1
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Sasaki A, Takeshima H, Yamashita S, Ichita C, Kawachi J, Naito W, Ohashi Y, Takeuchi C, Fukuda M, Furuichi Y, Yamamichi N, Ando T, Kobara H, Kotera T, Itoi T, Sumida C, Hamada A, Koizumi K, Ushijima T. Severe induction of aberrant DNA methylation by nodular gastritis in adults. J Gastroenterol 2024; 59:442-456. [PMID: 38499886 DOI: 10.1007/s00535-024-02094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Nodular gastritis (NG) is characterized by marked antral lymphoid follicle formation, and is a strong risk factor for diffuse-type gastric cancer in adults. However, it is unknown whether aberrant DNA methylation, which is induced by atrophic gastritis (AG) and is a risk for gastric cancer, is induced by NG. Here, we analyzed methylation induction by NG. METHODS Gastric mucosal samples were obtained from non-cancerous antral tissues of 16 NG and 20 AG patients with gastric cancer and 5 NG and 6 AG patients without, all age- and gender-matched. Genome-wide methylation analysis and expression analysis were conducted by a BeadChip array and RNA-sequencing, respectively. RESULTS Clustering analysis of non-cancerous antral tissues of NG and AG patients with gastric cancer was conducted using methylation levels of 585 promoter CpG islands (CGIs) of methylation-resistant genes, and a large fraction of NG samples formed a cluster with strong methylation induction. Promoter CGIs of CDH1 and DAPK1 tumor-suppressor genes were more methylated in NG than in AG. Notably, methylation levels of these genes were also higher in the antrum of NG patients without cancer. Genes related to lymphoid follicle formation, such as CXCL13/CXCR5 and CXCL12/CXCR4, had higher expression in NG, and genes involved in DNA demethylation TET2 and IDH1, had only half the expression in NG. CONCLUSIONS Severe aberrant methylation, involving multiple tumor-suppressor genes, was induced in the gastric antrum and body of patients with NG, in accordance with their high gastric cancer risk.
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Affiliation(s)
- Akiko Sasaki
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Chikamasa Ichita
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Jun Kawachi
- Department of General Surgery, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Wataru Naito
- Department of Diagnostic Pathology, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Yui Ohashi
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Chihiro Takeuchi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Masahide Fukuda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yumi Furuichi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Department of Gastroenterological Surgery, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Nobutake Yamamichi
- Center for Epidemiology and Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Hideki Kobara
- Department of Gastroenterology and Neurology, Kagawa University, Kagawa, Japan
| | - Tohru Kotera
- Department of Medical Examination, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Chihiro Sumida
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuya Koizumi
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
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2
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Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumourigenesis. Nat Cell Biol 2023; 25:323-336. [PMID: 36732631 DOI: 10.1038/s41556-022-01069-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/01/2022] [Indexed: 02/04/2023]
Abstract
Nuclear localization of HIPPO-YAP fusion proteins has been implicated in supratentorial ependymoma development. Here, unexpectedly, we find that liquid-liquid phase separation, rather than nuclear localization, of recurrent patient-derived YAP fusions, YAP-MAMLD1 and C11ORF95-YAP, underlies ependymoma tumourigenesis from neural progenitor cells. Mutagenesis and chimaera assays demonstrate that an intrinsically disordered region promotes oligomerization of the YAP fusions into nuclear, puncta-like, membrane-less condensates. Oligomerization and nuclear condensates induced by YAP fusion with a coiled-coil domain of transcriptional activator GCN4 also promote ependymoma formation. YAP-MAMLD1 concentrates transcription factors and co-activators, including BRD4, MED1 and TEAD, in condensates while excluding transcriptional repressive PRC2, and induces long-range enhancer-promoter interactions that promote transcription and oncogenic programmes. Blocking condensate-mediated transcriptional co-activator activity inhibits tumourigenesis, indicating a critical role of liquid phase separation for YAP fusion oncogenic activity in ependymoma. YAP fusions containing the intrinsically disordered region features are common in human tumours, suggesting that nuclear condensates could be targeted to treat YAP-fusion-induced cancers.
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Depletion of R270C Mutant p53 in Osteosarcoma Attenuates Cell Growth but Does Not Prevent Invasion and Metastasis In Vivo. Cells 2022; 11:cells11223614. [PMID: 36429043 PMCID: PMC9688353 DOI: 10.3390/cells11223614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/06/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022] Open
Abstract
Novel therapeutic targets are needed to better treat osteosarcoma, which is the most common bone malignancy. We previously developed mouse osteosarcoma cells, designated AX (accelerated bone formation) cells from bone marrow stromal cells. AX cells harbor both wild-type and mutant forms of p53 (R270C in the DNA-binding domain, which is equivalent to human R273C). In this study, we showed that mutant p53 did not suppress the transcriptional activation function of wild-type p53 in AX cells. Notably, AXT cells, which are cells derived from tumors originating from AX cells, lost wild-type p53 expression, were devoid of the intact transcription activation function, and were resistant to doxorubicin. ChIP-seq analyses revealed that this mutant form of p53 bound to chromatin in the vicinity of the transcription start sites of various genes but exhibited a different binding profile from wild-type p53. The knockout of mutant p53 in AX and AXT cells by CRISPR-Cas9 attenuated tumor growth but did not affect the invasion of these cells. In addition, depletion of mutant p53 did not prevent metastasis in vivo. Therefore, the therapeutic potency targeting R270C (equivalent to human R273C) mutant p53 is limited in osteosarcoma. However, considering the heterogeneous nature of osteosarcoma, it is important to further evaluate the biological and clinical significance of mutant p53 in various cases.
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4
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Sizer RE, Chahid N, Butterfield SP, Donze D, Bryant NJ, White RJ. TFIIIC-based chromatin insulators through eukaryotic evolution. Gene X 2022; 835:146533. [PMID: 35623477 DOI: 10.1016/j.gene.2022.146533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 11/04/2022] Open
Abstract
Eukaryotic chromosomes are divided into domains with distinct structural and functional properties, such as differing levels of chromatin compaction and gene transcription. Domains of relatively compact chromatin and minimal transcription are termed heterochromatic, whereas euchromatin is more open and actively transcribed. Insulators separate these domains and maintain their distinct features. Disruption of insulators can cause diseases such as cancer. Many insulators contain tRNA genes (tDNAs), examples of which have been shown to block the spread of activating or silencing activities. This characteristic of specific tDNAs is conserved through evolution, such that human tDNAs can serve as barriers to the spread of silencing in fission yeast. Here we demonstrate that tDNAs from the methylotrophic fungus Pichia pastoris can function effectively as insulators in distantly-related budding yeast. Key to the function of tDNAs as insulators is TFIIIC, a transcription factor that is also required for their expression. TFIIIC binds additional loci besides tDNAs, some of which have insulator activity. Although the mechanistic basis of TFIIIC-based insulation has been studied extensively in yeast, it is largely uncharacterized in metazoa. Utilising publicly-available genome-wide ChIP-seq data, we consider the extent to which mechanisms conserved from yeast to man may suffice to allow efficient insulation by TFIIIC in the more challenging chromatin environments of metazoa and suggest features that may have been acquired during evolution to cope with new challenges. We demonstrate the widespread presence at human tDNAs of USF1, a transcription factor with well-established barrier activity in vertebrates. We predict that tDNA-based insulators in higher organisms have evolved through incorporation of modules, such as binding sites for factors like USF1 and CTCF that are absent from yeasts, thereby strengthening function and providing opportunities for regulation between cell types.
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Affiliation(s)
- Rebecca E Sizer
- Department of Biology, The University of York, York YO10 5DD, UK
| | - Nisreen Chahid
- Department of Biology, The University of York, York YO10 5DD, UK
| | | | - David Donze
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Nia J Bryant
- Department of Biology, The University of York, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, The University of York, York YO10 5DD, UK.
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5
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Gupta R. Epigenetic regulation and targeting of ECM for cancer therapy. Am J Physiol Cell Physiol 2022; 322:C762-C768. [PMID: 35235427 PMCID: PMC8993518 DOI: 10.1152/ajpcell.00022.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The tumor microenvironment (TME) composed of different types of cells embedded in extracellular matrix (ECM) has crucial effects on cancer growth and metastasis. ECM is made of a variety of proteins that provide structural support to the cells and regulate biological functions by modulating the crosstalk among cells, thus effecting tumor growth and progression. In this mini-review, we discuss epigenetic modifications that regulate the expression of fibrous ECM proteins and glycoproteins and the prospects of targeting them for cancer therapy.
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Affiliation(s)
- Romi Gupta
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, United States.,O'Neal Comprehensive Cancer Center at The University of Alabama at Birmingham, Birmingham, AL, United States
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6
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Shah AT, Reshi ZA, Altaf M. DNA Methylation of ABC Transporters Differs in Native and Non-native Populations of Conyza canadensis L. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.781498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While differences in the methylation patterns of ABC transporters under different environmental conditions and their role in plant growth, development, and response to biotic and abiotic stresses are well documented, less is known about the variation in the methylation patterns of ABC transporters in plant species in the native and non-native ranges. In this study, we present the results of differences in methylation of ABC transporters of Conyza canadensis L. in its native (North America) and non-native (Kashmir Himalaya) ranges. Our data show that ABC transporter genes have reduced DNA methylation in Kashmir Himalaya than in North America. Furthermore, in the non-native range of Kashmir Himalaya, we found that ABC transporter genes have enriched RNA Pol-II binding and reduced nucleosome occupancy, both hallmarks of transcriptional activity. Taken together, our study showed differential DNA methylation in the ABC transporter genes in the native range of North America and non-native range of Kashmir Himalaya in Conyza canadensis and that the reduced DNA methylation and increased RNA Pol-II binding is one of the possible mechanisms through which this species in the non-native range of Kashmir Himalaya may show greater gene expression of ABC transporter genes. This increased ABC transporter gene expression may help the plant to grow in different environmental conditions in the non-native range. Furthermore, this study could pave way for more studies to better explain the enigmatic plant invasions of C. canadensis in the non-native range of Kashmir Himalaya.
