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Perycz M, Dabrowski MJ, Jardanowska-Kotuniak M, Roura AJ, Gielniewski B, Stepniak K, Dramiński M, Ciechomska IA, Kaminska B, Wojtas B. Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors. Acta Neuropathol Commun 2024; 12:72. [PMID: 38711090 PMCID: PMC11071216 DOI: 10.1186/s40478-024-01779-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] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The RE1-silencing transcription factor (REST) acts either as a repressor or activator of transcription depending on the genomic and cellular context. REST is a key player in brain cell differentiation by inducing chromatin modifications, including DNA methylation, in a proximity of its binding sites. Its dysfunction may contribute to oncogenesis. Mutations in IDH1/2 significantly change the epigenome contributing to blockade of cell differentiation and glioma development. We aimed at defining how REST modulates gene activation and repression in the context of the IDH mutation-related phenotype in gliomas. We studied the effects of REST knockdown, genome wide occurrence of REST binding sites, and DNA methylation of REST motifs in IDH wild type and IDH mutant gliomas. We found that REST target genes, REST binding patterns, and TF motif occurrence proximal to REST binding sites differed in IDH wild-type and mutant gliomas. Among differentially expressed REST targets were genes involved in glial cell differentiation and extracellular matrix organization, some of which were differentially methylated at promoters or gene bodies. REST knockdown differently impacted invasion of the parental or IDH1 mutant glioma cells. The canonical REST-repressed gene targets showed significant correlation with the GBM NPC-like cellular state. Interestingly, results of REST or KAISO silencing suggested the interplay between these TFs in regulation of REST-activated and repressed targets. The identified gene regulatory networks and putative REST cooperativity with other TFs, such as KAISO, show distinct REST target regulatory networks in IDH-WT and IDH-MUT gliomas, without concomitant DNA methylation changes. We conclude that REST could be an important therapeutic target in gliomas.
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Affiliation(s)
- Malgorzata Perycz
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michal J Dabrowski
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska-Kotuniak
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
- Doctoral School of Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Stepniak
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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2
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Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
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Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
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3
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Plaisance I, Chouvardas P, Sun Y, Nemir M, Aghagolzadeh P, Aminfar F, Shen S, Shim WJ, Rochais F, Johnson R, Palpant N, Pedrazzini T. A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovasc Res 2023; 119:1361-1376. [PMID: 36537036 PMCID: PMC10262180 DOI: 10.1093/cvr/cvac191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 03/25/2024] Open
Abstract
AIMS The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The human lncRNA CARMEN, which is known to dictate specification toward the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced isoforms. METHODS AND RESULTS The CARMEN locus can be manipulated to direct human primary cardiac precursor cells (CPCs) into specific cardiovascular fates. Investigating CARMEN isoform usage in differentiating CPCs represents therefore a unique opportunity to uncover isoform-specific functions in lncRNAs. Here, we identify one CARMEN isoform, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. CONCLUSIONS These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA. They further demonstrated the crucial importance of the lncRNA isoform CARMEN-201 in SMC specification during heart development.
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Affiliation(s)
- Isabelle Plaisance
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Yuliangzi Sun
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Mohamed Nemir
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Parisa Aghagolzadeh
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Farhang Aminfar
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Sophie Shen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Francesca Rochais
- Aix Marseille University, Marseille Medical Genetics, INSERM, U1251, Marseille, France
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University of Bern, Bern, Switzerland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nathan Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
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4
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Vega-Benedetti AF, Loi E, Moi L, Zavattari P. DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer. Clin Epigenetics 2023; 15:98. [PMID: 37301955 PMCID: PMC10257853 DOI: 10.1186/s13148-023-01514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND DNA methylation changes, frequent early events in cancer, can modulate the binding of transcription factors. RE1-silencing transcription factor (REST) plays a fundamental role in regulating the expression of neuronal genes, and in particular their silencing in non-neuronal tissues, by inducing chromatin modifications, including DNA methylation changes, not only in the proximity of its binding sites but also in the flanking regions. REST has been found aberrantly expressed in brain cancer and other cancer types. In this work, we investigated DNA methylation alterations at REST binding sites and their flanking regions in a brain cancer (pilocytic astrocytoma), two gastrointestinal tumours (colorectal cancer and biliary tract cancer) and a blood cancer (chronic lymphocytic leukemia). RESULTS Differential methylation analyses focused on REST binding sites and their flanking regions were conducted between tumour and normal samples from our experimental datasets analysed by Illumina microarrays and the identified alterations were validated using publicly available datasets. We discovered distinct DNA methylation patterns between pilocytic astrocytoma and the other cancer types in agreement with the opposite oncogenic and tumour suppressive role of REST in glioma and non-brain tumours. CONCLUSIONS Our results suggest that these DNA methylation alterations in cancer may be associated with REST dysfunction opening the enthusiastic possibility to develop novel therapeutic interventions based on the modulation of this master regulator in order to restore the aberrant methylation of its target regions into a normal status.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy.
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DNMT3B rs2424913 as a Risk Factor for Congenital Heart Defects in Down Syndrome. Genes (Basel) 2023; 14:genes14030576. [PMID: 36980848 PMCID: PMC10048502 DOI: 10.3390/genes14030576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Impairments of the genes that encode enzymes that are involved in one-carbon metabolism because of the presence of gene polymorphisms can affect the methylation pattern. The altered methylation profiles of the genes involved in cardiogenesis may result in congenital heart defects (CHDs). The aim of this study was to investigate the association between the MTHFR rs1801133, MTHFR rs1801131, MTRR rs1801394, DNMT1 rs2228611, DNMT3A rs1550117, DNMT3B rs1569686, and DNMT3B rs2424913 gene polymorphisms and congenital heart defects in Down syndrome (DS) individuals. The study was conducted on 350 participants, including 134 DS individuals with CHDs (DSCHD+), 124 DS individuals without CHDs (DSCHD−), and 92 individuals with non-syndromic CHD. The genotyping was performed using the PCR–RFLP method. A statistically significant higher frequency of the DNMT3B rs2424913 TT in the DSCHD+ individuals was observed. The DNMT3B rs2424913 TT genotype, as well as the T allele, had significantly higher frequencies in the individuals with DS and atrial septal defects (ASDs) in comparison with the individuals with DS and other CHDs. Furthermore, our results indicate a statistically significant effect of the DNMT3B rs1569686 TT genotype in individuals with non-syndromic CHDs. The results of the study suggest that the DNMT3B rs2424913 TT genotypes may be a possible predisposing factor for CHDs in DS individuals, and especially those with ASDs.
