifón J, Martín-Subero JI, Agirre X, Prosper F. Epigenomic profiling of myelofibrosis reveals widespread DNA methylation changes in enhancer elements and ZFP36L1 as a potential tumor suppressor gene that is epigenetically regulated. Haematologica 2019; 104:1572-1579. [PMID: 30655376 PMCID: PMC6669145 DOI: 10.3324/haematol.2018.204917] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022] Open
Abstract
In this study we interrogated the DNA methylome of myelofibrosis patients using high-density DNA methylation arrays. We detected 35,215 differentially methylated CpG, corresponding to 10,253 genes, between myelofibrosis patients and healthy controls. These changes were present both in primary and secondary myelofibrosis, which showed no differences between them. Remarkably, most differentially methylated CpG were located outside gene promoter regions and showed significant association with enhancer regions. This aberrant enhancer hypermethylation was negatively correlated with the expression of 27 genes in the myelofibrosis cohort. Of these, we focused on the ZFP36L1 gene and validated its decreased expression and enhancer DNA hypermethylation in an independent cohort of patients and myeloid cell-lines. In vitro reporter assay and 5’-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer. Furthermore, in vitro rescue of ZFP36L1 expression had an impact on cell proliferation and induced apoptosis in SET-2 cell line indicating a possible role of ZFP36L1 as a tumor suppressor gene in myelofibrosis. Collectively, we describe the DNA methylation profile of myelofibrosis, identifying extensive changes in enhancer elements and revealing ZFP36L1 as a novel candidate tumor suppressor gene.
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Affiliation(s)
- Nicolás Martínez-Calle
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Marien Pascual
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Raquel Ordoñez
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Edurne San José Enériz
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona
| | - Estíbaliz Miranda
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Elisabeth Guruceaga
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada, Universidad de Navarra, Pamplona
| | - Víctor Segura
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada, Universidad de Navarra, Pamplona
| | | | | | - María José Calasanz
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,CIMA Laboratory of Diagnostics, Universidad de Navarra, Pamplona
| | - Carles Besses
- Departmento de Hematología, Hospital del Mar, Barcelona
| | - José Rifón
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona
| | - José I Martín-Subero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona.,Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona
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20
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Gandin V, Khalkar P, Braude J, Fernandes AP. Organic selenium compounds as potential chemotherapeutic agents for improved cancer treatment. Free Radic Biol Med 2018; 127:80-97. [PMID: 29746900 DOI: 10.1016/j.freeradbiomed.2018.05.001] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/12/2018] [Accepted: 05/01/2018] [Indexed: 12/16/2022]
Abstract
Selenium(Se)-containing compounds have attracted a growing interest as anticancer agents over recent decades, with mounting reports demonstrating their high efficacy and selectivity against cancer cells. Typically, Se compounds exert their cytotoxic effects by acting as pro-oxidants that alter cellular redox homeostasis. However, the precise intracellular targets, signalling pathways affected and mechanisms of cell death engaged following treatment vary with the chemical properties of the selenocompound and its metabolites, as well as the cancer model that is used. Naturally occurring organic Se compounds, besides encompassing a significant antitumor activity with an apparent ability to prevent metastasis, also seem to have fewer side effects and less systemic effects as reported for many inorganic Se compounds. On this basis, many novel organoselenium compounds have also been synthesized and examined as potential chemotherapeutic agents. This review aims to summarize the most well studied natural and synthetic organoselenium compounds and provide the most recent developments in our understanding of the molecular mechanisms that underlie their potential anticancer effects.
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Affiliation(s)
- Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Prajakta Khalkar
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jeremy Braude
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Aristi P Fernandes
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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21
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Benetatos L, Vartholomatos G. Enhancer DNA methylation in acute myeloid leukemia and myelodysplastic syndromes. Cell Mol Life Sci 2018; 75:1999-2009. [PMID: 29484447 PMCID: PMC11105366 DOI: 10.1007/s00018-018-2783-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 12/13/2022]
Abstract
DNA methylation (CpG methylation) exerts an important role in normal differentiation and proliferation of hematopoietic stem cells and their differentiated progeny, while it has also the ability to regulate myeloid versus lymphoid fate. Mutations of the epigenetic machinery are observed in hematological malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) resulting in hyper- or hypo-methylation affecting several different pathways. Enhancers are cis-regulatory elements which promote transcription activation and are characterized by histone marks including H3K27ac and H3K4me1/2. These gene subunits are target gene expression 'fine-tuners', are differentially used during the hematopoietic differentiation, and, in contrast to promoters, are not shared by the different hematopoietic cell types. Although the interaction between gene promoters and DNA methylation has extensively been studied, much less is known about the interplay between enhancers and DNA methylation. In hematopoiesis, DNA methylation at enhancers has the potential to discriminate between fetal and adult erythropoiesis, and also is a regulatory mechanism in granulopoiesis through repression of neutrophil-specific enhancers in progenitor cells during maturation. The interplay between DNA methylation at enhancers is disrupted in AML and MDS and mainly hyper-methylation at enhancers raising early during myeloid lineage commitment is acquired during malignant transformation. Interactions between mutated epigenetic drivers and other oncogenic mutations also affect enhancers' activity with final result, myeloid differentiation block. In this review, we have assembled recent data regarding DNA methylation and enhancers' activity in normal and mainly myeloid malignancies.