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7
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ARID1A loss-of-function induces CpG island methylator phenotype. Cancer Lett 2022; 532:215587. [DOI: 10.1016/j.canlet.2022.215587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
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8
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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9
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Nguyen K, Dobrowolski C, Shukla M, Cho WK, Luttge B, Karn J. Inhibition of the H3K27 demethylase UTX enhances the epigenetic silencing of HIV proviruses and induces HIV-1 DNA hypermethylation but fails to permanently block HIV reactivation. PLoS Pathog 2021; 17:e1010014. [PMID: 34673825 PMCID: PMC8562785 DOI: 10.1371/journal.ppat.1010014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/02/2021] [Accepted: 10/07/2021] [Indexed: 01/09/2023] Open
Abstract
One strategy for a functional cure of HIV-1 is "block and lock", which seeks to permanently suppress the rebound of quiescent HIV-1 by epigenetic silencing. For the bivalent promoter in the HIV LTR, both histone 3 lysine 27 tri-methylation (H3K27me3) and DNA methylation are associated with viral suppression, while H3K4 tri-methylation (H3K4me3) is correlated with viral expression. However, H3K27me3 is readily reversed upon activation of T-cells through the T-cell receptor. In an attempt to suppress latent HIV-1 in a stable fashion, we knocked down the expression or inhibited the activity of UTX/KDM6A, the major H3K27 demethylase, and investigated its impact on latent HIV-1 reactivation in T cells. Inhibition of UTX dramatically enhanced H3K27me3 levels at the HIV LTR and was associated with increased DNA methylation. In latently infected cells from patients, GSK-J4, which is a potent dual inhibitor of the H3K27me3/me2-demethylases JMJD3/KDM6B and UTX/KDM6A, effectively suppressed the reactivation of latent HIV-1 and also induced DNA methylation at specific sites in the 5'LTR of latent HIV-1 by the enhanced recruitment of DNMT3A to HIV-1. Nonetheless, suppression of HIV-1 through epigenetic silencing required the continued treatment with GSK-J4 and was rapidly reversed after removal of the drug. DNA methylation was also rapidly lost after removal of drug, suggesting active and rapid DNA-demethylation of the HIV LTR. Thus, induction of epigenetic silencing by histone and DNA methylation appears to be insufficient to permanently silence HIV-1 proviral transcription.
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Affiliation(s)
- Kien Nguyen
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Curtis Dobrowolski
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia, United States of America
| | - Meenakshi Shukla
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Won-Kyung Cho
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine (KIOM), Dong-gu, Daegu, Republic of Korea
| | - Benjamin Luttge
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
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10
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Gebhard C, Mulet-Lazaro R, Glatz D, Schwarzfischer-Pfeilschifter L, Schirmacher P, Gaedcke J, Weichert W, Reuschel E, Dietmaier W, Rehli M. Aberrant DNA methylation patterns in microsatellite stable human colorectal cancers define a new marker panel for the CpG island methylator phenotype. Int J Cancer 2021; 150:617-625. [PMID: 34591983 DOI: 10.1002/ijc.33831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
A distinct group of colorectal carcinomas (CRCs) referred to as the "CpG island methylator phenotype" (CIMP) shows an extremely high incidence of de novo DNA methylation and may share common pathological, clinical or molecular features. However, there is limited consensus about which CpG islands (CGIs) define a CIMP, particularly in microsatellite stable (MSS) carcinomas. To study this phenotype in a systematic manner, we analyzed genome-wide CGI DNA methylation profiles of 19 MSS CRC using methyl-CpG immunoprecipitation (MCIp) and hybridization on 244K CGI oligonucleotide microarrays, determined KRAS and BRAF mutation status and compared disease-related DNA methylation changes to chromosomal instability as detected by microarray-based comparative genomic hybridization. Results were validated using mass spectrometry analysis of bisulfite-converted DNA at a subset of 76 individual CGIs in 120 CRC and 43 matched normal tissue samples. Both genome-wide profiling and CpG methylation fine mapping segregated a group of CRC showing pronounced and frequent de novo DNA methylation of a distinct group of CGIs that only partially overlapped with previously established classifiers. The CIMP group defined in our study revealed significant association with colon localization, either KRAS or BRAF mutation, and mostly minor chromosomal losses but no association with known histopathological features. Our data provide a basis for defining novel marker panels that may enable a more reliable classification of CIMP in all CRCs, independently of the MS status.
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Affiliation(s)
- Claudia Gebhard
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Medical Center Regensburg, Regensburg, Germany.,Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | | | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jochen Gaedcke
- Department of General and Visceral Surgery, University Medical Center, Göttingen, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Germany
| | - Wolfgang Dietmaier
- Institute of Pathology, University Hospital Regensburg, Regensburg, Germany
| | - Michael Rehli
- Regensburg Center for Interventional Immunology (RCI), University Regensburg and University Medical Center Regensburg, Regensburg, Germany.,Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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11
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Katsuda Y, Tanaka K, Mori T, Narita M, Takeshima H, Kondo T, Yamabe Y, Matsufuji M, Sato D, Hamada Y, Yamaguchi K, Ushijima T, Inada E, Kuzumaki N, Iseki M, Narita M. Histone modification of pain-related gene expression in spinal cord neurons under a persistent postsurgical pain-like state by electrocautery. Mol Brain 2021; 14:146. [PMID: 34544461 PMCID: PMC8451106 DOI: 10.1186/s13041-021-00854-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/08/2021] [Indexed: 11/10/2022] Open
Abstract
Chronic postsurgical pain (CPSP) is a serious problem. We developed a mouse model of CPSP induced by electrocautery and examined the mechanism of CPSP. In this mouse model, while both incision and electrocautery each produced acute allodynia, persistent allodynia was only observed after electrocautery. Under these conditions, we found that the mRNA levels of Small proline rich protein 1A (Sprr1a) and Annexin A10 (Anxa10), which are the key modulators of neuropathic pain, in the spinal cord were more potently and persistently increased by electrocautery than by incision. Furthermore, these genes were overexpressed almost exclusively in chronic postsurgical pain-activated neurons. This event was associated with decreased levels of tri-methylated histone H3 at Lys27 and increased levels of acetylated histone H3 at Lys27 at their promoter regions. On the other hand, persistent allodynia and overexpression of Sprr1a and Anxa10 after electrocautery were dramatically suppressed by systemic administration of GSK-J4, which is a selective H3K27 demethylase inhibitor. These results suggest that the effects of electrocautery contribute to CPSP along with synaptic plasticity and epigenetic modification.
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Affiliation(s)
- Yosuke Katsuda
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Kenichi Tanaka
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Tomohisa Mori
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Michiko Narita
- Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashige Kondo
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Yoshiyuki Yamabe
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Misa Matsufuji
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Daisuke Sato
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Yusuke Hamada
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.,Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Keisuke Yamaguchi
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Anesthesiology and Pain Medicine, Juntendo Tokyo Koto Geriatric Medical Center, 3-3-20 Shinsuna, Koto-ku, Tokyo, 136-0075, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Eiichi Inada
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Naoko Kuzumaki
- Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Masako Iseki
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Minoru Narita
- Department of Anesthesiology and Pain Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan. .,Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan. .,Division of Cancer Pathophysiology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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12
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Yasukawa Y, Hattori N, Iida N, Takeshima H, Maeda M, Kiyono T, Sekine S, Seto Y, Ushijima T. SAA1 is upregulated in gastric cancer-associated fibroblasts possibly by its enhancer activation. Carcinogenesis 2021; 42:180-189. [PMID: 33284950 DOI: 10.1093/carcin/bgaa131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/08/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) tend to have tumor-promoting capacity, and can provide therapeutic targets. Even without cancer cells, CAF phenotypes are stably maintained, and DNA methylation and H3K27me3 changes have been shown to be involved. Here, we searched for a potential therapeutic target in primary CAFs from gastric cancer and a mechanism for its dysregulation. Expression microarray using eight CAFs and seven non-CAFs (NCAFs) revealed that serum amyloid A1 (SAA1), which encodes an acute phase secreted protein, was second most upregulated in CAFs, following IGF2. Conditioned medium (CM) derived from SAA1-overexpressing NCAFs was shown to increase migration of gastric cancer cells compared with that from control NCAFs, and its tumor-promoting effect was comparable to that of CM from CAFs. In addition, increased migration of cancer cells by CM from CAFs was mostly canceled with CM from CAFs with SAA1 knockdown. Chromatin immunoprecipitation (ChIP)-quantitative PCR showed that CAFs had higher levels of H3K27ac, an active enhancer mark, in the promoter and the two far upstream regions of SAA1 than NCAFs. Also, BET bromodomain inhibitors, JQ1 and mivebresib, decreased SAA1 expression and tumor-promoting effects in CAFs, suggesting SAA1 upregulation by enhancer activation in CAFs. Our present data showed that SAA1 is a candidate therapeutic target from gastric CAFs and indicated that increased enhancer acetylation is important for its overexpression.
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Affiliation(s)
- Yoshimi Yasukawa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Maeda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tohru Kiyono
- Division of Cell Culture Technology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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13
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Takeshima H, Niwa T, Yamashita S, Takamura-Enya T, Iida N, Wakabayashi M, Nanjo S, Abe M, Sugiyama T, Kim YJ, Ushijima T. TET repression and increased DNMT activity synergistically induce aberrant DNA methylation. J Clin Invest 2021; 130:5370-5379. [PMID: 32663196 DOI: 10.1172/jci124070] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 07/07/2020] [Indexed: 01/15/2023] Open
Abstract
Chronic inflammation is deeply involved in various human disorders, such as cancer, neurodegenerative disorders, and metabolic disorders. Induction of epigenetic alterations, especially aberrant DNA methylation, is one of the major mechanisms, but how it is induced is still unclear. Here, we found that expression of TET genes, methylation erasers, was downregulated in inflamed mouse and human tissues, and that this was caused by upregulation of TET-targeting miRNAs such as MIR20A, MIR26B, and MIR29C, likely due to activation of NF-κB signaling downstream of IL-1β and TNF-α. However, TET knockdown induced only mild aberrant methylation. Nitric oxide (NO), produced by NOS2, enhanced enzymatic activity of DNA methyltransferases (DNMTs), methylation writers, and NO exposure induced minimal aberrant methylation. In contrast, a combination of TET knockdown and NO exposure synergistically induced aberrant methylation, involving genomic regions not methylated by either alone. The results showed that a vicious combination of TET repression, due to NF-κB activation, and DNMT activation, due to NO production, is responsible for aberrant methylation induction in human tissues.