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Zhang D, Ning J, Ramprasath T, Yu C, Zheng X, Song P, Xie Z, Zou MH. Kynurenine promotes neonatal heart regeneration by stimulating cardiomyocyte proliferation and cardiac angiogenesis. Nat Commun 2022; 13:6371. [PMID: 36289221 PMCID: PMC9606021 DOI: 10.1038/s41467-022-33734-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 09/29/2022] [Indexed: 12/25/2022] Open
Abstract
Indoleamine 2,3 dioxygenase-1 (IDO1) catalyzes tryptophan-kynurenine metabolism in many inflammatory and cancer diseases. Of note, acute inflammation that occurs immediately after heart injury is essential for neonatal cardiomyocyte proliferation and heart regeneration. However, the IDO1-catalyzed tryptophan metabolism during heart regeneration is largely unexplored. Here, we find that apical neonatal mouse heart resection surgery led to rapid and consistent increases in cardiac IDO1 expression and kynurenine accumulation. Cardiac deletion of Ido1 gene or chemical inhibition of IDO1 impairs heart regeneration. Mechanistically, elevated kynurenine triggers cardiomyocyte proliferation by activating the cytoplasmic aryl hydrocarbon receptor-SRC-YAP/ERK pathway. In addition, cardiomyocyte-derived kynurenine transports to endothelial cells and stimulates cardiac angiogenesis by promoting aryl hydrocarbon receptor nuclear translocation and enhancing vascular endothelial growth factor A expression. Notably, Ahr deletion prevents indoleamine 2,3 dioxygenase -kynurenine-associated heart regeneration. In summary, increasing indoleamine 2,3 dioxygenase-derived kynurenine level promotes cardiac regeneration by functioning as an endogenous regulator of cardiomyocyte proliferation and cardiac angiogenesis.
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Affiliation(s)
- Donghong Zhang
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Jinfeng Ning
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Tharmarajan Ramprasath
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Changjiang Yu
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Xiaoxu Zheng
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Ping Song
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Zhonglin Xie
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA
| | - Ming-Hui Zou
- Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street North East, Atlanta, GA, 30303, USA.
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7
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Li J, Cheng C, Xu J, Zhang T, Tokat B, Dolios G, Ramakrishnan A, Shen L, Wang R, Xu PX. The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and REST-binding sequences to maintain nephron progenitor identity. Nucleic Acids Res 2022; 50:10343-10359. [PMID: 36130284 PMCID: PMC9561260 DOI: 10.1093/nar/gkac760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022] Open
Abstract
Eya1 is critical for establishing and maintaining nephron progenitor cells (NPCs). It belongs to a family of proteins called phosphatase-transcriptional activators but without intrinsic DNA-binding activity. However, the spectrum of the Eya1-centered networks is underexplored. Here, we combined transcriptomic, genomic and proteomic approaches to characterize gene regulation by Eya1 in the NPCs. We identified Eya1 target genes, associated cis-regulatory elements and partner proteins. Eya1 preferentially occupies promoter sequences and interacts with general transcription factors (TFs), RNA polymerases, different types of TFs, chromatin-remodeling factors with ATPase or helicase activity, and DNA replication/repair proteins. Intriguingly, we identified REST-binding motifs in 76% of Eya1-occupied sites without H3K27ac-deposition, which were present in many Eya1 target genes upregulated in Eya1-deficient NPCs. Eya1 copurified REST-interacting chromatin-remodeling factors, histone deacetylase/lysine demethylase, and corepressors. Coimmunoprecipitation validated physical interaction between Eya1 and Rest/Hdac1/Cdyl/Hltf in the kidneys. Collectively, our results suggest that through interactions with chromatin-remodeling factors and specialized DNA-binding proteins, Eya1 may modify chromatin structure to facilitate the assembly of regulatory complexes that regulate transcription positively or negatively. These findings provide a mechanistic basis for how Eya1 exerts its activity by forming unique multiprotein complexes in various biological processes to maintain the cellular state of NPCs.
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Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Chunming Cheng
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Bengu Tokat
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | | | - Li Shen
- Department of Neurosciences, New York, NY 10029, USA
| | - Rong Wang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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8
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PGC-1α4 Interacts with REST to Upregulate Neuronal Genes and Augment Energy Consumption in Developing Cardiomyocytes. Cells 2022; 11:cells11192944. [PMID: 36230906 PMCID: PMC9564192 DOI: 10.3390/cells11192944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 02/02/2023] Open
Abstract
Transcriptional coactivator PGC-1α is a main regulator of cardiac energy metabolism. In addition to canonical PGC-1α1, other PGC-1α isoforms have been found to exert specific biological functions in a variety of tissues. We investigated the expression patterns and the biological effects of the non-canonical isoforms in the heart. We used RNA sequencing data to identify the expression patterns of PGC-1α isoforms in the heart. To evaluate the biological effects of the alternative isoform expression, we generated a transgenic mouse with cardiac-specific overexpression of PGC-1α4 and analysed the cardiac phenotype with a wide spectrum of physiological and biophysical tools. Our results show that non-canonical isoforms are expressed in the heart, and that the main variant PGC-1α4 is induced by β-adrenergic signalling in adult cardiomyocytes. Cardiomyocyte specific PGC-1α4 overexpression in mice relieves the RE1-Silencing Transcription factor (REST)-mediated suppression of neuronal genes during foetal heart development. The resulting de-repression of REST target genes induces a cardiac phenotype with increased cellular energy consumption, resulting in postnatal dilated cardiomyopathy. These results propose a new concept for actions of the PGC-1α protein family where activation of the Pgc-1α gene, through its isoforms, induces a phenotype with concurrent supply and demand for cellular energy. These data highlight the biological roles of the different PGC-1α isoforms, which should be considered when future therapies are developed.
