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Wei X, Li J, Cheng Z, Wei S, Yu G, Olsen ML. Decoding the Epigenetic Landscape: Insights into 5mC and 5hmC Patterns in Mouse Cortical Cell Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602342. [PMID: 39026756 PMCID: PMC11257419 DOI: 10.1101/2024.07.06.602342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The DNA modifications, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), represent powerful epigenetic regulators of temporal and spatial gene expression. Yet, how the cooperation of these genome-wide, epigenetic marks determine unique transcriptional signatures across different brain cell populations is unclear. Here we applied Nanopore sequencing of native DNA to obtain a complete, genome-wide, single-base resolution atlas of 5mC and 5hmC modifications in neurons, astrocytes and microglia in the mouse cortex (99% genome coverage, 40 million CpG sites). In tandem with RNA sequencing, analysis of 5mC and 5hmC patterns across cell types reveals astrocytes drive uniquely high brain 5hmC levels and support two decades of research regarding methylation patterns, gene expression and alternative splicing, benchmarking this resource. As such, we provide the most comprehensive DNA methylation data in mouse brain as an interactive, online tool (NAM-Me, https://olsenlab.shinyapps.io/NAMME/) to serve as a resource dataset for those interested in the methylome landscape.
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Affiliation(s)
- Xiaoran Wei
- Biomedical and Veterinary Sciences Graduate Program, Virginia Tech, Blacksburg, VA, the United States
- School of Neuroscience, Virginia Tech, Blacksburg, VA, the United States
| | - Jiangtao Li
- School of Neuroscience, Virginia Tech, Blacksburg, VA, the United States
- Genetics, Bioinformatics and Computational Biology Graduate Program, Virginia Tech, Blacksburg, VA, the United States
| | - Zuolin Cheng
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, the United States
| | - Songtao Wei
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, the United States
| | - Guoqiang Yu
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, the United States
| | - Michelle L Olsen
- School of Neuroscience, Virginia Tech, Blacksburg, VA, the United States
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Chalkley MBL, Guerin LN, Iyer T, Mallahan S, Nelson S, Sahin M, Hodges E, Ess KC, Ihrie RA. Human TSC2 Mutant Cells Exhibit Aberrations in Early Neurodevelopment Accompanied by Changes in the DNA Methylome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597443. [PMID: 38895266 PMCID: PMC11185654 DOI: 10.1101/2024.06.04.597443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tuberous Sclerosis Complex (TSC) is a debilitating developmental disorder characterized by a variety of clinical manifestations. While benign tumors in the heart, lungs, kidney, and brain are all hallmarks of the disease, the most severe symptoms of TSC are often neurological, including seizures, autism, psychiatric disorders, and intellectual disabilities. TSC is caused by loss of function mutations in the TSC1 or TSC2 genes and consequent dysregulation of signaling via mechanistic Target of Rapamycin Complex 1 (mTORC1). While TSC neurological phenotypes are well-documented, it is not yet known how early in neural development TSC1/2-mutant cells diverge from the typical developmental trajectory. Another outstanding question is the contribution of homozygous-mutant cells to disease phenotypes and whether such phenotypes are also seen in the heterozygous-mutant populations that comprise the vast majority of cells in patients. Using TSC patient-derived isogenic induced pluripotent stem cells (iPSCs) with defined genetic changes, we observed aberrant early neurodevelopment in vitro, including misexpression of key proteins associated with lineage commitment and premature electrical activity. These alterations in differentiation were coincident with hundreds of differentially methylated DNA regions, including loci associated with key genes in neurodevelopment. Collectively, these data suggest that mutation or loss of TSC2 affects gene regulation and expression at earlier timepoints than previously appreciated, with implications for whether and how prenatal treatment should be pursued.