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Affiliation(s)
- Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takeji Takamura-Enya
- Department of Applied Chemistry, Kanagawa Institute of Technology, Kanagawa, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Sohachi Nanjo
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Masanobu Abe
- Department of Oral and Maxillofacial Surgery, University of Tokyo Hospital, Tokyo, Japan.,Division for Health Service Promotion, University of Tokyo, Tokyo, Japan
| | - Toshiro Sugiyama
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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14
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Chen J, Liu A, Lin Z, Wang B, Chai X, Chen S, Lu W, Zheng M, Cao T, Zhong M, Li R, Wu M, Lu Z, Pang W, Huang W, Xiao L, Lin D, Wang Z, Lei F, Chen X, Long W, Zheng Y, Chen Q, Zeng J, Ren D, Li J, Zhang X, Huang Y. Downregulation of the circadian rhythm regulator HLF promotes multiple-organ distant metastases in non-small cell lung cancer through PPAR/NF-κb signaling. Cancer Lett 2020; 482:56-71. [PMID: 32289442 DOI: 10.1016/j.canlet.2020.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 12/24/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death due to its early recurrence and widespread metastatic potential. Accumulating studies have reported that dysregulation of circadian rhythms-associated regulators is implicated in the recurrence and metastasis of NSCLC. Therefore, identification of metastasis-associated circadian rhythm genes is clinically necessary. Here we report that the circadian gene hepatic leukemia factor (HLF), which was dramatically reduced in early-relapsed NSCLC tissues, was significantly correlated with early progression and distant metastasis in NSCLC patients. Upregulating HLF inhibited, while silencing HLF promoted lung colonization, as well as metastasis of NSCLC cells to bone, liver and brain in vivo. Importantly, downexpression of HLF promoted anaerobic metabolism to support anchorage-independent growth of NSCLC cells under low nutritional condition by activating NF-κB/p65 signaling through disrupting translocation of PPARα and PPARγ. Further investigations revealed that both genetic deletion and methylation contribute to downexpression of HLF in NSCLC tissues. In conclusion, our results shed light on a plausible mechanism by which HLF inhibits distant metastasis in NSCLC, suggesting that HLF may serve as a novel target for clinical intervention in NSCLC.
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Affiliation(s)
- Jiarong Chen
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Aibin Liu
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Bin Wang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China
| | - Xingxing Chai
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Laboratory Animal Center, Guangdong Medical University, Zhanjiang, 524023, China
| | - Shasha Chen
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China
| | - Wenjie Lu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Ting Cao
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Meigong Zhong
- Department of Pharmacy, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, 529030, China
| | - Ronggang Li
- Department of Pathology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Minyan Wu
- Department of Basic Medicine, Guangdong Jiangmen Chinese Medical College, Jiangmen, 529030, China
| | - Zhuming Lu
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Wenguang Pang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Lin Xiao
- Department of Radiotherapy Center, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Daren Lin
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Zhihui Wang
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Fangyong Lei
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Xiangmeng Chen
- Department of Radiology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Wansheng Long
- Department of Radiology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Yan Zheng
- Department of Research and Development, Research and Development Center for Molecular Diagnosis Engineering Technology of Human Papillomavirus (HPV) Related Diseases of Guangdong Province, Hybribio Limited, Changzhou, 521021, China
| | - Qiong Chen
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jincheng Zeng
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China
| | - Dong Ren
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China
| | - Jun Li
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China.
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China.
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15
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Maeda M, Takeshima H, Iida N, Hattori N, Yamashita S, Moro H, Yasukawa Y, Nishiyama K, Hashimoto T, Sekine S, Ishii G, Ochiai A, Fukagawa T, Katai H, Sakai Y, Ushijima T. Cancer cell niche factors secreted from cancer-associated fibroblast by loss of H3K27me3. Gut 2020; 69:243-251. [PMID: 31085554 DOI: 10.1136/gutjnl-2018-317645] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/25/2019] [Accepted: 04/21/2019] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Cancer-associated fibroblasts (CAFs), a major component of cancer stroma, can confer aggressive properties to cancer cells by secreting multiple factors. Their phenotypes are stably maintained, but the mechanisms are not fully understood. We aimed to show the critical role of epigenetic changes in CAFs in maintaining their tumour-promoting capacity and to show the validity of the epigenomic approach in identifying therapeutic targets from CAFs to starve cancer cells. DESIGN Twelve pairs of primary gastric CAFs and their corresponding non-CAFs (NCAFs) were established from surgical specimens. Genome-wide DNA methylation and H3K27me3 analyses were conducted by BeadArray 450K and ChIP-on-Chip, respectively. Functions of potential a therapeutic target were analysed by inhibiting it, and prognostic impact was assessed in a database. RESULTS CAFs had diverse and distinct DNA methylation and H3K27me3 patterns compared with NCAFs. Loss of H3K27me3, but not DNA methylation, in CAFs was enriched for genes involved in stem cell niche, cell growth, tissue development and stromal-epithelial interactions, such as WNT5A, GREM1, NOG and IGF2. Among these, we revealed that WNT5A, which had been considered to be derived from cancer cells, was highly expressed in cancer stromal fibroblasts, and was associated with poor prognosis. Inhibition of secreted WNT5A from CAFs suppressed cancer cell growth and migration. CONCLUSIONS H3K27me3 plays a crucial role in defining tumour-promoting capacities of CAFs, and multiple stem cell niche factors were secreted from CAFs due to loss of H3K27me3. The validity of the epigenetic approach to uncover therapeutic targets for cancer-starving therapy was demonstrated.
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Affiliation(s)
- Masahiro Maeda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastrointestinal Surgery, Faculty of Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroshi Moro
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshimi Yasukawa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhiro Nishiyama
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Taiki Hashimoto
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Shigeki Sekine
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Genichiro Ishii
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, Chiba, Japan
| | - Atsushi Ochiai
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Takeo Fukagawa
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiharu Sakai
- Department of Gastrointestinal Surgery, Faculty of Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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16
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Yamashita S, Nanjo S, Rehnberg E, Iida N, Takeshima H, Ando T, Maekita T, Sugiyama T, Ushijima T. Distinct DNA methylation targets by aging and chronic inflammation: a pilot study using gastric mucosa infected with Helicobacter pylori. Clin Epigenetics 2019; 11:191. [PMID: 31829249 PMCID: PMC6907118 DOI: 10.1186/s13148-019-0789-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background Aberrant DNA methylation is induced by aging and chronic inflammation in normal tissues. The induction by inflammation is widely recognized as acceleration of age-related methylation. However, few studies addressed target genomic regions and the responsible factors in a genome-wide manner. Here, we analyzed methylation targets by aging and inflammation, taking advantage of the potent methylation induction in human gastric mucosa by Helicobacter pylori infection-triggered inflammation. Results DNA methylation microarray analysis of 482,421 CpG probes, grouped into 270,249 genomic blocks, revealed that high levels of methylation were induced in 44,461 (16.5%) genomic blocks by inflammation, even after correction of the influence of leukocyte infiltration. A total of 61.8% of the hypermethylation was acceleration of age-related methylation while 21.6% was specific to inflammation. Regions with H3K27me3 were frequently hypermethylated both by aging and inflammation. Basal methylation levels were essential for age-related hypermethylation while even regions with little basal methylation were hypermethylated by inflammation. When limited to promoter CpG islands, being a microRNA gene and high basal methylation levels strongly enhanced hypermethylation while H3K27me3 strongly enhanced inflammation-induced hypermethylation. Inflammation was capable of overriding active transcription. In young gastric mucosae, genes with high expression and frequent mutations in gastric cancers were more frequently methylated than in old ones. Conclusions Methylation by inflammation was not simple acceleration of age-related methylation. Targets of aberrant DNA methylation were different between young and old gastric mucosae, and driver genes were preferentially methylated in young gastric mucosa.
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Affiliation(s)
- Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Sohachi Nanjo
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Emil Rehnberg
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Takao Maekita
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Toshiro Sugiyama
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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17
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Gonzalez-Molina J, Gramolelli S, Liao Z, Carlson JW, Ojala PM, Lehti K. MMP14 in Sarcoma: A Regulator of Tumor Microenvironment Communication in Connective Tissues. Cells 2019; 8:cells8090991. [PMID: 31466240 PMCID: PMC6770050 DOI: 10.3390/cells8090991] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
Sarcomas are deadly malignant tumors of mesenchymal origin occurring at all ages. The expression and function of the membrane-type matrix metalloproteinase MMP14 is closely related to the mesenchymal cell phenotype, and it is highly expressed in most sarcomas. MMP14 regulates the activity of multiple extracellular and plasma membrane proteins, influencing cell–cell and cell–extracellular matrix (ECM) communication. This regulation mediates processes such as ECM degradation and remodeling, cell invasion, and cancer metastasis. Thus, a comprehensive understanding of the biology of MMP14 in sarcomas will shed light on the mechanisms controlling the key processes in these diseases. Here, we provide an overview of the function and regulation of MMP14 and we discuss their relationship with clinical and pre-clinical MMP14 data in both adult and childhood sarcomas.
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Affiliation(s)
- Jordi Gonzalez-Molina
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17177 Stockholm, Sweden.
- Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden.
| | - Silvia Gramolelli
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Zehuan Liao
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17177 Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Joseph W Carlson
- Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Päivi M Ojala
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Section of Virology, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1NY, UK
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17177 Stockholm, Sweden.
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland.