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Nishizaki SS, Boyle AP. SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. BMC Bioinformatics 2022; 23:317. [PMID: 35927613 PMCID: PMC9351228 DOI: 10.1186/s12859-022-04865-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
MOTIVATION Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor's motif. RESULTS SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease. AVAILABILITY AND IMPLEMENTATION SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe .
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Affiliation(s)
- Sierra S Nishizaki
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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Wang W, Lu G, Liu H, Xiong Z, Leung H, Cao R, Pang AL, Su X, Law PWN, Zhao Z, Chen Z, Chan W. Pten Regulates Cardiomyocyte Differentiation by Modulating Non-CG Methylation via Dnmt3. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100849. [PMID: 34247447 PMCID: PMC8425920 DOI: 10.1002/advs.202100849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/04/2021] [Indexed: 06/13/2023]
Abstract
The regulation of cardiomyocyte differentiation is a fundamental aspect of cardiac development and regenerative medicine. PTEN plays important roles during embryonic development. However, its role in cardiomyocyte differentiation remains unknown. In this study, a low-cost protocol for cardiomyocyte differentiation from mouse embryonic stem cells (ESCs) is presented and it is shown that Pten deletion potently suppresses cardiomyocyte differentiation. Transcriptome analysis shows that the expression of a series of cardiomyocyte marker genes is downregulated in Pten-/- cardiomyocytes. Pten ablation induces Dnmt3b expression via the AKT/FoxO3a pathway and regulates the expression of a series of imprinted genes, including Igf2. Double knockout of Dnmt3l and Dnmt3b rescues the deficiency of cardiomyocyte differentiation of Pten-/- ESCs. The DNA methylomes from wild-type and Pten-/- embryoid bodies and cardiomyocytes are analyzed by whole-genome bisulfite sequencing. Pten deletion significantly promotes the non-CG (CHG and CHH) methylation levels of genomic DNA during cardiomyocyte differentiation, and the non-CG methylation levels of cardiomyocyte genes and Igf2 are increased in Pten-/- cardiomyocytes. Igf2 or Igf1r deletion also suppresses cardiomyocyte differentiation through the MAPK/ERK signaling pathway, and IGF2 supplementation partially rescues the cardiomyocyte differentiation. Finally, Pten conditional knockout mice are generated and the role of PTEN in cardiomyocyte differentiation is verified in vivo.
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Affiliation(s)
- Wuming Wang
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
| | - Gang Lu
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
| | - Hong‐Bin Liu
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
| | - Zhiqiang Xiong
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
- SDIVF R&D Centre12W, Hong Kong Science ParkShatinHong KongChina
| | - Ho‐Duen Leung
- SDIVF R&D Centre12W, Hong Kong Science ParkShatinHong KongChina
| | - Ruican Cao
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
| | - Alan Lap‐Yin Pang
- R&D DivisionTGD Life Company Limited15W, Hong Kong Science ParkShatinHong KongChina
| | - Xianwei Su
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
- SDIVF R&D Centre12W, Hong Kong Science ParkShatinHong KongChina
| | - Patrick Wai Nok Law
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
| | - Zhiju Zhao
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
| | - Zi‐Jiang Chen
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
| | - Wai‐Yee Chan
- CUHK‐SDU Joint Laboratory on Reproductive GeneticsSchool of Biomedical SciencesThe Chinese University of Hong KongHong KongChina
- National Research Center for Assisted Reproductive Technology and Reproductive GeneticsJinan250001China
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11
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m6A modification promotes miR-133a repression during cardiac development and hypertrophy via IGF2BP2. Cell Death Discov 2021; 7:157. [PMID: 34226535 PMCID: PMC8257704 DOI: 10.1038/s41420-021-00552-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/09/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
Both N6-methyladenosine (m6A) RNA modification and microRNAs (miRNAs) are common regulatory mechanisms for gene post-transcription by modulating mRNA stability and translation. They also share the same 3′-untranslated regions (UTRs) regions for their target gene. However, little is known about their potential interaction in cell development and biology. Here, we aimed to investigate how m6A regulates the specific miRNA repression during cardiac development and hypertrophy. Our multiple lines of bioinformatic and molecular biological evidence have shown that m6A modification on cardiac miR-133a target sequence promotes miR-133a repressive effect via AGO2-IGF2BP2 (Argonaute 2—Insulin-like growth factor 2 mRNA binding protein 2) complex. Among 139 cardiac miRNAs, only the seed sequence of miR-133a was inversely complement to m6A consensus motif “GGACH” by sequence alignment analysis. Immunofluorescence staining, luciferase reporter, and m6A-RIP (RNA immunoprecipitation) assays revealed that m6A modification facilitated miR-133a binding to and repressing their targets. The inhibition of the miR-133a on cardiac proliferation and hypertrophy could be prevented by silencing of Fto (FTO alpha-ketoglutarate dependent dioxygenase) which induced m6A modification. IGF2BP2, an m6A binding protein, physically interacted with AGO2 and increased more miR-133a accumulation on its target site, which was modified by m6A. In conclusion, our study revealed a novel and precise regulatory mechanism that the m6A modification promoted the repression of specific miRNA during heart development and hypertrophy. Targeting m6A modification might provide a strategy to repair hypertrophic gene expression induced by miR-133a.