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Affiliation(s)
- Mary-Bronwen L. Chalkley
- Department of Cell & Developmental Biology, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lindsey N. Guerin
- Department of Biochemistry, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Tenhir Iyer
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Samantha Mallahan
- Department of Cell & Developmental Biology, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Sydney Nelson
- Department of Cell & Developmental Biology, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mustafa Sahin
- Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Emily Hodges
- Department of Biochemistry, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin C. Ess
- Department of Cell & Developmental Biology, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Denver, Colorado, United States of America
| | - Rebecca A. Ihrie
- Department of Cell & Developmental Biology, School of Medicine Basic Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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Skardžiūtė K, Kvederavičiūtė K, Pečiulienė I, Narmontė M, Gibas P, Ličytė J, Klimašauskas S, Kriukienė E. One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci. Cell Chem Biol 2024; 31:607-621.e9. [PMID: 38154461 PMCID: PMC10962225 DOI: 10.1016/j.chembiol.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and DNA hydroxymethylation-from a single library. The approach is based on chemo-enzymatic covalent tagging of unmodified CG sites and hydroxymethylated cytosine (5hmC) along with GC sites in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation of the approach revealed its sensitivity and informativity in evaluating chromatin accessibility and DNA modification interactions that drive transcriptional regulation. We employed the technology in a study of chromatin and DNA demethylation dynamics during in vitro neuronal differentiation. The study highlighted the involvement of gene body 5hmC in modulating an extensive decoupling between promoter accessibility and transcription. The importance of 5hmC in chromatin remodeling was further demonstrated by the observed resistance of the developmentally acquired open loci to the global 5hmC erasure in neuronal progenitors.
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Affiliation(s)
- Kotryna Skardžiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Inga Pečiulienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania.
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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Xue X, Wang Z, Wang Y, Zhou X. Disease Diagnosis Based on Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2114-2127. [PMID: 37527510 DOI: 10.1021/acschembio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid modifications include a wide range of epigenetic and epitranscriptomic factors and impact a wide range of nucleic acids due to their profound influence on biological inheritance, growth, and metabolism. The recently developed methods of mapping and characterizing these modifications have promoted their discovery as well as large-scale studies in eukaryotes, especially in humans. Because of these pioneering strategies, nucleic acid modifications have been shown to have a great impact on human disorders such as cancer. Therefore, whether nucleic acid modifications could become a new type of biomarker remains an open question. In this review, we briefly look back at classical nucleic acid modifications and then focus on the progress made in investigating these modifications as diagnostic biomarkers in clinical therapy and present our perspective on their development prospects.
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Affiliation(s)
- Xiaochen Xue
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiying Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Department of Chemistry, College of Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Cross Research Institute of Zhongnan Hospital, Wuhan University, Wuhan 430071, China
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Kouter K, Šalamon Arčan I, Videtič Paska A. Epigenetics in psychiatry: Beyond DNA methylation. World J Psychiatry 2023; 13:319-330. [PMID: 37383287 PMCID: PMC10294132 DOI: 10.5498/wjp.v13.i6.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/31/2023] [Accepted: 04/25/2023] [Indexed: 06/19/2023] Open
Abstract
The global burden of psychopathologies appears to be underestimated, since the global psychiatric disorder burden is exceeding other medical burdens. To be able to address this problem more effectively, we need to better understand the etiology of psychiatric disorders. One of the hallmarks of psychiatric disorders appears to be epigenetic dysregulation. While some epigenetic modifications (such as DNA methylation) are well known and studied, the roles of others have been investigated much less. DNA hydroxymethylation is a rarely studied epigenetic modification, which as well as being an intermediate stage in the DNA demethylation cycle is also an independent steady cell state involved in neurodevelopment and plasticity. In contrast to DNA methylation, DNA hydroxymethylation appears to be related to an increase in gene expression and subsequent protein expression. Although no particular gene or genetic locus can be at this point linked to changes in DNA hydroxymethylation in psychiatric disorders, the epigenetic marks present good potential for biomarker identification because the epigenetic landscape is a result of the interplay between genes and environment, which both influence the development of psychiatric disorders, and because hydoxymethylation changes are particularly enriched in the brain and in synapse-related genes.