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18
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Xu A, Chen J, Peng H, Han G, Cai H. Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences. Front Genet 2019; 10:236. [PMID: 30984238 PMCID: PMC6448130 DOI: 10.3389/fgene.2019.00236] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/04/2019] [Indexed: 11/21/2022] Open
Abstract
Recent advances in high-throughput sequencing have accelerated the accumulation of omics data on the same tumor tissue from multiple sources. Intensive study of multi-omics integration on tumor samples can stimulate progress in precision medicine and is promising in detecting potential biomarkers. However, current methods are restricted owing to highly unbalanced dimensions of omics data or difficulty in assigning weights between different data sources. Therefore, the appropriate approximation and constraints of integrated targets remain a major challenge. In this paper, we proposed an omics data integration method, named high-order path elucidated similarity (HOPES). HOPES fuses the similarities derived from various omics data sources to solve the dimensional discrepancy, and progressively elucidate the similarities from each type of omics data into an integrated similarity with various high-order connected paths. Through a series of incremental constraints for commonality, HOPES can take both specificity of single data and consistency between different data types into consideration. The fused similarity matrix gives global insight into patients' correlation and efficiently distinguishes subgroups. We tested the performance of HOPES on both a simulated dataset and several empirical tumor datasets. The test datasets contain three omics types including gene expression, DNA methylation, and microRNA data for five different TCGA cancer projects. Our method was shown to achieve superior accuracy and high robustness compared with several benchmark methods on simulated data. Further experiments on five cancer datasets demonstrated that HOPES achieved superior performances in cancer classification. The stratified subgroups were shown to have statistically significant differences in survival. We further located and identified the key genes, methylation sites, and microRNAs within each subgroup. They were shown to achieve high potential prognostic value and were enriched in many cancer-related biological processes or pathways.
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Affiliation(s)
- Aodan Xu
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Jiazhou Chen
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hong Peng
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - GuoQiang Han
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongmin Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China
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19
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Takeshima H, Ushijima T. Accumulation of genetic and epigenetic alterations in normal cells and cancer risk. NPJ Precis Oncol 2019; 3:7. [PMID: 30854468 PMCID: PMC6403339 DOI: 10.1038/s41698-019-0079-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/11/2019] [Indexed: 12/17/2022] Open
Abstract
Cancers develop due to the accumulation of genetic and epigenetic alterations. Genetic alterations are induced by aging, mutagenic chemicals, ultraviolet light, and other factors; whereas, epigenetic alterations are mainly by aging and chronic inflammation. The accumulation and patterns of alterations in normal cells reflect our past exposure levels and life history. Most accumulated alterations are considered as passengers, but their accumulation is correlated with cancer drivers. This has been shown for aberrant DNA methylation but has only been speculated for genetic alterations. However, recent technological advancements have enabled measurement of rare point mutations, and studies have shown that their accumulation levels are indeed correlated with cancer risk. When the accumulation levels of aberrant DNA methylation and point mutations are combined, risk prediction becomes even more accurate. When high levels of alterations accumulate, the tissue has a high risk of developing cancer or even multiple cancers and is considered as a “cancerization field”, with or without expansion of physiological patches of clonal cells. In this review, we describe the formation of a cancerization field and how we can apply its detection in precision cancer risk diagnosis.
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Affiliation(s)
- Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, 104-0045 Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, 104-0045 Tokyo, Japan
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20
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Easwaran H, Baylin SB. Origin and Mechanisms of DNA Methylation Dynamics in Cancers. RNA TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-14792-1_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Novel epigenetic markers for gastric cancer risk stratification in individuals after Helicobacter pylori eradication. Gastric Cancer 2018; 21:745-755. [PMID: 29427040 DOI: 10.1007/s10120-018-0803-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/27/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND The risk stratification of healthy individuals after Helicobacter pylori eradication is an urgent issue. The assessment of aberrant DNA methylation accumulated in gastric tissues with normal appearance, which can reflect overall epigenomic damage, is a promising strategy. We aimed to establish novel epigenetic cancer risk markers for H. pylori-eradicated individuals. METHODS Gastric mucosa was collected from eight healthy volunteers without H. pylori infection (G1), 75 healthy individuals with gastric atrophy (G2), and 94 gastric cancer patients (G3) after H. pylori eradication. Genome-wide analysis was conducted using Infinium 450 K and differentially methylated probes were screened using large difference and iEVORA-based methods. Bisulfite pyrosequencing was used for validation. RESULTS Screening, using 8 G1, 12 G2, and 12 G3 samples, isolated 57 candidates unmethylated in G1 and differentially methylated in G3 compared with G2. Validation for nine candidate markers (FLT3, LINC00643, RPRM, JAM2, ELMO1, BHLHE22, RIMS1, GUSBP5, and ZNF3) in 63 G2 and 82 G3 samples showed that all of them had significantly higher methylation levels in G3 than in G2 (P < 0.0001). Their methylation levels were highly correlated, which indicated that they reflect overall epigenomic damage. The candidates had sufficient performance (AUC: 0.70-0. 80) and high odds ratios (5.43-23.41), some of which were superior to a previous marker, miR-124a-3. The methylation levels of our novel markers were not associated with gastric atrophy, gender, or age. CONCLUSIONS Novel epigenetic markers for gastric cancer risk optimized for H. pylori-eradicated individuals were established.
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22
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DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
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Arai E, Miura F, Totoki Y, Yamashita S, Tian Y, Gotoh M, Ojima H, Nakagawa H, Takahashi Y, Nakamura H, Hama N, Kato M, Kimura H, Suzuki Y, Ito T, Shibata T, Kanai Y. Epigenome mapping of human normal purified hepatocytes: personal epigenome variation and genome-epigenome correlation. Epigenomics 2018; 10:955-979. [PMID: 29972026 DOI: 10.2217/epi-2017-0111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
AIM The aim of this study was to reveal the epigenome landscape of human normal hepatocytes. MATERIALS & METHODS Cells purified from partial hepatectomy specimens of Japanese patients were subjected to whole-genome bisulfite sequencing using postbisulfite adaptor tagging, chromatin immunoprecipitation sequencing, RNA sequencing and whole-genome sequencing. RESULTS CHG and CHH methylations were inversely associated with gene expression. Histone modification profiles of personal differentially methylated regions (pDMRs) differed considerably among samples. pDMRs were observed around the transcription start sites of genes whose expression is reportedly regulated by CpG methylation. pDMRs were frequently observed in the vicinity of single-nucleotide variations and insertions/deletions. CONCLUSION Genetic variations may induce epigenetic variations, generating individual differences in the phenotypes of normal hepatocytes through variations in expression.
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Affiliation(s)
- Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Fumihito Miura
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yasushi Totoki
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Masahiro Gotoh
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Hidenori Ojima
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Hiroyuki Nakagawa
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd, Tokyo 105-6215, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd, Tokyo 105-6215, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroshi Kimura
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Graduate School of Bioscience & Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yutaka Suzuki
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Takashi Ito
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Tatsuhiro Shibata
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
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Okochi-Takada E, Hattori N, Ito A, Niwa T, Wakabayashi M, Kimura K, Yoshida M, Ushijima T. Establishment of a high-throughput detection system for DNA demethylating agents. Epigenetics 2018; 13:147-155. [PMID: 27935410 DOI: 10.1080/15592294.2016.1267887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic alterations underlie various human disorders, including cancer, and this has resulted in the development of drugs targeting epigenetic alterations. Although DNA demethylating agents are one of the major epigenetic drugs, only two compounds-5-azacytidine (5-aza-CR, azacitidine) and 5-aza-2'-deoxycytidine (5-aza-dC, decitabine)-have obtained clinical approval. Here, we aimed to establish a detection system for DNA demethylating agents suitable for a high-throughput screening (HTS) in mammalian cells. We inserted luciferase and EGFP reporter genes under the UCHL1 promoter, which is methylation-silenced in human colon cancers and can be readily demethylated to drive strong expression. Methylated UCHL1 promoter was introduced into HCT116 colon cancer cells, and transfectants with methylated exogenous UCHL1 promoter were obtained. By screening subclones from each of the epigenetically heterogeneous transfectant clones, we finally obtained three optimal subclones that expressed luciferase and EGFP after 5-aza-dC treatment with high signal-to-noise ratios. Nucleosomes with H3K9me2 were present around the exogenous UCHL1 promoter in all three subclones. Using one of the subclones (HML58-3), HTS was conducted using 19,840 small molecules. Two hit compounds were obtained, and these turned out to be 5-aza-dC and 5-aza-CR. The assay system constructed here demonstrates a robust response to DNA demethylating agents, along with high specificity, and will be useful for screening and biological assays in epigenetics.