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12
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Suppression of m6A mRNA modification by DNA hypermethylated ALKBH5 aggravates the oncological behavior of KRAS mutation/LKB1 loss lung cancer. Cell Death Dis 2021; 12:518. [PMID: 34016959 PMCID: PMC8137886 DOI: 10.1038/s41419-021-03793-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 02/04/2023]
Abstract
Oncogenic KRAS mutations combined with the loss of the LKB1 tumor-suppressor gene (KL) are strongly associated with aggressive forms of lung cancer. N6-methyladenosine (m6A) in mRNA is a crucial epigenetic modification that controls cancer self-renewal and progression. However, the regulation and role of m6A modification in this cancer are unclear. We found that decreased m6A levels correlated with the disease progression and poor survival for KL patients. The correlation was mediated by a special increase in ALKBH5 (AlkB family member 5) levels, an m6A demethylase. ALKBH5 gain- or loss-of function could effectively reverse LKB1 regulated cell proliferation, colony formation, and migration of KRAS-mutated lung cancer cells. Mechanistically, LKB1 loss upregulated ALKBH5 expression by DNA hypermethylation of the CTCF-binding motif on the ALKBH5 promoter, which inhibited CTCF binding but enhanced histone modifications, including H3K4me3, H3K9ac, and H3K27ac. This effect could successfully be rescued by LKB1 expression. ALKBH5 demethylation of m6A stabilized oncogenic drivers, such as SOX2, SMAD7, and MYC, through a pathway dependent on YTHDF2, an m6A reader protein. The above findings were confirmed in clinical KRAS-mutated lung cancer patients. We conclude that loss of LKB1 promotes ALKBH5 transcription by a DNA methylation mechanism, reduces m6A modification, and increases the stability of m6A target oncogenes, thus contributing to aggressive phenotypes of KRAS-mutated lung cancer.
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13
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Yoshizaki K, Kimura R, Kobayashi H, Oki S, Kikkawa T, Mai L, Koike K, Mochizuki K, Inada H, Matsui Y, Kono T, Osumi N. Paternal age affects offspring via an epigenetic mechanism involving REST/NRSF. EMBO Rep 2021; 22:e51524. [PMID: 33399271 PMCID: PMC7857438 DOI: 10.15252/embr.202051524] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
Advanced paternal age can have deleterious effects on various traits in the next generation. Here, we establish a paternal‐aging model in mice to understand the molecular mechanisms of transgenerational epigenetics. Whole‐genome target DNA methylome analyses of sperm from aged mice reveal more hypo‐methylated genomic regions enriched in REST/NRSF binding motifs. Gene set enrichment analyses also reveal the upregulation of REST/NRSF target genes in the forebrain of embryos from aged fathers. Offspring derived from young mice administrated with a DNA de‐methylation drug phenocopy the abnormal vocal communication of pups derived from aged fathers. In conclusion, hypo‐methylation of sperm DNA can be a key molecular feature modulating neurodevelopmental programs in offspring by causing fluctuations in the expression of REST/NRSF target genes.
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Affiliation(s)
- Kaichi Yoshizaki
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Disease Model, Aichi Developmental Disability Center, Aichi, Japan
| | - Ryuichi Kimura
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.,Department of Embryology, Nara Medical University, Nara, Japan.,The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takako Kikkawa
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Lingling Mai
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kohei Koike
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Physiology, Center for Integrative Physiology and Molecular Medicine, Saarland University School of Medicine, Homburg, Germany
| | - Kentaro Mochizuki
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hitoshi Inada
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Laboratory of Health and Sports Science, Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Yasuhisa Matsui
- The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, Japan.,Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tomohiro Kono
- The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, Japan.,Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, Japan
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14
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Crosstalk between cardiomyocytes and noncardiomyocytes is essential to prevent cardiomyocyte apoptosis induced by proteasome inhibition. Cell Death Dis 2020; 11:783. [PMID: 32951004 PMCID: PMC7502079 DOI: 10.1038/s41419-020-03005-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 02/08/2023]
Abstract
Heart is a multi-cellular organ made up of various cell types interacting with each other. Cardiomyocytes may benefit or suffer from crosstalk with noncardiomyocytes in response to diverse kinds of cardiac stresses. Proteasome dysfunction is a common cardiac stress which causes cardiac proteotoxicity and contributes to cardiac diseases such as heart failure and myocardial infarction. The role of crosstalk between cardiomyocytes and noncardiomyocytes in defense of cardiac proteotoxicity remains unknown. Here, we report a cardiomyocyte-specific survival upon proteasome inhibition in a heterogeneous culture consisting of cardiomyocytes and other three major cardiac cell types. Conversely, cardiomyocyte apoptosis is remarkably induced by proteasome inhibition in a homogeneous culture consisting of a majority of cardiomyocytes, demonstrating an indispensable role of noncardiomyocytes in the prevention of cardiomyocyte apoptosis resulting from proteasome inhibition. We further show that cardiomyocytes express brain natriuretic peptide (BNP) as an extracellular molecule in response to proteasome inhibition. Blockade of BNP receptor on noncardiomyocytes significantly exacerbated the cardiomyocyte apoptosis, indicating a paracrine function of cardiomyocyte-released extracellular BNP in activation of a protective feedback from noncardiomyocytes. Finally, we demonstrate that proteasome inhibition-activated transcriptional up-regulation of BNP in cardiomyocytes was associated with the dissociation of repressor element 1 silencing transcription factor (REST)/ histone deacetylase 1 (HDAC1) repressor complex from BNP gene promoter. Consistently, the induction of BNP could be further augmented by the treatment of HDAC inhibitors. We conclude that the crosstalk between cardiomyocytes and noncardiomyocytes plays a crucial role in the protection of cardiomyocytes from proteotoxicity stress, and identify cardiomyocyte-released BNP as a novel paracrine signaling molecule mediating this crosstalk. These findings provide new insights into the key regulators and cardioprotective mechanism in proteasome dysfunction-related cardiac diseases.