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Affiliation(s)
- Katarina Kouter
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Iris Šalamon Arčan
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Alja Videtič Paska
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana 1000, Slovenia
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Li C, Pang M, Li Y, Han L, Fan Y, Xin X, Zhang X, Zhang N, Qin Y. Protective effect of vitamin C against tetrachlorobenzoquinone-induced 5-hydroxymethylation-dependent apoptosis in HepG2 cells mainly via the mitochondrial apoptosis pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 260:115097. [PMID: 37271103 DOI: 10.1016/j.ecoenv.2023.115097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Tetrachlorobenzoquinone (TCBQ) is an active metabolite of pentachlorophenol, and stimulates the accumulation of ROS to trigger apoptosis. The preventive effect of vitamin C (Vc) against TCBQ-induced apoptosis in HepG2 cells is unknown. And there is little known about TCBQ-triggered 5-hydromethylcytosine (5hmC)-dependent apoptosis. Here, we confirmed that Vc alleviated TCBQ-induced apoptosis. Through investigating the underlying mechanism, we found TCBQ downregulated 5hmC levels of genomic DNA in a Tet-dependent manner, with a particularly pronounced decrease in the promoter region, using UHPLC-MS-MS analysis and hydroxymethylated DNA immunoprecipitation sequencing. Notably, TCBQ exposure resulted in alterations of 5hmC abundance to ∼91% of key genes at promoters in the mitochondrial apoptosis pathway, along with changes of mRNA expression in 87% of genes. By contrast, 5hmC abundance of genes only exhibited slight changes in the death receptor/ligand pathway. Interestingly, the pretreatment with Vc, a positive stimulator of 5hmC generation, restored 5hmC in the genomic DNA to near-normal levels. More notably, Vc pretreatment further counter-regulated TCBQ-induced alteration of 5hmC abundance in the promoter with 100% of genes, accompanying the reverse modulation of mRNA expressions in 89% of genes. These data from Vc pretreatment supported the relationship between TCBQ-induced apoptosis and the altered 5hmC abundance. Additionally, Vc also suppressed TCBQ-stimulated generation of ROS, and further increased the stability of mitochondria. Our study illuminates a new mechanism of TCBQ-induced 5hmC-dependent apoptosis, and the dual mechanisms of Vc against TCBQ-stimulated apoptosis via reversely regulating 5hmC levels and scavenging ROS. The work also provided a possible strategy for the detoxification of TCBQ.
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Affiliation(s)
- Cuiping Li
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China.
| | - Mengfan Pang
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Yaping Li
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China.
| | - Lirong Han
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Yajiao Fan
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xuelian Xin
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xian Zhang
- School of Public Health, Hebei University, Baoding 071002, PR China; Key Laboratory of Public Health Safety of Hebei Province, PR China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Ning Zhang
- College of Chemistry and Chemical Engineering, Dezhou University, Shandong 253023, PR China
| | - Yan Qin
- Central Laboratory, Affiliated Hospital of Hebei University, Baoding 071002, PR China
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Kumar A, Kos MZ, Roybal D, Carless MA. A pilot investigation of differential hydroxymethylation levels in patient-derived neural stem cells implicates altered cortical development in bipolar disorder. Front Psychiatry 2023; 14:1077415. [PMID: 37139321 PMCID: PMC10150707 DOI: 10.3389/fpsyt.2023.1077415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Bipolar disorder (BD) is a chronic mental illness characterized by recurrent episodes of mania and depression and associated with social and cognitive disturbances. Environmental factors, such as maternal smoking and childhood trauma, are believed to modulate risk genotypes and contribute to the pathogenesis of BD, suggesting a key role in epigenetic regulation during neurodevelopment. 5-hydroxymethylcytosine (5hmC) is an epigenetic variant of particular interest, as it is highly expressed in the brain and is implicated in neurodevelopment, and psychiatric and neurological disorders. Methods Induced pluripotent stem cells (iPSCs) were generated from the white blood cells of two adolescent patients with bipolar disorder and their same-sex age-matched unaffected siblings (n = 4). Further, iPSCs were differentiated into neuronal stem cells (NSCs) and characterized for purity using immuno-fluorescence. We used reduced representation hydroxymethylation profiling (RRHP) to perform genome-wide 5hmC profiling of iPSCs and NSCs, to model 5hmC changes during neuronal differentiation and assess their impact on BD risk. Functional annotation and enrichment testing of genes harboring differentiated 5hmC loci were performed with the online tool DAVID. Results Approximately 2 million sites were mapped and quantified, with the majority (68.8%) located in genic regions, with elevated 5hmC levels per site observed for 3' UTRs, exons, and 2-kb shorelines of CpG islands. Paired t-tests of normalized 5hmC counts between iPSC and NSC cell lines revealed global hypo-hydroxymethylation in NSCs and enrichment of differentially hydroxymethylated sites within genes associated with plasma membrane (FDR = 9.1 × 10-12) and axon guidance (FDR = 2.1 × 10-6), among other neuronal processes. The most significant difference was observed for a transcription factor binding site for the KCNK9 gene (p = 8.8 × 10-6), encoding a potassium channel protein involved in neuronal activity and migration. Protein-protein-interaction (PPI) networking showed significant connectivity (p = 3.2 × 10-10) between proteins encoded by genes harboring highly differentiated 5hmC sites, with genes involved in axon guidance and ion transmembrane transport forming distinct sub-clusters. Comparison of NSCs of BD cases and unaffected siblings revealed additional patterns of differentiation in hydroxymethylation levels, including sites in genes with functions related to synapse formation and regulation, such as CUX2 (p = 2.4 × 10-5) and DOK-7 (p = 3.6 × 10-3), as well as an enrichment of genes involved in the extracellular matrix (FDR = 1.0 × 10-8). Discussion Together, these preliminary results lend evidence toward a potential role for 5hmC in both early neuronal differentiation and BD risk, with validation and more comprehensive characterization to be achieved through follow-up study.