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Affiliation(s)
- Eriko Okochi-Takada
- a Division of Epigenomics , National Cancer Center Research Institute , 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 , Japan
| | - Naoko Hattori
- a Division of Epigenomics , National Cancer Center Research Institute , 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 , Japan
| | - Akihiro Ito
- b Chemical Genetics Laboratory , RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 , Japan.,c Chemical Genomics Research Group , RIKEN Center for Sustainable Resource Science , 2-1 Hirosawa, Wako, Saitama 351-0198 , Japan
| | - Tohru Niwa
- a Division of Epigenomics , National Cancer Center Research Institute , 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 , Japan
| | - Mika Wakabayashi
- a Division of Epigenomics , National Cancer Center Research Institute , 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 , Japan
| | - Kana Kimura
- a Division of Epigenomics , National Cancer Center Research Institute , 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 , Japan
| | - Minoru Yoshida
- b Chemical Genetics Laboratory , RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 , Japan.,c Chemical Genomics Research Group , RIKEN Center for Sustainable Resource Science , 2-1 Hirosawa, Wako, Saitama 351-0198 , Japan.,d Seed Compounds Exploratory Unit for Drug Discovery Platform , RIKEN Center for Sustainable Resource Science , 2-1 Hirosawa, Wako, Saitama 351-0198 , Japan
| | - Toshikazu Ushijima
- a Division of Epigenomics , National Cancer Center Research Institute , 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 , Japan
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Tsubota S, Kishida S, Shimamura T, Ohira M, Yamashita S, Cao D, Kiyonari S, Ushijima T, Kadomatsu K. PRC2-Mediated Transcriptomic Alterations at the Embryonic Stage Govern Tumorigenesis and Clinical Outcome in MYCN-Driven Neuroblastoma. Cancer Res 2017; 77:5259-5271. [PMID: 28807939 DOI: 10.1158/0008-5472.can-16-3144] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/23/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022]
Abstract
Pediatric cancers such as neuroblastoma are thought to involve a dysregulation of embryonic development. However, it has been difficult to identify the critical events that trigger tumorigenesis and differentiate them from normal development. In this study, we report the establishment of a spheroid culture method that enriches early-stage tumor cells from TH-MYCN mice, a preclinical model of neuroblastoma. Using this method, we found that tumorigenic cells were evident as early as day E13.5 during embryo development, when the MYC and PRC2 transcriptomes were significantly altered. Ezh2, an essential component of PRC2, was expressed in embryonic and postnatal tumor lesions and physically associated with N-MYC and we observed that H3K27me3 was increased at PRC2 target genes. PRC2 inhibition suppressed in vitro sphere formation, derepressed its target genes, and suppressed in situ tumor growth. In clinical specimens, expression of MYC and PRC2 target genes correlated strongly and predicted survival outcomes. Together, our findings highlighted PRC2-mediated transcriptional control during embryogenesis as a critical step in the development and clinical outcome of neuroblastoma. Cancer Res; 77(19); 5259-71. ©2017 AACR.
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Affiliation(s)
- Shoma Tsubota
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Kishida
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miki Ohira
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Dongliang Cao
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichi Kiyonari
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenji Kadomatsu
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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Targeting of super-enhancers and mutant BRAF can suppress growth of BRAF -mutant colon cancer cells via repression of MAPK signaling pathway. Cancer Lett 2017; 402:100-109. [DOI: 10.1016/j.canlet.2017.05.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 11/24/2022]
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27
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Takeshima H, Niwa T, Toyoda T, Wakabayashi M, Yamashita S, Ushijima T. Degree of methylation burden is determined by the exposure period to carcinogenic factors. Cancer Sci 2017; 108:316-321. [PMID: 27992956 PMCID: PMC5378290 DOI: 10.1111/cas.13136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/08/2016] [Accepted: 12/10/2016] [Indexed: 12/25/2022] Open
Abstract
Aberrant DNA methylation accumulated in normal tissues, namely methylation burden, is associated with risk of carcinogenesis. The levels of methylation burden are known to be influenced by multiple factors, such as genetic factors and strengths of carcinogenic factors. However, the impact of the degree of exposure to a carcinogenic factor is still unclear. Here, using a Mongolian gerbil model of Helicobacter pylori (H. pylori)‐induced gastritis, we aimed to clarify the impact of the degree of exposure on methylation burden in normal gastric tissues. DNA methylation levels of four CpG islands, HE6, SA9, SB5, and SD2, increased by H. pylori infection, depending upon the infection period. After eradication of H. pylori, DNA methylation levels decreased, but tended to be higher in gastric mucosae with a longer infection period. DNA molecules with dense methylation, but not those with sparse methylation, increased depending upon the infection period. DNA methylation levels of one of the four CpG islands, SA9, tended to be higher in gastric mucosae of gerbils infected with H. pylori, even 50 weeks after eradication than in those of non‐infected gerbils. These results showed for the first time that the levels of methylation burden in normal tissues are influenced by the degree of exposure to a carcinogenic factor.
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Affiliation(s)
- Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takeshi Toyoda
- Division of Pathology, National Institute of Health Sciences, Tokyo, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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28
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Kochmanski J, Montrose L, Goodrich JM, Dolinoy DC. Environmental Deflection: The Impact of Toxicant Exposures on the Aging Epigenome. Toxicol Sci 2017; 156:325-335. [PMID: 28087834 PMCID: PMC6256948 DOI: 10.1093/toxsci/kfx005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Epigenetic drift and age-related methylation have both been used in the literature to describe changes in DNA methylation that occurs with aging. However, ambiguity remains regarding the exact definition of both of these terms, and neither of these fields of study explicitly considers the impact of environmental factors on the aging epigenome. Recent twin studies have demonstrated longitudinal, pair-specific discordance in DNA methylation patterns, suggesting an effect of the environment on age-related methylation and/or epigenetic drift. Supporting this idea, other new reports have shown clear environment- and toxicant-mediated shifts away from the baseline rates of age-related methylation and epigenetic drift within an organism, a process we now term "environmental deflection." By defining and delineating environmental deflection, this contemporary review aims to highlight the effects of specific toxicological factors on the rate of DNA methylation changes that occur over the life course. In an effort to inform future epigenetics-based toxicology studies, a field of research now classified as toxicoepigenetics, we provide clear definitions and examples of "epigenetic drift" and "age-related methylation," summarize the recent evidence for environmental deflection of the aging epigenome, and discuss the potential functional effects of environmental deflection.
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Affiliation(s)
| | | | | | - Dana C. Dolinoy
- Environmental Health Sciences
- Nutritional Sciences, School of Public Health, University of Michigan, Washington Heights, Ann Arbor, Michigan 48109
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29
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Savio AJ, Bapat B. Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer. Epigenetics 2017; 12:441-448. [PMID: 28304185 DOI: 10.1080/15592294.2017.1305527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the MLH1 promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the MLH1 shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the MLH1 CpG island in which it is located.
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Affiliation(s)
- Andrea J Savio
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Bharati Bapat
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada.,c Department of Pathology , University Health Network , Toronto , Ontario , Canada
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30
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Savio AJ, Mrkonjic M, Lemire M, Gallinger S, Knight JA, Bapat B. The dynamic DNA methylation landscape of the mutL homolog 1 shore is altered by MLH1-93G>A polymorphism in normal tissues and colorectal cancer. Clin Epigenetics 2017; 9:26. [PMID: 28293327 PMCID: PMC5345264 DOI: 10.1186/s13148-017-0326-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/02/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Colorectal cancers (CRCs) undergo distinct genetic and epigenetic alterations. Expression of mutL homolog 1 (MLH1), a mismatch repair gene that corrects DNA replication errors, is lost in up to 15% of sporadic tumours due to mutation or, more commonly, due to DNA methylation of its promoter CpG island. A single nucleotide polymorphism (SNP) in the CpG island of MLH1 (MLH1-93G>A or rs1800734) is associated with CpG island hypermethylation and decreased MLH1 expression in CRC tumours. Further, in peripheral blood mononuclear cell (PBMC) DNA of both CRC cases and non-cancer controls, the variant allele of rs1800734 is associated with hypomethylation at the MLH1 shore, a region upstream of its CpG island that is less dense in CpG sites. RESULTS To determine whether this genotype-epigenotype association is present in other tissue types, including colorectal tumours, we assessed DNA methylation in matched normal colorectal tissue, tumour, and PBMC DNA from 349 population-based CRC cases recruited from the Ontario Familial Colorectal Cancer Registry. Using the semi-quantitative real-time PCR-based MethyLight assay, MLH1 shore methylation was significantly higher in tumour tissue than normal colon or PBMCs (P < 0.01). When shore methylation levels were stratified by SNP genotype, normal colorectal DNA and PBMC DNA were significantly hypomethylated in association with variant SNP genotype (P < 0.05). However, this association was lost in tumour DNA. Among distinct stages of CRC, metastatic stage IV CRC tumours incurred significant hypomethylation compared to stage I-III cases, irrespective of genotype status. Shore methylation of MLH1 was not associated with MSI status or promoter CpG island hypermethylation, regardless of genotype. To confirm these results, bisulfite sequencing was performed in matched tumour and normal colorectal specimens from six CRC cases, including two cases per genotype (wildtype, heterozygous, and homozygous variant). Bisulfite sequencing results corroborated the methylation patterns found by MethyLight, with significant hypomethylation in normal colorectal tissue of variant SNP allele carriers. CONCLUSIONS These results indicate that the normal tissue types tested (colorectum and PBMC) experience dynamic genotype-associated epigenetic alterations at the MLH1 shore, whereas tumour DNA incurs aberrant hypermethylation compared to normal DNA.
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Affiliation(s)
- Andrea J. Savio
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
| | - Miralem Mrkonjic
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3 Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
- Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3 Canada
- Ontario Familial Colorectal Cancer Registry, Cancer Care Ontario, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Surgery, University Health Network, 200 Elizabeth St., Toronto, ON M5G 2C4 Canada
| | - Julia A. Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON M5T 3M7 Canada
| | - Bharat Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
- Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, ON M5G 2C4 Canada
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Mechanisms for the induction of gastric cancer by Helicobacter pylori infection: aberrant DNA methylation pathway. Gastric Cancer 2017; 20:8-15. [PMID: 27718135 DOI: 10.1007/s10120-016-0650-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/23/2016] [Indexed: 02/07/2023]
Abstract
Multiple pathogenic mechanisms by which Helicobacter pylori infection induces gastric cancer have been established in the last two decades. In particular, aberrant DNA methylation is induced in multiple driver genes, which inactivates them. Methylation profiles in gastric cancer are associated with specific subtypes, such as microsatellite instability. Recent comprehensive and integrated analyses showed that many cancer-related pathways are more frequently altered by aberrant DNA methylation than by mutations. Aberrant DNA methylation can even be present in noncancerous gastric mucosae, producing an "epigenetic field for cancerization." Mechanistically, H. pylori-induced chronic inflammation, but not H. pylori itself, plays a direct role in the induction of aberrant DNA methylation. The expression of three inflammation-related genes, Il1b, Nos2, and Tnf, is highly associated with the induction of aberrant DNA methylation. Importantly, the degree of accumulated aberrant DNA methylation is strongly correlated with gastric cancer risk. A recent multicenter prospective cohort study demonstrated the utility of epigenetic cancer risk diagnosis for metachronous gastric cancer. Suppression of aberrant DNA methylation by a demethylating agent was shown to inhibit gastric cancer development in an animal model. Induction of aberrant DNA methylation is the major pathway by which H. pylori infection induces gastric cancer, and this can be utilized for translational opportunities.