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15
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Mu J, Zhang D, Tian Y, Xie Z, Zou MH. BRD4 inhibition by JQ1 prevents high-fat diet-induced diabetic cardiomyopathy by activating PINK1/Parkin-mediated mitophagy in vivo. J Mol Cell Cardiol 2020; 149:1-14. [PMID: 32941882 DOI: 10.1016/j.yjmcc.2020.09.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022]
Abstract
BRD4 is a member of the BET family of epigenetic regulators. Inhibition of BRD4 by the selective bromodomain inhibitor JQ1, alleviates thoracic aortic constriction-induced cardiac hypertrophy and heart failure. However, whether BRD4 inhibition by JQ1 has therapeutic effect on diabetic cardiomyopathy, a major cause of heart failure in patients with Type 2 diabetes, remains unknown. Here, we discover a novel link between BRD4 and PINK1/Parkin-mediated mitophagy during diabetic cardiomyopathy. Upregulation of BRD4 in diabetic mouse hearts inhibits PINK1/Parkin-mediated mitophagy, resulting in accumulation of damaged mitochondria and subsequent impairment of cardiac structure and function. BRD4 inhibition by JQ1 improves mitochondrial function, and repairs the cardiac structure and function of the diabetic heart. These effects depended on rewiring of the BRD4-driven transcription and repression of PINK1. Deletion of Pink1 suppresses mitophagy, exacerbates cardiomyopathy, and abrogates the therapeutic effect of JQ1 on diabetic cardiomyopathy. Our results illustrate a valid therapeutic strategy for treating diabetic cardiomyopathy by inhibition of BRD4.
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Affiliation(s)
- Jing Mu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States of America; Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA 30303, United States of America
| | - Donghong Zhang
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA 30303, United States of America
| | - Yunli Tian
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA 30303, United States of America
| | - Zhonglin Xie
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA 30303, United States of America.
| | - Ming-Hui Zou
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States of America; Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA 30303, United States of America.
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16
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Zhang S, Zeng T, Hu B, Zhang YH, Feng K, Chen L, Niu Z, Li J, Huang T, Cai YD. Discriminating Origin Tissues of Tumor Cell Lines by Methylation Signatures and Dys-Methylated Rules. Front Bioeng Biotechnol 2020; 8:507. [PMID: 32528944 PMCID: PMC7264161 DOI: 10.3389/fbioe.2020.00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for multiple biological processes. DNA methylation in mammals acts as an epigenetic mark of transcriptional repression. Aberrant levels of DNA methylation can be observed in various types of tumor cells. Thus, DNA methylation has attracted considerable attention among researchers to provide new and feasible tumor therapies. Conventional studies considered single-gene methylation or specific loci as biomarkers for tumorigenesis. However, genome-scale methylated modification has not been completely investigated. Thus, we proposed and compared two novel computational approaches based on multiple machine learning algorithms for the qualitative and quantitative analyses of methylation-associated genes and their dys-methylated patterns. This study contributes to the identification of novel effective genes and the establishment of optimal quantitative rules for aberrant methylation distinguishing tumor cells with different origin tissues.
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Affiliation(s)
- Shiqi Zhang
- School of Life Sciences, Shanghai University, Shanghai, China.,Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Tao Zeng
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China
| | - Bin Hu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic, Guangzhou, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Zhibin Niu
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jianhao Li
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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17
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Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res 2020; 47:D145-D154. [PMID: 30380113 PMCID: PMC6323897 DOI: 10.1093/nar/gky1005] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/10/2018] [Indexed: 12/17/2022] Open
Abstract
Several recent studies have portrayed DNA methylation as a new player in the recruitment of transcription factors (TF) within chromatin, highlighting a need to connect TF binding sites (TFBS) with their respective DNA methylation profiles. However, current TFBS databases are restricted to DNA binding motif sequences. Here, we present MethMotif, a two-dimensional TFBS database that records TFBS position weight matrices along with cell type specific CpG methylation information computed from a combination of ChIP-seq and whole genome bisulfite sequencing datasets. Integrating TFBS motifs with TFBS DNA methylation better portrays the features of DNA loci recognised by TFs. In particular, we found that DNA methylation patterns within TFBS can be cell specific (e.g. MAFF). Furthermore, for a given TF, different DNA methylation profiles are associated with different DNA binding motifs (e.g. REST). To date, MethMotif database records over 500 TFBSs computed from over 2000 ChIP-seq datasets in 11 different cell types. MethMotif portal is accessible through an open source web interface (https://bioinfo-csi.nus.edu.sg/methmotif) that allows users to intuitively explore the entire dataset and perform both single, and batch queries.
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Affiliation(s)
- Quy Xiao Xuan Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Stephanie Sian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Thieffry
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure (IBENS), INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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18
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Jinesh GG, Brohl AS. The genetic script of metastasis. Biol Rev Camb Philos Soc 2020; 95:244-266. [PMID: 31663259 DOI: 10.1111/brv.12562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/24/2023]
Abstract
Metastasis is a pivotal event that changes the course of cancers from benign and treatable to malignant and difficult to treat, resulting in the demise of patients. Understanding the genetic control of metastasis is thus crucial to develop efficient and sustainable targeted therapies. Here we discuss the alterations in epigenetic mechanisms, transcription, chromosomal instability, chromosome imprinting, non-coding RNAs, coding RNAs, mutant RNAs, enhancers, G-quadruplexes, and copy number variation to dissect the genetic control of metastasis. We conclude that the genetic control of metastasis is predominantly executed through epithelial to mesenchymal transition and evasion of cell death. We discuss how genetic regulatory mechanisms can be harnessed for therapeutic purposes to achieve sustainable control over cancer metastasis.