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Affiliation(s)
- Ashish Kumar
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Mark Z. Kos
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, San Antonio, TX, United States
| | - Donna Roybal
- Traditions Behavioral Health, Larkspur, CA, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Melanie A. Carless
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- Brain Health Consortium, The University of Texas at San Antonio, San Antonio, TX, United States
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Cheng Y, Song H, Ming GL, Weng YL. Epigenetic and epitranscriptomic regulation of axon regeneration. Mol Psychiatry 2023; 28:1440-1450. [PMID: 36922674 PMCID: PMC10650481 DOI: 10.1038/s41380-023-02028-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Effective axonal regeneration in the adult mammalian nervous system requires coordination of elevated intrinsic growth capacity and decreased responses to the inhibitory environment. Intrinsic regenerative capacity largely depends on the gene regulatory network and protein translation machinery. A failure to activate these pathways upon injury is underlying a lack of robust axon regeneration in the mature mammalian central nervous system. Epigenetics and epitranscriptomics are key regulatory mechanisms that shape gene expression and protein translation. Here, we provide an overview of different types of modifications on DNA, histones, and RNA, underpinning the regenerative competence of axons in the mature mammalian peripheral and central nervous systems. We highlight other non-neuronal cells and their epigenetic changes in determining the microenvironment for tissue repair and axon regeneration. We also address advancements of single-cell technology in charting transcriptomic and epigenetic landscapes that may further facilitate the mechanistic understanding of differential regenerative capacity in neuronal subtypes. Finally, as epigenetic and epitranscriptomic processes are commonly affected by brain injuries and psychiatric disorders, understanding their alterations upon brain injury would provide unprecedented mechanistic insights into etiology of injury-associated-psychiatric disorders and facilitate the development of therapeutic interventions to restore brain function.
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Affiliation(s)
- Yating Cheng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, 77030, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, 77030, USA.
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, 77030, USA.
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Baral I, Shirude MB, Jothi DL, Mukherjee A, Dutta D. Characterization of a Distinct State in the Continuum of Pluripotency Facilitated by Inhibition of PKCζ in Mouse Embryonic Stem Cells. Stem Cell Rev Rep 2023; 19:1098-1115. [PMID: 36781773 DOI: 10.1007/s12015-023-10513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Inhibition of PKC (PKCi) signaling maintains pluripotency of embryonic stem cells (ESCs) across different mammalian species. However, the position of PKCi maintained ESCs in the pluripotency continuum is largely unknown. Here we demonstrate that mouse ESCs when cultured continuously, with PKCi, for 75 days are retained in naïve state of pluripotency. Gene expression analysis and proteomics studies demonstrated enhanced naïve character of PKCi maintained ESCs in comparison to classical serum/LIF (S/L) supported ESCs. Molecular analysis revealed that activation of PKCζ isoform associate with primed state of pluripotency, present in epiblast-like stem cells generated in vitro while inhibition of PKCζ phosphorylation associated with naïve state of pluripotency in vitro and in vivo. Phosphoproteomics and chromatin modification enzyme array based studies showed loss in DNA methyl transferase 3B (DNMT3B) and its phosphorylation level upon functional inhibition of PKCζ as one of the crucial components of this regulatory pathway. Unlike ground state of pluripotency maintained by MEK/GSK3 inhibitor in addition to LIF (2i/LIF), loss in DNMT3B is a reversible phenomenon in PKCi maintained ESCs. Absence of phosphorylation of c-MYC, RAF1, SPRY4 while presence of ERF, DUSP6, CIC and YAP1 phosphorylation underlined the phosphoproteomics signature of PKCi mediated maintenance of naïve pluripotency. States of pluripotency represent the developmental continuum and the existence of PKCi mediated mouse ESCs in a distinct state in the continuum of pluripotency (DiSCo) might contribute to the establishment of stages of murine embryonic development that were non-permissible till date.