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Chronic treatment of non-small-cell lung cancer cells with gefitinib leads to an epigenetic loss of epithelial properties associated with reductions in microRNA-155 and -200c. PLoS One 2017; 12:e0172115. [PMID: 28225782 PMCID: PMC5321411 DOI: 10.1371/journal.pone.0172115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 01/31/2017] [Indexed: 12/24/2022] Open
Abstract
Background The EGFR tyrosine kinase inhibitor gefitinib is used in therapy for non-small-cell lung cancer (NSCLC). However, its application is limited by resistance-accelerated disease progression, which is accompanied by the epithelial-to-mesenchymal transition (EMT). In the present study, we performed multiple expression analyses of microRNAs (miRNAs) and quantified the expression of several related EMT players in gefitinib-resistant NSCLC cells. Methods and results To establish gefitinib-resistant NSCLC cells, gefitinib-sensitive HCC827 cells, which exhibit an in-frame deletion [E746-A750] in EGFR exon 19, were exposed to gefitinib for at least 1.5 months. Next, to profile “gefitinib-resistant HCC827 (HCC827GR)” cells, which have a secondary T790M mutation in EGFR exon 20, a miRNA array analysis was performed in HCC827 and HCC827GR cells. The greatest differences were seen in the levels of miR-155 and miR-200c, which essentially disappeared in HCC827GR cells. In addition to these reductions, the levels of smad2 and zeb1, which are both key players in EMT and targets for miR-155 and miR-200c, respectively, were dramatically increased in HCC827GR cells. In HCC827GR cells, the expression of epithelial-cadherin (E-cadherin) was greatly reduced with repressive histone modifications, whereas vimentin, which is expressed in mesenchymal cells, was dramatically increased with active histone modifications. In another gefitinib-resistant NSCLC cell line (H1975 cells), similar to the findings in HCC827GR cells, both miR-155 and miR-200c were absent, and the EMT was induced along with epigenetic modifications. Interestingly, the inhibition of both miR-155 and miR-200c in HCC827 cells without gefitinib induced significant increases in smad2 and zeb1 along with a dramatic decrease in E-cadherin and a slight increase in vimentin. Furthermore, although the inhibition of these miRNAs in HCC827 cells decreased gefitinib sensitivity, this dual-inhibition in HCC827 cells without gefitinib did not produce a secondary T790M mutation in EGFR exon 20. Conclusion and implications These results suggest that chronic treatment of NSCLC cells with gefitinib changes the expression of miRNAs, including dramatic reductions in miR-155 and miR-200c along with an EGFR mutation. Furthermore, this depletion of miR-155 and miR-200c may be associated with the EMT along with histone modifications, and may contribute to the decrease in the sensitivity to gefitinib independent of a secondary EGFR mutation.
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Ambrosi C, Manzo M, Baubec T. Dynamics and Context-Dependent Roles of DNA Methylation. J Mol Biol 2017; 429:1459-1475. [PMID: 28214512 DOI: 10.1016/j.jmb.2017.02.008] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/26/2017] [Accepted: 02/09/2017] [Indexed: 12/22/2022]
Abstract
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing and plays important roles during mammalian development. Its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements, and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity. The genome-wide distribution and dynamic behaviour of this mark have been studied in great detail in a variety of tissues and cell lines, including early embryonic development and in embryonic stem cells. In combination with functional studies, these genome-wide maps of DNA methylation revealed interesting features of this mark and provided important insights into its dynamic nature and potential functional role in genome regulation. In this review, we discuss how these recent observations, in combination with insights obtained from biochemical and functional genetics studies, have expanded our current knowledge about the regulation and context-dependent roles of DNA methylation in mammalian genomes.
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Affiliation(s)
- Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Nakamura T, Yamashita S, Fukumura K, Nakabayashi J, Tanaka K, Tamura K, Tateishi K, Kinoshita M, Fukushima S, Takami H, Fukuoka K, Yamazaki K, Matsushita Y, Ohno M, Miyakita Y, Shibui S, Kubo A, Shuto T, Kocialkowski S, Yamanaka S, Mukasa A, Sasayama T, Mishima K, Maehara T, Kawahara N, Nagane M, Narita Y, Mano H, Ushijima T, Ichimura K. Genome-wide DNA methylation profiling identifies primary central nervous system lymphoma as a distinct entity different from systemic diffuse large B-cell lymphoma. Acta Neuropathol 2017; 133:321-324. [PMID: 28058506 DOI: 10.1007/s00401-016-1664-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/24/2016] [Accepted: 12/24/2016] [Indexed: 10/20/2022]
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Al-Hadid Q, Yang Y. R-loop: an emerging regulator of chromatin dynamics. Acta Biochim Biophys Sin (Shanghai) 2016; 48:623-31. [PMID: 27252122 DOI: 10.1093/abbs/gmw052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/29/2016] [Indexed: 12/27/2022] Open
Abstract
The dynamic structure of chromatin, which exists in two conformational states: heterochromatin and euchromatin, alters the accessibility of the DNA to regulatory factors during transcription, replication, recombination, and DNA damage repair. Chemical modifications of histones and DNA, as well as adenosine triphospahate-dependent nucleosome remodeling, have been the major focus of research on chromatin dynamics over the past two decades. However, recent studies using a DNA-RNA hybrid-specific antibody and next-generation sequencing approaches have revealed that the formation of R-loops, one of the most common non-canonical DNA structures, is an emerging regulator of chromatin states. This review focuses on recent insights into the interplay between R-loop formation and the epigenetic modifications of chromatin in normal and disease states.
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Affiliation(s)
- Qais Al-Hadid
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA 91010, USA
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Abe M, Yamashita S, Mori Y, Abe T, Saijo H, Hoshi K, Ushijima T, Takato T. High-risk oral leukoplakia is associated with aberrant promoter methylation of multiple genes. BMC Cancer 2016; 16:350. [PMID: 27255271 PMCID: PMC4891845 DOI: 10.1186/s12885-016-2371-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/19/2016] [Indexed: 01/26/2023] Open
Abstract
Background Early detection of oral squamous cell carcinomas (OSCCs) is urgently needed to improve the prognosis and quality of life (QOL) of patients. Oral leukoplakias (OLs), known as the most common premalignant lesions in the oral cavity, often precede OSCCs. Especially, OLs with dysplasia are known to have a high risk of malignant transformation. Here, we searched for the promoter methylation characteristic of high-risk OLs. Methods To identify methylation-silenced genes, a combined analysis of methylated DNA immunoprecipitation (MeDIP) − CpG island (CGI) microarray analysis and expression microarray analysis after treatment with a demethylating agent was performed in two OSCC cell lines (Ca9–22 and HSC-2). The methylation statuses of each gene were examined by methylation-specific PCR. Results A total of 52 genes were identified as candidates for methylation-silenced genes in Ca9-22 or HSC-2. The promoter regions of 13 genes among the 15 genes randomly selected for further analysis were confirmed to be methylated in one or more of five cell lines. In OSCC tissues (n = 26), 8 of the 13 genes, TSPYL5, EGFLAM, CLDN11, NKX2-3, RBP4, CMTM3, TRPC4, and MAP6, were methylated. In OL tissues (n = 24), seven of the eight genes, except for EGFLAM, were found to be methylated in their promoter regions. There were significantly greater numbers of methylated genes in OLs with dysplasia than in those without dysplasia (p < 0.0001). Conclusions OLs at high risk for malignant transformation were associated with aberrant promoter methylation of multiple genes. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2371-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masanobu Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Division for Health Service Promotion, University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshiyuki Mori
- Department of Dentistry, Oral & Maxillofacial Surgery, Jichi Medical University, Tochigi, Japan
| | - Takahiro Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hideto Saijo
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuto Hoshi
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tsuyoshi Takato
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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Nakazato H, Takeshima H, Kishino T, Kubo E, Hattori N, Nakajima T, Yamashita S, Igaki H, Tachimori Y, Kuniyoshi Y, Ushijima T. Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis. PLoS One 2016; 11:e0147372. [PMID: 26812616 PMCID: PMC4728064 DOI: 10.1371/journal.pone.0147372] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/04/2016] [Indexed: 01/26/2023] Open
Abstract
The SWI/SNF chromatin remodeling complex is frequently inactivated by somatic mutations of its various components in various types of cancers, and also by aberrant DNA methylation. However, its somatic mutations and aberrant methylation in esophageal squamous cell carcinomas (ESCCs) have not been fully analyzed. In this study, we aimed to clarify in ESCC, what components of the SWI/SNF complex have somatic mutations and aberrant methylation, and when somatic mutations of the SWI/SNF complex occur. Deep sequencing of components of the SWI/SNF complex using a bench-top next generation sequencer revealed that eight of 92 ESCCs (8.7%) had 11 somatic mutations of 7 genes, ARID1A, ARID2, ATRX, PBRM1, SMARCA4, SMARCAL1, and SMARCC1. The SMARCA4 mutations were located in the Forkhead (85Ser>Leu) and SNF2 family N-terminal (882Glu>Lys) domains. The PBRM1 mutations were located in a bromodomain (80Asn>Ser) and an HMG-box domain (1,377Glu>Lys). For most mutations, their mutant allele frequency was 31–77% (mean 61%) of the fraction of cancer cells in the same samples, indicating that most of the cancer cells in individual ESCC samples had the SWI/SNF mutations on one allele, when present. In addition, a BeadChip array analysis revealed that a component of the SWI/SNF complex, ACTL6B, had aberrant methylation at its promoter CpG island in 18 of 52 ESCCs (34.6%). These results showed that genetic and epigenetic alterations of the SWI/SNF complex are present in ESCCs, and suggested that genetic alterations are induced at an early stage of esophageal squamous cell carcinogenesis.