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Affiliation(s)
- Goodwin G Jinesh
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A.,Sarcoma Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A
| | - Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A.,Chemical Biology and Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A
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19
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Association of N 6-methyladenine DNA with plaque progression in atherosclerosis via myocardial infarction-associated transcripts. Cell Death Dis 2019; 10:909. [PMID: 31797919 PMCID: PMC6892866 DOI: 10.1038/s41419-019-2152-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 01/14/2023]
Abstract
Modification of the novel N6-methyladenine (m6A) DNA implicates this epigenetic mark in human malignant disease, but its role in atherosclerosis (AS) is largely unknown. Here, we found that the leukocyte level of m6A but not 5mC DNA modification was decreased with increasing of carotid plaque size and thickness in 207 AS patients as compared with 142 sex- and age-matched controls. Serum low-density lipoprotein (LDL) and leukocyte m6A levels were associated with the progression of carotid plaque size and thickness. Both LDL level and plaque thickness were also independently and negatively related to m6A level. Reduced m6A level was further confirmed in leukocytes and endothelium in western diet-induced AS mice and in oxidized-LDL (ox-LDL)-treated human endothelium and monocyte cells. Decreased m6A level was closely related to the upregulation of AlkB homolog 1 (ALKBH1), the demethylase of m6A. Silencing of ALKBH1 or hypoxia-inducible factor 1α (HIF1α) could rescue the ox-LDL–increased level of MIAT, a hypoxia-response gene. Mechanically, ox-LDL induced HIF1α for transfer into the nucleus. Nuclear HIF1α bound to the ALKBH1-demethylated MIAT promoter and transcriptionally upregulated its expression. Therefore, elevated ALKBH1 level in endothelium and leukocytes reduced m6A level, which is a novel and sensitive biomarker for AS progression.
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20
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Abstract
Supplemental Digital Content is available in the text. If unifying principles could be revealed for how the same genome encodes different eukaryotic cells and for how genetic variability and environmental input are integrated to impact cardiovascular health, grand challenges in basic cell biology and translational medicine may succumb to experimental dissection. A rich body of work in model systems has implicated chromatin-modifying enzymes, DNA methylation, noncoding RNAs, and other transcriptome-shaping factors in adult health and in the development, progression, and mitigation of cardiovascular disease. Meanwhile, deployment of epigenomic tools, powered by next-generation sequencing technologies in cardiovascular models and human populations, has enabled description of epigenomic landscapes underpinning cellular function in the cardiovascular system. This essay aims to unpack the conceptual framework in which epigenomes are studied and to stimulate discussion on how principles of chromatin function may inform investigations of cardiovascular disease and the development of new therapies.
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Affiliation(s)
- Manuel Rosa-Garrido
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles
| | - Douglas J Chapski
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles
| | - Thomas M Vondriska
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles.
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21
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Liu Y, Lu P, Wang Y, Morrow BE, Zhou B, Zheng D. Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis. J Am Heart Assoc 2019; 8:e012941. [PMID: 31322043 PMCID: PMC6761639 DOI: 10.1161/jaha.119.012941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Background Heart tube looping to form a 4-chambered heart is a critical stage of embryonic heart development, but the gene drivers and their regulatory targets have not been extensively characterized at the cell-type level. Methods and Results To study the interaction of signaling pathways, transcription factors (TFs), and genetic networks in the process, we constructed gene co-expression networks and identified gene modules highly activated in individual cardiomyocytes at multiple anatomical regions and developmental stages using previously published single-cell RNA-seq data. Function analyses of the modules uncovered major pathways important for spatiotemporal cardiomyocyte differentiation. Interestingly, about half of the pathways were highly active in cardiomyocytes at the outflow tract (OFT) and atrioventricular canal, including well-known pathways for cardiac development and many newly identified ones. We predicted that these OFT-atrioventricular canal pathways were regulated by a large number of TFs actively expressed at the OFT-atrioventricular canal cardiomyocytes, with the prediction supported by motif enrichment analysis, including 10 TFs that have not been previously associated with cardiac development (eg, Etv5, Rbpms, and Baz2b). Furthermore, we found that TF targets in the OFT-atrioventricular canal modules were most significantly enriched with genes associated with mouse heart developmental abnormalities and human congenital heart defects, in comparison with TF targets in other modules, consistent with the critical developmental roles of OFT. Conclusions By analyzing gene co-expression at single cardiomyocytes, our systematic study has uncovered many known and additional new important TFs and their regulated molecular signaling pathways that are spatiotemporally active during heart looping.
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Affiliation(s)
- Yang Liu
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Pengfei Lu
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Yidong Wang
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Bernice E. Morrow
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of Ob/Gyn and PediatricsAlbert Einstein College of MedicineBronxNY
| | - Bin Zhou
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of Ob/Gyn and PediatricsAlbert Einstein College of MedicineBronxNY
- Department of MedicineAlbert Einstein College of MedicineBronxNY
| | - Deyou Zheng
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of NeurologyAlbert Einstein College of MedicineBronxNY
- Department of NeuroscienceAlbert Einstein College of MedicineBronxNY
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22
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Wu L, Wu D, Ning J, Liu W, Zhang D. Changes of N6-methyladenosine modulators promote breast cancer progression. BMC Cancer 2019; 19:326. [PMID: 30953473 PMCID: PMC6451293 DOI: 10.1186/s12885-019-5538-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 03/28/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Breast cancer (BC) displays striking genetic, epigenetic and phenotypic diversity. N6-methyladenosine (m6A) in mRNA has emerged as a crucial epitranscriptomic modification that controls cancer self-renewal and cell fate. However, the key enzymes of m6A expression and function in human breast carcinogenesis remain unclear. METHODS The expression of m6A methylases (METTL3, METTL14 and WTAP) and demethylases (FTO and ALKBH5) were analyzed by using ONCOMINE and The Cancer Genome Atlas databases and in 36 pairs of BC and adjacent non-cancerous tissue. The level of m6A in BC patients was detected by ELISA, and the function of m6A was analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, colony formation assay and transwell assay. The database of bc-GenExMiner v4.0, Kaplan-Meier Plotter and cBioPortal were queried for correlation, mutation and prognosis analysis of BC. RESULTS The m6A methylases and demethylases were dysregulated in several major malignant tumors. Specifically, the expression of all m6A methylases was reduced in BC as compared with normal controls, but the demethylase ALKBH5 was induced in ONCOMINE databases and confirmed in clinical patients. METTL14 expression was positively correlated with METTL3 expression, and both showed high expression in normal breast-like and luminal-A and -B BC. Functionally, reducing m6A expression by overexpressing METTL14 and/or knockdown of ALKBH5 could inhibit breast cell viability, colony formation and cell migration. Furthermore, Kaplan-Meier, meta-analysis and univariate Cox assay showed that the expression of m6A members including METTL3, METTL14, WTAP and FTO but not their gene mutation and amplification, was tightly associated with cancer progression and poor survival. CONCLUSIONS Changes of m6A modulators reduced m6A may promote tumorigenesis and predict poor prognosis in BC.