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Affiliation(s)
- Ishita Baral
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Mayur Balkrishna Shirude
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Dhana Lakshmi Jothi
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Ananda Mukherjee
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.
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Qi J, Shi Y, Tan Y, Zhang Q, Zhang J, Wang J, Huang C, Ci W. Regional gain and global loss of 5-hydroxymethylcytosine coexist in genitourinary cancers and regulate different oncogenic pathways. Clin Epigenetics 2022; 14:117. [PMID: 36127710 PMCID: PMC9491006 DOI: 10.1186/s13148-022-01333-4] [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: 05/20/2022] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA 5-hydroxymethylcytosine (5hmC) is produced by dynamic 5mC oxidation process contributing to tissue specification, and loss of 5hmC has been reported in multiple cancers including genitourinary cancers. However, 5hmC is also cell-type specific, and its variability may exist between differentiated tumor cells and cancer stem cells. Thus, cancer-associated changes in 5hmC may be contributed by distinct sets of tumor cells within the tumor tissues. RESULTS Here, we applied a sensitive immunoprecipitation-based method (hMeDIP-seq) to analyze 5hmC changes during genitourinary carcinogenesis (including prostate, urothelial and kidney). We confirmed the tissue-specific distribution of 5hmC in genitourinary tissues and identified regional gain and global loss of 5hmC coexisting in genitourinary cancers. The genes with gain of 5hmC during tumorigenesis were functionally enriched in regulating stemness and hypoxia, whereas were associated with poor clinical prognosis irrespective of their differences in tumor type. We identified that gain of 5hmC occurred in soft fibrin gel-induced 3D tumor spheres with a tumor-repopulating phenotype in two prostate cancer cell lines, 22RV1 and PC3, compared with conventional two-dimensional (2D) rigid dishes. Then, we defined a malignant signature derived from the differentially hydroxymethylated regions affected genes of cancer stem-like cells, which could predict a worse clinical outcome and identified phenotypically malignant populations of cells from prostate cancer tumors. Notably, an oxidation-resistant vitamin C derivative, ascorbyl phosphate magnesium, restored 5hmC and killed the cancer stem cell-like cells leading to apoptosis in prostate cancer cell lines. CONCLUSIONS Collectively, our study dissects the regional gain of 5hmC in maintaining cancer stem-like cells and related to poor prognosis, which provides proof of concept for an epigenetic differentiation therapy with vitamin C by 5hmC reprogramming.
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Affiliation(s)
- Jie Qi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianye Zhang
- Institute of Urology, Peking University, Beijing, 100034, China.,Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, 100034, China
| | - Jilu Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Cong Huang
- Institute of Urology, Peking University, Beijing, 100034, China.,Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, 100034, China
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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12
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Li J, Wu X, Ke J, Lee M, Lan Q, Li J, Yu J, Huang Y, Sun DQ, Xie R. TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation. Nat Commun 2022; 13:3907. [PMID: 35798741 PMCID: PMC9263144 DOI: 10.1038/s41467-022-31611-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/17/2022] [Indexed: 12/02/2022] Open
Abstract
Existing knowledge of the role of epigenetic modifiers in pancreas development has exponentially increased. However, the function of TET dioxygenases in pancreatic endocrine specification remains obscure. We set out to tackle this issue using a human embryonic stem cell (hESC) differentiation system, in which TET1/TET2/TET3 triple knockout cells display severe defects in pancreatic β-cell specification. The integrative whole-genome analysis identifies unique cell-type-specific hypermethylated regions (hyper-DMRs) displaying reduced chromatin activity and remarkable enrichment of FOXA2, a pioneer transcription factor essential for pancreatic endoderm specification. Intriguingly, TET depletion leads to significant changes in FOXA2 binding at the pancreatic progenitor stage, in which gene loci with decreased FOXA2 binding feature low levels of active chromatin modifications and enriches for bHLH motifs. Transduction of full-length TET1 but not the TET1-catalytic-domain in TET-deficient cells effectively rescues β-cell differentiation accompanied by restoring PAX4 hypomethylation. Taking these findings together with the defective generation of functional β-cells upon TET1-inactivation, our study unveils an essential role of TET1-dependent demethylation in establishing β-cell identity. Moreover, we discover a physical interaction between TET1 and FOXA2 in endodermal lineage intermediates, which provides a mechanistic clue regarding the complex crosstalk between TET dioxygenases and pioneer transcription factors in epigenetic regulation during pancreas specification. Here the authors show that TET1 is required for the generation of functional insulin-producing cells, FOXA2 physically interacts with TET1 and contributes to specific recruitment of TET1 to mediate chromatin opening at the regulatory elements of pancreatic lineage determinants.