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Affiliation(s)
- Hidetsugu Nakazato
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Esophageal Surgery Division, National Cancer Center Hospital, Tokyo, Japan
- Department of Thoracic and Cardiovascular Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Emi Kubo
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takeshi Nakajima
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroyasu Igaki
- Esophageal Surgery Division, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Tachimori
- Esophageal Surgery Division, National Cancer Center Hospital, Tokyo, Japan
| | - Yukio Kuniyoshi
- Department of Thoracic and Cardiovascular Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
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Kishino T, Niwa T, Yamashita S, Takahashi T, Nakazato H, Nakajima T, Igaki H, Tachimori Y, Suzuki Y, Ushijima T. Integrated analysis of DNA methylation and mutations in esophageal squamous cell carcinoma. Mol Carcinog 2016; 55:2077-2088. [PMID: 26756304 DOI: 10.1002/mc.22452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]
Abstract
The recent development of next-generation sequencing technology for extensive mutation analysis, and beadarray technology for genome-wide DNA methylation analysis has made it possible to obtain integrated pictures of genetic and epigenetic alterations, using the same cancer samples. In this study, we aimed to characterize such a picture in esophageal squamous cell carcinomas (ESCCs). Base substitutions of 55 cancer-related genes and copy number alterations (CNAs) of 28 cancer-related genes were analyzed by targeted sequencing. Forty-four of 57 ESCCs (77%) had 64 non-synonymous somatic mutations, and 24 ESCCs (42%) had 35 CNAs. A genome-wide DNA methylation analysis using an Infinium HumanMethylation450 BeadChip array showed that the CpG island methylator phenotype was unlikely to be present in ESCCs, a different situation from gastric and colon cancers. Regarding individual pathways affected in ESCCs, the WNT pathway was activated potentially by aberrant methylation of its negative regulators, such as SFRP1, SFRP2, SFRP4, SFRP5, SOX17, and WIF1 (33%). The p53 pathway was inactivated by TP53 mutations (70%), and potentially by aberrant methylation of its downstream genes. The cell cycle was deregulated by mutations of CDKN2A (9%), deletions of CDKN2A and RB1 (32%), and by aberrant methylation of CDKN2A and CHFR (9%). In conclusion, ESCCs had unique methylation profiles different from gastric and colon cancers. The genes involved in the WNT pathway were affected mainly by epigenetic alterations, and those involved in the p53 pathway and cell cycle regulation were affected mainly by genetic alterations. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan.,Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takamasa Takahashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hidetsugu Nakazato
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Takeshi Nakajima
- Division of Endoscopy, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyasu Igaki
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Tachimori
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuyuki Suzuki
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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Demura M, Saijoh K. The Role of DNA Methylation in Hypertension. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 956:583-598. [PMID: 27888489 DOI: 10.1007/5584_2016_80] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is the covalent modification of DNA that affects its function, without altering DNA sequences. Three important roles of DNA methylation include intrauterine programming, acquired predisposition, and transgenerational inheritance. A wide variety of factors can affect DNA methylation. Intrauterine programming involves drastic changes in DNA methylation patterns during cellular development and differentiation, which have a long-lasting effect on the predisposition of offspring. Influences from the mother, including maternal nutritional status, modify intrauterine epigenetic programming. In contrast to the rapid and drastic changes in utero, postnatal factors in daily life can also continue to slowly and dynamically change DNA methylation patterns in both somatic and germ cells. Epigenetic changes occurring in germ cell DNA exert a transgenerational impact on the phenotype of future generations, thus providing a means for ancestral transmission of environmental experiences. Despite adaptive ability, mismatch effect of transgenerational inheritance could be potentially harmful to health if environment has changed, and the acquired acclimatization is no longer beneficial. Increasing evidence from both human and animal studies indicates that DNA methylation exerts a causal impact on the development of hypertension. Therefore, an adverse outcome of maternal malnutrition could be the development of hypertension in offspring, whereby nutritional factors or disease conditions could induce phenotypes susceptible to hypertension through alteration of DNA methylation patterns. These factors are likely to alter DNA methylation patterns in all tissues including germ cells, and despite no direct evidence of an association between transgenerational epigenetic inheritance and hypertension, it is likely to play a role.
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Affiliation(s)
- Masashi Demura
- Department of Hygiene, Graduate School of Medical Science, Kanazawa University, Kanazawa, 920-8640, Japan.
| | - Kiyofumi Saijoh
- Department of Hygiene, Graduate School of Medical Science, Kanazawa University, Kanazawa, 920-8640, Japan
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Jiang Y, Yan B, Lai W, Shi Y, Xiao D, Jia J, Liu S, Li H, Lu J, Li Z, Chen L, Chen X, Sun L, Muegge K, Cao Y, Tao Y. Repression of Hox genes by LMP1 in nasopharyngeal carcinoma and modulation of glycolytic pathway genes by HoxC8. Oncogene 2015; 34:6079-91. [PMID: 25745994 PMCID: PMC4564361 DOI: 10.1038/onc.2015.53] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 12/26/2022]
Abstract
Epstein-Barr virus (EBV) causes human lymphoid malignancies, and the EBV product latent membrane protein 1 (LMP1) has been identified as an oncogene in epithelial carcinomas such as nasopharyngeal carcinoma (NPC). EBV can epigenetically reprogram lymphocyte-specific processes and induce cell immortalization. However, the interplay between LMP1 and the NPC host cell remains largely unknown. Here, we report that LMP1 is important to establish the Hox gene expression signature in NPC cell lines and tumor biopsies. LMP1 induces repression of several Hox genes in part via stalling of RNA polymerase II (RNA Pol II). Pol II stalling can be overcome by irradiation involving the epigenetic regulator TET3. Furthermore, we report that HoxC8, one of the genes silenced by LMP1, has a role in tumor growth. Ectopic expression of HoxC8 inhibits NPC cell growth in vitro and in vivo, modulates glycolysis and regulates the expression of tricarboxylic acid (TCA) cycle-related genes. We propose that viral latency products may repress via stalling key mediators that in turn modulate glycolysis.
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Affiliation(s)
- Yiqun Jiang
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Bin Yan
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Weiwei Lai
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Ying Shi
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078 China
| | - Jiantao Jia
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, 410008 China
| | - Shuang Liu
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan, 410008 China
| | - Hongde Li
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Jinchen Lu
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Zhi Li
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, 410008 China
| | - Ling Chen
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Xue Chen
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Lunqun Sun
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, 410008 China
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, National Cancer Institute, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Ya Cao
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
| | - Yongguang Tao
- Cancer Research Institute, Central South University, Changsha, Hunan, 410078 China
- Center for Molecular Imaging, Central South University, Changsha, Hunan, 410078 China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, 410078 China
- Key Laboratory of Carcinogenesis, Ministry of Health, Hunan, 410078 China
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Kasai H, Kawai K, Li YS. Free radical-mediated cytosine C-5 methylation triggers epigenetic changes during carcinogenesis. Biomol Concepts 2015; 4:213-20. [PMID: 25436577 DOI: 10.1515/bmc-2012-0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 01/18/2013] [Indexed: 01/19/2023] Open
Abstract
The methylation of the C-5 position of deoxycytidine (dC) in the promoter regions of tumor suppressor genes is often observed in cancer cells. We found that various environmental agents, as well as endogenous compounds such as methionine sulfoxide (MetO), generate methyl radicals and modify dC to form 5-methyl-dC in DNA in vitro. We confirmed that both DNA methylation and cancer incidence in the liver were increased by the administration of MetO to oxidatively stressed mice. In this review, we summarize previous reports on methyl radical generation in vitro and in vivo and DNA modifications by methyl radicals, including our discoveries, as well as our recent experimental evidence suggesting that free radical-mediated dC methylation triggers epigenetic changes.
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Monk D. Germline-derived DNA methylation and early embryo epigenetic reprogramming: The selected survival of imprints. Int J Biochem Cell Biol 2015; 67:128-38. [PMID: 25966912 DOI: 10.1016/j.biocel.2015.04.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/27/2015] [Indexed: 12/27/2022]
Abstract
DNA methylation is an essential epigenetic mechanism involved in many essential cellular processes. During development epigenetic reprograming takes place during gametogenesis and then again in the pre-implantation embryo. These two reprograming windows ensure genome-wide removal of methylation in the primordial germ cells so that sex-specific signatures can be acquired in the sperm and oocyte. Following fertilization the majority of this epigenetic information is erased to give the developing embryo an epigenetic profile coherent with pluripotency. It is estimated that ∼65% of the genome is differentially methylated between the gametes, however following embryonic reprogramming only parent-of-origin methylation at known imprinted loci remains. This suggests that trans-acting factors such as Zfp57 can discriminate imprinted differentially methylated regions (DMRs) from the thousands of CpG rich regions that are differentially marked in the gametes. Recently transient imprinted DMRs have been identified suggesting that these loci are also protected from pre-implantation reprograming but succumb to de novo remethylation at the implantation stage. This highlights that "ubiquitous" imprinted loci are also resilient to gaining methylation by protecting their unmethylated alleles. In this review I examine the processes involved in epigenetic reprograming and the mechanisms that ensure allelic methylation at imprinted loci is retained throughout the life of the organism, discussing the critical differences between mouse and humans. This article is part of a Directed Issue entitled: Epigenetics Dynamics in development and disease.
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Affiliation(s)
- David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08908, Spain.