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Affiliation(s)
- Lianpin Wu
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, 325027, Zhejiang, China
| | - Dengying Wu
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, 325027, Zhejiang, China
| | - Jinfeng Ning
- The Thoracic Department of Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Donghong Zhang
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, 325027, Zhejiang, China. .,Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street SE, Atlanta, GA, 30303, USA.
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23
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Wu L, Zhang D, Zhou L, Pei Y, Zhuang Y, Cui W, Chen J. FUN14 domain-containing 1 promotes breast cancer proliferation and migration by activating calcium-NFATC1-BMI1 axis. EBioMedicine 2019; 41:384-394. [PMID: 30803933 PMCID: PMC6442990 DOI: 10.1016/j.ebiom.2019.02.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND FUN14 domain-containing 1 (FUNDC1), as a novel member of mitochondria-associated endoplasmic reticulum (ER) membranes associates with mitochondrial division and mitophagy. However, the expression profile and functional roles of FUNDC1 remain largely unclear in human cancer biology, including breast cancer (BC). METHODS Immunohistochemistry and western blot analysis were used to determine the expression of FUNDC1 and BMI1 polycomb ring finger oncogene (BMI1). CCK8, cell counting and transwell assays were used to analyze cell proliferation, migration and invasion, respectively. Luciferase reporter and chromatin immunoprecipitation (ChIP) assays were used to detect the transcriptional regulation of Nuclear factor of activated T-cells, cytoplasmic 1 (NFATC1). The prognostic merit of NFATC1 expression was assessed by Kaplan-Meier assay. FINDINGS Immunohistochemistry revealed strong immunostaining for FUNDC1 in cytoplasmic and nuclear membrane distribution in BC tissues as compared with normal breast epithelium. Kaplan-Meier survival analysis showed worse outcome for BC patients with high FUNDC1 expression. In vitro assay of gain- and loss-of-function of FUNDC1 suggested that FUNDC1 could stimulate BC cell proliferation, migration and invasion. Furthermore, elevated FUNDC1 level promoted Ca2+ cytosol influx from ER and extracellular, as well as NFATC1 nuclear translocation and activity. Nuclear NFATC1 bound to the BMI1 gene promoter and transcriptionally upregulated its expression. Notably, BMI1 overexpression could rescue the loss of function of FUNDC1. Co-expression of FUNDC1 and BMI1 in BC patients predicted worse prognosis than without either expression. INTERPRETATION FUNDC1 might promote BC progression by activating the Ca2+-NFATC1-BMI1 axis. This pathway may be promising for developing multiple targets for BC therapy.
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Affiliation(s)
- Lianpin Wu
- Department of Cardiology, The Second Affiliated Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou 325027, Zhejiang, PR China
| | - Donghong Zhang
- Center for Molecular and Translational Medicine, Georgia State University, Research Science Center, 157 Decatur St SE, Atlanta, GA 30303. USA
| | - Li Zhou
- Department of Gynecological Oncology, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, PR China
| | - Yuqing Pei
- Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, PR China
| | - Yixuan Zhuang
- Oncological Research Lab, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, PR China
| | - Wei Cui
- Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, PR China
| | - Jiongyu Chen
- Oncological Research Lab, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou 515031, PR China.
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Clare CE, Brassington AH, Kwong WY, Sinclair KD. One-Carbon Metabolism: Linking Nutritional Biochemistry to Epigenetic Programming of Long-Term Development. Annu Rev Anim Biosci 2019; 7:263-287. [DOI: 10.1146/annurev-animal-020518-115206] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One-carbon (1C) metabolism comprises a series of interlinking metabolic pathways that include the methionine and folate cycles that are central to cellular function, providing 1C units (methyl groups) for the synthesis of DNA, polyamines, amino acids, creatine, and phospholipids. S-adenosylmethionine is a potent aminopropyl and methyl donor within these cycles and serves as the principal substrate for methylation of DNA, associated proteins, and RNA. We propose that 1C metabolism functions as a key biochemical conduit between parental environment and epigenetic regulation of early development and that interindividual and ethnic variability in epigenetic-gene regulation arises because of genetic variants within 1C genes, associated epigenetic regulators, and differentially methylated target DNA sequences. We present evidence to support these propositions, drawing upon studies undertaken in humans and animals. We conclude that future studies should assess the epigenetic effects of cumulative (multigenerational) dietary imbalances contemporaneously in both parents, as this better represents the human experience.
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Affiliation(s)
- Constance E. Clare
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Amey H. Brassington
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Wing Yee Kwong
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Kevin D. Sinclair
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
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25
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Abstract
Textbook and scientific papers addressing DNA methylation usually still cite “DNA methylation occurs at CpG cytosines”. Methylation at cytosines outside the CpG nucleotide, the so-called “non-CpG methylation”, is usually considered a minor and not biologically relevant process. However, the technical improvements and additional studies in epigenetics have demonstrated that non-CpG methylation is present with frequency higher than previously thought and retains biological activity, potentially relevant to the understanding and the treatment of human diseases.