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Affiliation(s)
- Jianfang Li
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.,Innovation Center for Advanced Interdisciplinary Medicine, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510530, China.,Guangzhou Laboratory, Guangzhou, 510005, China
| | - Xinwei Wu
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.,Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jie Ke
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Minjung Lee
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Qingping Lan
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - De-Qiang Sun
- Innovation Center for Advanced Interdisciplinary Medicine, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510530, China. .,Cardiology Department, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
| | - Ruiyu Xie
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China. .,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, 999078, China.
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13
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Besaratinia A, Caceres A, Tommasi S. DNA Hydroxymethylation in Smoking-Associated Cancers. Int J Mol Sci 2022; 23:2657. [PMID: 35269796 PMCID: PMC8910185 DOI: 10.3390/ijms23052657] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/01/2023] Open
Abstract
5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (A.C.); (S.T.)
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14
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Mlodawska OW, Saini P, Parker JB, Wei JJ, Bulun SE, Simon MA, Chakravarti D. Epigenomic and enhancer dysregulation in uterine leiomyomas. Hum Reprod Update 2022; 28:518-547. [PMID: 35199155 PMCID: PMC9247409 DOI: 10.1093/humupd/dmac008] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/16/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Uterine leiomyomas, also known as uterine fibroids or myomas, are the most common benign gynecological tumors and are found in women of reproductive and postmenopausal age. There is an exceptionally high prevalence of this tumor in women by the age of 50 years. Black women are particularly affected, with an increased incidence, earlier age of onset, larger and faster growing fibroids and greater severity of symptoms as compared to White women. Although advances in identifying genetic and environmental factors to delineate these fibroids have already been made, only recently has the role of epigenomics in the pathogenesis of this disease been considered. OBJECTIVE AND RATIONALE Over recent years, studies have identified multiple epigenomic aberrations that may contribute to leiomyoma development and growth. This review will focus on the most recent discoveries in three categories of epigenomic changes found in uterine fibroids, namely aberrant DNA methylation, histone tail modifications and histone variant exchange, and their translation into altered target gene architecture and transcriptional outcome. The findings demonstrating how the altered 3D shape of the enhancer can regulate gene expression from millions of base pairs away will be discussed. Additionally, translational implications of these discoveries and potential roadblocks in leiomyoma treatment will be addressed. SEARCH METHODS A comprehensive PubMed search was performed to identify published articles containing keywords relevant to the focus of the review, such as: uterine leiomyoma, uterine fibroids, epigenetic alterations, epigenomics, stem cells, chromatin modifications, extracellular matrix [ECM] organization, DNA methylation, enhancer, histone post-translational modifications and dysregulated gene expression. Articles until September 2021 were explored and evaluated to identify relevant updates in the field. Most of the articles focused on in the discussion were published between 2015 and 2021, although some key discoveries made before 2015 were included for background information and foundational purposes. We apologize to the authors whose work was not included because of space restrictions or inadvertent omission. OUTCOMES Chemical alterations to the DNA structure and of nucleosomal histones, without changing the underlying DNA sequence, have now been implicated in the phenotypic manifestation of uterine leiomyomas. Genome-wide DNA methylation analysis has revealed subsets of either suppressed or overexpressed genes accompanied by aberrant promoter methylation. Furthermore, differential promoter access resulting from altered 3D chromatin structure and histone modifications plays a role in regulating transcription of key genes thought to be involved in leiomyoma etiology. The dysregulated genes function in tumor suppression, apoptosis, angiogenesis, ECM formation, a variety of cancer-related signaling pathways and stem cell differentiation. Aberrant DNA methylation or histone modification is also observed in altering enhancer architecture, which leads to changes in enhancer-promoter contact strength, producing novel explanations for the overexpression of high mobility group AT-hook 2 and gene dysregulation found in mediator complex subunit 12 mutant fibroids. While many molecular mechanisms and epigenomic features have been investigated, the basis for the racial disparity observed among those in the Black population remains unclear. WIDER IMPLICATIONS A comprehensive understanding of the exact pathogenesis of uterine leiomyoma is lacking and requires attention as it can provide clues for prevention and viable non-surgical treatment. These findings will widen our knowledge of the role epigenomics plays in the mechanisms related to uterine leiomyoma development and highlight novel approaches for the prevention and identification of epigenome targets for long-term non-invasive treatment options of this significantly common disease.