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Dynamic regulation of the angiotensinogen gene by DNA methylation, which is influenced by various stimuli experienced in daily life. Hypertens Res 2015; 38:519-27. [PMID: 25809578 DOI: 10.1038/hr.2015.42] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/28/2015] [Accepted: 02/03/2015] [Indexed: 12/17/2022]
Abstract
Angiotensinogen (AGT) has a central role in maintaining blood pressure and fluid balance. DNA methylation is an epigenomic modification maintaining a steady pattern in somatic cells. Herein we summarize the link between AGT regulation and DNA methylation. DNA methylation negatively regulates AGT expression and dynamically changes in response to continuous AGT promoter stimulation. High-salt intake and excess circulating aldosterone cause DNA demethylation around the CCAAT enhancer-binding protein-binding sites, thereby converting the phenotype of AGT expression from an inactive to an active state in visceral adipose tissue. Salt-dependent hypertension may be partially affected by increased adipose AGT expression. Because angiotensin II is a well-established aldosterone-releasing hormone, stimulation of adipose AGT by aldosterone creates a positive feedback loop. This effect is pathologically associated with obesity-related hypertension, although it would be physiologically favorable for humans to efficiently retain their body fluid. The clear difference in DNA demethylation patterns between aldosterone and cortisol indicates a difference in the respective target DNA-binding sites between mineralocorticoid and glucocorticoid receptors in the AGT promoter. Stimulation-induced interactions between transcription factors and target DNA-binding sites trigger DNA demethylation. Dynamic changes in DNA methylation occur in relaxed chromatin regions both where transcription factors actively interact and where transcription is initiated. In contrast to rapid histone modifications, DNA demethylation and remethylation will progress relatively slowly over days or years. A wide variety of stimuli in daily life will continue to slowly and dynamically change DNA methylation patterns throughout life. Wise choices of beneficial stimuli will improve health.
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Yamaguchi T, Mukai H, Yamashita S, Fujii S, Ushijima T. Comprehensive DNA Methylation and Extensive Mutation Analyses of HER2-Positive Breast Cancer. Oncology 2015; 88:377-84. [DOI: 10.1159/000369904] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/11/2014] [Indexed: 11/19/2022]
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Yoda Y, Takeshima H, Niwa T, Kim JG, Ando T, Kushima R, Sugiyama T, Katai H, Noshiro H, Ushijima T. Integrated analysis of cancer-related pathways affected by genetic and epigenetic alterations in gastric cancer. Gastric Cancer 2015; 18:65-76. [PMID: 24510342 DOI: 10.1007/s10120-014-0348-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/18/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND The profiles of genetic and epigenetic alterations in cancer-related pathways are considered to be useful for selection of patients likely to respond to specific drugs, including molecular-targeted and epigenetic drugs. In this study, we aimed to characterize such profiles in gastric cancers (GCs). METHODS Genetic alterations of 55 cancer-related genes were analyzed by a benchtop next-generation sequencer. DNA methylation statuses were analyzed by a bead array with 485,512 probes. RESULTS The WNT pathway was activated by mutations of CTNNB1 in 2 GCs and potentially by aberrant methylation of its negative regulators, such as DKK3, NKD1, and SFRP1, in 49 GCs. The AKT/mTOR pathway was activated by mutations of PIK3CA and PTPN11 in 4 GCs. The MAPK pathway was activated by mutations and gene amplifications of ERBB2, FLT3, and KRAS in 11 GCs. Cell-cycle regulation was affected by aberrant methylation of CDKN2A and CHFR in 13 GCs. Mismatch repair was affected by a mutation of MLH1 in 1 GC and by aberrant methylation of MLH1 in 2 GCs. The p53 pathway was inactivated by mutations of TP53 in 19 GCs and potentially by aberrant methylation of its downstream genes in 38 GCs. Cell adhesion was affected by mutations of CDH1 in 2 GCs. CONCLUSIONS Genes involved in cancer-related pathways were more frequently affected by epigenetic alterations than by genetic alterations. The profiles of genetic and epigenetic alterations are expected to be useful for selection of the patients who are likely to benefit from specific drugs.
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Affiliation(s)
- Yukie Yoda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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Takeshima H, Wakabayashi M, Hattori N, Yamashita S, Ushijima T. Identification of coexistence of DNA methylation and H3K27me3 specifically in cancer cells as a promising target for epigenetic therapy. Carcinogenesis 2014; 36:192-201. [PMID: 25477340 DOI: 10.1093/carcin/bgu238] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alterations of epigenetic modifications are promising targets for cancer therapy, and several epigenetic drugs are now being clinically utilized. At the same time, individual epigenetic modifications have physiological functions in normal cells, and cancer cell specificity is considered difficult to achieve using a drug against a single epigenetic modification. To overcome this limitation, a combination of epigenetic modifications specifically or preferentially present in cancer cells is a candidate target. In this study, we aimed to demonstrate (i) the presence of a cancer cell-specific combination of epigenetic modifications by focusing on DNA methylation and trimethylation of histone H3 lysine 27 (H3K27me3) and (ii) the therapeutic efficacy of a combination of DNA demethylation and EZH2 inhibition. Analyses of DNA methylation and H3K27me3 in human colon, breast and prostate cancer cell lines revealed that 24.7±4.1% of DNA methylated genes had both DNA methylation and H3K27me3 (dual modification) in cancer cells, while it was 11.8±7.1% in normal cells. Combined treatment with a DNA demethylating agent, 5-aza-2'-deoxycytidine (5-aza-dC) and an EZH2 inhibitor, GSK126, induced marked re-expression of genes with the dual modification, including known tumor-suppressor genes such as IGFBP7 and SFRP1, and showed an additive inhibitory effect on growth of cancer cells in vitro. Finally, an in vivo combined treatment with 5-aza-dC and GSK126 inhibited growth of xenograft tumors more efficiently than a single treatment with 5-aza-dC. These results showed that the dual modification exists specifically in cancer cells and is a promising target for cancer cell-specific epigenetic therapy.
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Affiliation(s)
- Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Mika Wakabayashi
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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Frequent involvement of chromatin remodeler alterations in gastric field cancerization. Cancer Lett 2014; 357:328-338. [PMID: 25462860 DOI: 10.1016/j.canlet.2014.11.038] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/18/2014] [Accepted: 11/18/2014] [Indexed: 12/22/2022]
Abstract
A field for cancerization, or a field defect, is formed by the accumulation of genetic and epigenetic alterations in normal-appearing tissues, and is involved in various cancers, especially multiple cancers. Epigenetic alterations are frequently present in chronic inflammation-exposed tissues, but information on individual genes involved in the formation of a field defect is still fragmental. Here, using non-cancerous gastric tissues of cancer patients, we isolated 16 aberrantly methylated genes, and identified chromatin remodelers ACTL6B and SMARCA1 as novel genes frequently methylated in non-cancerous tissues. SMARCA1 was expressed at high levels in normal gastric tissues, but was frequently silenced by aberrant methylation in gastric cancer cells. Moreover, somatic mutations of additional chromatin remodelers, such as ARID1A, SMARCA2, and SMARCA4, were found in 30% of gastric cancers. Mutant allele frequency suggested that the majority of cancer cells harbored a mutation when present. Depletion of a chromatin remodeler, SMARCA1 or SMARCA2, in cancer cell lines promoted their growth. These results showed that epigenetic and genetic alterations of chromatin remodelers are induced at an early stage of carcinogenesis and are frequently involved in the formation of a field defect.
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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Provençal N, Suderman MJ, Guillemin C, Vitaro F, Côté SM, Hallett M, Tremblay RE, Szyf M. Association of childhood chronic physical aggression with a DNA methylation signature in adult human T cells. PLoS One 2014; 9:e89839. [PMID: 24691403 PMCID: PMC3972178 DOI: 10.1371/journal.pone.0089839] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 01/27/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Chronic physical aggression (CPA) is characterized by frequent use of physical aggression from early childhood to adolescence. Observed in approximately 5% of males, CPA is associated with early childhood adverse environments and long-term negative consequences. Alterations in DNA methylation, a covalent modification of DNA that regulates genome function, have been associated with early childhood adversity. AIMS To test the hypothesis that a trajectory of chronic physical aggression during childhood is associated with a distinct DNA methylation profile during adulthood. METHODS We analyzed genome-wide promoter DNA methylation profiles of T cells from two groups of adult males assessed annually for frequency of physical aggression between 6 and 15 years of age: a group with CPA and a control group. Methylation profiles covering the promoter regions of 20 000 genes and 400 microRNAs were generated using MeDIP followed by hybridization to microarrays. RESULTS In total, 448 distinct gene promoters were differentially methylated in CPA. Functionally, many of these genes have previously been shown to play a role in aggression and were enriched in biological pathways affected by behavior. Their locations in the genome tended to form clusters spanning millions of bases in the genome. CONCLUSIONS This study provides evidence of clustered and genome-wide variation in promoter DNA methylation in young adults that associates with a history of chronic physical aggression from 6 to 15 years of age. However, longitudinal studies of methylation during early childhood will be necessary to determine if and how this methylation variation in T cells DNA plays a role in early development of chronic physical aggression.
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Affiliation(s)
- Nadine Provençal
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
| | - Matthew J. Suderman
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
| | - Claire Guillemin
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
| | - Frank Vitaro
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- School of Psycho-Education, University of Montreal, Montréal, Quebec, Canada
| | - Sylvana M. Côté
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- School of Social and Preventive Medicine, University of Montreal, Montréal, Quebec, Canada
| | - Michael Hallett
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
| | - Richard E. Tremblay
- Research Unit on Children's Psycho-Social Maladjustment and Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Canada
- Department of Psychology and Pediatrics, University of Montreal, Montreal, Quebec, Canada
- School of Public Health, Physiotherapy and Population Sciences, University College Dublin, Dublin, Ireland
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec, Canada
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Baubec T, Schübeler D. Genomic patterns and context specific interpretation of DNA methylation. Curr Opin Genet Dev 2014; 25:85-92. [PMID: 24614011 DOI: 10.1016/j.gde.2013.11.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/29/2013] [Indexed: 12/21/2022]
Abstract
Methylation of CpG dinucleotides is a reversible modification of DNA that is highly prevalent throughout mammalian genomes. Recent advances generated genomic DNA methylation maps during cellular differentiation at unprecedented resolution. Combined with functional assays this revealed that dynamics in DNA methylation coincide with changes in regulatory activity and that transcription factors play an important role in shaping methylation patterns. This tightly links DNA methylation with underlying DNA sequence features and suggests that a substantial fraction of methylation changes occur downstream of gene regulation. Here we discuss our current understanding of the context-dependent readout of DNA methylation and criteria that need to be fulfilled for this modification to be instructive for gene regulation.
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Affiliation(s)
- Tuncay Baubec
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland.
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland; University of Basel, Faculty of Science, Petersplatz 1, Basel 4003, Switzerland.
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