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22
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Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP. Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis. Free Radic Biol Med 2018; 117:247-257. [PMID: 29438720 DOI: 10.1016/j.freeradbiomed.2018.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 01/19/2023]
Abstract
Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.
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Affiliation(s)
- Prajakta Khalkar
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Hani Abdulkadir Ali
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Paula Codó
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Nuria Díaz Argelich
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Organic and Pharmaceutical Chemistry, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, E-31008 Pamplona, Spain
| | - Anni Martikainen
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Mohsen Karimi Arzenani
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Sören Lehmann
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Julian Walfridsson
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Ungerstedt
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Aristi P Fernandes
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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23
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Li Y, Zhao H, Xu Q, Lv N, Jing Y, Wang L, Wang X, Guo J, Zhou L, Liu J, Chen G, Chen C, Li Y, Yu L. Detection of prognostic methylation markers by methylC-capture sequencing in acute myeloid leukemia. Oncotarget 2017; 8:110444-110459. [PMID: 29299160 PMCID: PMC5746395 DOI: 10.18632/oncotarget.22789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022] Open
Abstract
Clinical and genetic features incompletely predict outcome in acute myeloid leukemia (AML). The value of clinical methylation assays for prognostic markers has not been extensively explored. We assess the prognostic implications of methylC-capture sequencing (MCC-Seq) in patients with de novo AML by integrating DNA methylation and genetic risk stratification. MCC-Seq assessed DNA methylation level in 44 samples. The differentially methylated regions associated with prognostic genetic information were identified. The selected prognostic DNA methylation markers were independently validated in two sets. MCC-Seq exhibited good performance in AML patients. A panel of 12 differentially methylated genes was identified with promoter hyper-differentially methylated regions associated with the outcome. Compared with a low M-value, a high M-value was associated with failure to achieve complete remission (p = 0.024), increased hazard for disease-free survival in the study set (p = 0.039) and poor overall survival in The Cancer Genome Atlas set (p = 0.038). Hematopoietic stem cell transplantation and survival outcomes were not adversely affected by a high M-value (p = 0.271). Our study establishes that MCC-Seq is a stable, reproducible, and cost-effective methylation assay in AML. A 12-gene M-value encompassing epigenetic and genetic prognostic information represented a valid prognostic marker for patients with AML.
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Affiliation(s)
- Yan Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, China
| | - Hongmei Zhao
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Qingyu Xu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Na Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
| | - Yu Jing
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Lili Wang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaowen Wang
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Lei Zhou
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guofeng Chen
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Chongjian Chen
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Yonghui Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Yu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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24
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Impact of DNA methylation programming on normal and pre-leukemic hematopoiesis. Semin Cancer Biol 2017; 51:89-100. [PMID: 28964938 DOI: 10.1016/j.semcancer.2017.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/30/2022]
Abstract
Epigenome regulation is a critical mechanism that governs cell identity, lineage specification and developmental cell fates. With the advent of low-input and single-cell technologies as well as sophisticated cell labeling techniques, our understanding of transcriptional and epigenetic regulation of hematopoiesis is currently undergoing dramatic changes. Increasingly, evidence suggests that the epigenome conformation acts as a critical decision-making mechanism that instructs self-renewal, differentiation and developmental fates of hematopoietic progenitor cells. When dysregulated, this leads to the evolution of disease states such as leukemia. Indeed, aberrations in DNA methylation, histone modifications and genome architecture are characteristic features of many hematopoietic neoplasms in which epigenetic enzymes are frequently mutated. Sequencing studies and characterization of the epigenetic landscape in lymphomas, leukemias and in aged healthy individuals with clonal hematopoiesis have been indispensible to identify epigenetic regulators that play a role in transformation or pre-disposition to hematopoietic malignancies. In this review, we outline the current view of the hematopoietic system and the epigenetic mechanisms regulating hematopoiesis under homeostatic conditions, with a particular focus on the role of DNA methylation in this process. We will also summarize the current knowledge on the mechanisms underlying dysregulated DNA methylation in hematologic malignancies and how this contributes to our understanding of the physiological functions of epigenetic regulators in hematopoiesis.
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