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Affiliation(s)
| | | | - J Brandon Parker
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jian-Jun Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Melissa A Simon
- Department of Obstetrics and Gynecology, Center for Health Equity Transformation, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Debabrata Chakravarti
- Correspondence address. Department of Obstetrics and Gynecology, Northwestern University, Feinberg School of Medicine, 303 E Superior Street, Lurie 4-119, Chicago, IL 60611, USA. E-mail:
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15
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Coker SJ, Smith-Díaz CC, Dyson RM, Vissers MCM, Berry MJ. The Epigenetic Role of Vitamin C in Neurodevelopment. Int J Mol Sci 2022; 23:ijms23031208. [PMID: 35163133 PMCID: PMC8836017 DOI: 10.3390/ijms23031208] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/07/2023] Open
Abstract
The maternal diet during pregnancy is a key determinant of offspring health. Early studies have linked poor maternal nutrition during gestation with a propensity for the development of chronic conditions in offspring. These conditions include cardiovascular disease, type 2 diabetes and even compromised mental health. While multiple factors may contribute to these outcomes, disturbed epigenetic programming during early development is one potential biological mechanism. The epigenome is programmed primarily in utero, and during this time, the developing fetus is highly susceptible to environmental factors such as nutritional insults. During neurodevelopment, epigenetic programming coordinates the formation of primitive central nervous system structures, neurogenesis, and neuroplasticity. Dysregulated epigenetic programming has been implicated in the aetiology of several neurodevelopmental disorders such as Tatton-Brown-Rahman syndrome. Accordingly, there is great interest in determining how maternal nutrient availability in pregnancy might affect the epigenetic status of offspring, and how such influences may present phenotypically. In recent years, a number of epigenetic enzymes that are active during embryonic development have been found to require vitamin C as a cofactor. These enzymes include the ten-eleven translocation methylcytosine dioxygenases (TETs) and the Jumonji C domain-containing histone lysine demethylases that catalyse the oxidative removal of methyl groups on cytosines and histone lysine residues, respectively. These enzymes are integral to epigenetic regulation and have fundamental roles in cellular differentiation, the maintenance of pluripotency and development. The dependence of these enzymes on vitamin C for optimal catalytic activity illustrates a potentially critical contribution of the nutrient during mammalian development. These insights also highlight a potential risk associated with vitamin C insufficiency during pregnancy. The link between vitamin C insufficiency and development is particularly apparent in the context of neurodevelopment and high vitamin C concentrations in the brain are indicative of important functional requirements in this organ. Accordingly, this review considers the evidence for the potential impact of maternal vitamin C status on neurodevelopmental epigenetics.
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Affiliation(s)
- Sharna J. Coker
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Carlos C. Smith-Díaz
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
| | - Rebecca M. Dyson
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Margreet C. M. Vissers
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
- Correspondence: (M.C.M.V.); (M.J.B.)
| | - Mary J. Berry
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
- Correspondence: (M.C.M.V.); (M.J.B.)
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16
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Zhu X, Xiong L, Lyu R, Shen Y, Liu L, Li S, Argueta C, Tan L. Regulation of TET2 gene expression and 5mC oxidation in breast cancer cells by estrogen signaling. Biochem Biophys Res Commun 2021; 589:240-246. [PMID: 34929447 DOI: 10.1016/j.bbrc.2021.12.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/14/2021] [Indexed: 11/02/2022]
Abstract
Estrogen signaling plays important roles in diverse physiological and pathophysiological processes. However, the relationship between estrogen signaling and epigenetic regulation is not fully understood. Here, we explored the effect of estrogen signaling on the expression of Ten-Eleven Translocation (TET) family genes and DNA hydroxylmethylation in estrogen receptor alpha positive (ERα+) breast cancer cells. By analyzing the RNA-seq data, we identified TET2 as an estradiol (E2)-responsive gene in ERα+ MCF7 cells. RT-qPCR and Western blot analyses confirmed that both the mRNA and protein levels of TET2 gene were upregulated in MCF7 cells by E2 treatment. ChIP-seq and qPCR analyses showed that the enrichment of ERα and H3K27ac on the upstream regulatory regions of TET2 gene was increased in MCF7 cells upon E2 treatment. Moreover, E2 treatment also led to a significant increase in the global 5-hydroxymethylcytosine (5hmC) level, while knockout of TET2 abolished such E2-induced 5hmC increase. Conversely, treatment with ICI 182780, a potent and selective estrogen receptor degrader (SERD), inhibited TET2 gene expression and down-regulated the 5hmC level in MCF7 cells. Taken together, our study identified an ERα/TET2/5hmC epigenetic pathway, which may participate in the estrogen-associated physiological and pathophysiological processes.