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26
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Chromosome 19 miRNA cluster and CEBPB expression specifically mark and potentially drive triple negative breast cancers. PLoS One 2018; 13:e0206008. [PMID: 30335837 PMCID: PMC6193703 DOI: 10.1371/journal.pone.0206008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022] Open
Abstract
Triple negative breast cancers (TNBCs) are known to express low PGR, ESR1, and ERBB2, and high KRT5, KRT14, and KRT17. However, the reasons behind the increased expressions of KRT5, KRT14, KRT17 and decreased expressions of PGR, ESR1, and ERBB2 in TNBCs are not fully understood. Here we show that, expression of chromosome 19 miRNA cluster (C19MC) specifically marks human TNBCs. Low REST and high CEBPB correlate with expression of C19MC, KRT5, KRT14, and KRT17 and enhancers of these genes/cluster are regulated by CEBPB and REST binding sites. The C19MC miRNAs in turn can potentially target REST to offer a positive feedback loop, and might target PGR, ESR1, ERBB2, GATA3, SCUBE2, TFF3 mRNAs to contribute towards TNBC phenotype. Thus our study demonstrates that C19MC miRNA expression marks TNBCs and that C19MC miRNAs and CEBPB might together determine the TNBC marker expression pattern.
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27
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Larsen K, Kristensen KK, Callesen H. DNA methyltransferases and tRNA methyltransferase DNMT2 in developing pig brain - expression and promoter methylation. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Cui D, Xu X. DNA Methyltransferases, DNA Methylation, and Age-Associated Cognitive Function. Int J Mol Sci 2018; 19:E1315. [PMID: 29710796 PMCID: PMC5983821 DOI: 10.3390/ijms19051315] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/20/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
Ageing, a leading cause of the decline/deficits in human learning, memory, and cognitive abilities, is a major risk factor for age-associated neurodegenerative disorders such as Alzheimer’s disease. Emerging evidence suggests that epigenetics, an inheritable but reversible biochemical process, plays a crucial role in the pathogenesis of age-related neurological disorders. DNA methylation, the best-known epigenetic mark, has attracted most attention in this regard. DNA methyltransferases (DNMTs) are key enzymes in mediating the DNA methylation process, by which a methyl group is transferred, faithfully or anew, to genomic DNA sequences. Biologically, DNMTs are important for gene imprinting. Accumulating evidence suggests that DNMTs not only play critical roles, including gene imprinting and transcription regulation, in early development stages of the central nervous system (CNS), but also are indispensable in adult learning, memory, and cognition. Therefore, the impact of DNMTs and DNA methylation on age-associated cognitive functions and neurodegenerative diseases has emerged as a pivotal topic in the field. In this review, the effects of each DNMT on CNS development and healthy and pathological ageing are discussed.
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Affiliation(s)
- Di Cui
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
| | - Xiangru Xu
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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29
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Zhu Q, Stöger R, Alberio R. A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline. Front Cell Dev Biol 2018; 6:24. [PMID: 29637072 PMCID: PMC5880922 DOI: 10.3389/fcell.2018.00024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine (5mC) on CpG dinucleotides has been viewed as the major epigenetic modification in eukaryotes for a long time. Apart from 5mC, additional DNA modifications have been discovered in eukaryotic genomes. Many of these modifications are thought to be solely associated with DNA damage. However, growing evidence indicates that some base modifications, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC), and N6-methadenine (6mA), may be of biological relevance, particularly during early stages of embryo development. Although abundance of these DNA modifications in eukaryotic genomes can be low, there are suggestions that they cooperate with other epigenetic markers to affect DNA-protein interactions, gene expression, defense of genome stability and epigenetic inheritance. Little is still known about their distribution in different tissues and their functions during key stages of the animal lifecycle. This review discusses current knowledge and future perspectives of these novel DNA modifications in the mammalian genome with a focus on their dynamic distribution during early embryonic development and their potential function in epigenetic inheritance through the germ line.
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Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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30
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Zhang D, Wang Y, Lu P, Wang P, Yuan X, Yan J, Cai C, Chang CP, Zheng D, Wu B, Zhou B. REST regulates the cell cycle for cardiac development and regeneration. Nat Commun 2017; 8:1979. [PMID: 29215012 PMCID: PMC5719406 DOI: 10.1038/s41467-017-02210-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
Despite the importance of cardiomyocyte proliferation in cardiac development and regeneration, the mechanisms that promote cardiomyocyte cell cycle remain incompletely understood. RE1 silencing transcription factor (REST) is a transcriptional repressor of neuronal genes. Here we show that REST also regulates the cardiomyocyte cell cycle. REST binds and represses the cell cycle inhibitor gene p21 and is required for mouse cardiac development and regeneration. Rest deletion de-represses p21 and inhibits the cardiomyocyte cell cycle and proliferation in embryonic or regenerating hearts. By contrast, REST overexpression in cultured cardiomyocytes represses p21 and increases proliferation. We further show that p21 knockout rescues cardiomyocyte cell cycle and proliferation defects resulting from Rest deletion. Our study reveals a REST-p21 regulatory axis as a mechanism for cell cycle progression in cardiomyocytes, which might be exploited therapeutically to enhance cardiac regeneration.
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Affiliation(s)
- Donghong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Yidong Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Pengfei Lu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Xinchun Yuan
- Department of Medical Ultrasound, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Jianyun Yan
- Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute, and The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chenleng Cai
- Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute, and The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ching-Pin Chang
- Department of Medicine, Indian University School of Medicine, Indianapolis, IN, 46202, USA
| | - Deyou Zheng
- Departments of Genetics, Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bingruo Wu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bin Zhou
- Departments of Genetics, Pediatrics, and Medicine (Cardiology), The Wilf Cardiovascular Research Institute, The Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Cardiology of First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 210029, China.
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