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Affiliation(s)
- Xuguo Zhu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lijun Xiong
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruitu Lyu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yinghui Shen
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lu Liu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Shuangqi Li
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Christian Argueta
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Li Tan
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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Abstract
DNA methylation is one of the most important components of epigenetics, which plays essential roles in maintaining genome stability and regulating gene expression. In recent years, DNA methylation measuring methods have been continuously optimized. Combined with next generation sequencing technologies, these approaches have enabled the detection of genome-wide cytosine methylation at single-base resolution. In this paper, we review the development of 5-methylcytosine and its oxidized derivatives measuring methods, and recent advancement of single-cell epigenome sequencing technologies, offering more referable information for the selection and optimization of DNA methylation sequencing technologies and related research.
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18
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Li X, Shi X, Gong Y, Guo W, Liu Y, Peng C, Xu Y. Selective Chemical Labeling and Sequencing of 5-Hydroxymethylcytosine in DNA at Single-Base Resolution. Front Genet 2021; 12:749211. [PMID: 34868220 PMCID: PMC8635956 DOI: 10.3389/fgene.2021.749211] [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: 07/29/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022] Open
Abstract
5-Hydroxymethylcytosine (5hmC), the oxidative product of 5-methylcytosine (5mC) catalyzed by ten-eleven translocation enzymes, plays an important role in many biological processes as an epigenetic mediator. Prior studies have shown that 5hmC can be selectively labeled with chemically modified glucose moieties and enriched using click chemistry with biotin affinity approaches. Besides, DNA deaminases of the AID/APOBEC family can discriminate modified 5hmC bases from cytosine (C) or 5mC. Herein, we developed a method based on embryonic stem cell (ESC) whole-genome analysis, which could enrich 5hmC-containing DNA by selective chemical labeling and locate 5hmC sites at single-base resolution with enzyme-based deamination. The combination experimental design is an extension of previous methods, and we hope that this cost-effective single-base resolution 5hmC sequencing method could be used to promote the mechanism and diagnosis research of 5hmC.
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Affiliation(s)
- Xiaogang Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Xinxin Shi
- Gastrointestinal Surgery Department of the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yin Gong
- School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Wenting Guo
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuanrui Liu
- Characteristic Medical Center of the Chinese People’s Armed Police Force, Tianjin, China
| | - Chunwei Peng
- Gastrointestinal Surgery Department of the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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19
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Lyu R, Zhu X, Shen Y, Xiong L, Liu L, Liu H, Wu F, Argueta C, Tan L. Tumour suppressor TET2 safeguards enhancers from aberrant DNA methylation and epigenetic reprogramming in ERα-positive breast cancer cells. Epigenetics 2021; 17:1180-1194. [PMID: 34689714 DOI: 10.1080/15592294.2021.1997405] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Aberrant DNA methylation is an epigenetic hallmark of malignant tumours. The DNA methylation level is regulated by not only DNA methyltransferases (DNMTs) but also Ten-Eleven Translocation (TET) family proteins. However, the exact role of TET genes in breast cancer remains controversial. Here, we uncover that the ERα-positive breast cancer patients with high TET2 mRNA expression had better overall survival rates. Consistently, knockout of TET2 promotes the tumorigenesis of ERα-positive MCF7 breast cancer cells. Mechanistically, TET2 loss leads to aberrant DNA methylation (gain of 5mC) at a large proportion of enhancers, accompanied by significant reduction in H3K4me1 and H3K27ac enrichment. By analysing the epigenetically reprogrammed enhancers, we identify oestrogen responsive element (ERE) as one of the enriched motifs of transcriptional factors. Importantly, TET2 loss impairs 17beta-oestradiol (E2)-induced transcription of the epigenetically reprogrammed EREs-associated genes through attenuating the binding of ERα. Taken together, these findings shed light on our understanding of the epigenetic mechanisms underlying the enhancer reprogramming during breast cancer pathogenesis.
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Affiliation(s)
- Ruitu Lyu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xuguo Zhu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yinghui Shen
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lijun Xiong
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lu Liu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hang Liu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feizhen Wu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Christian Argueta
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Li Tan
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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20
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Ten-eleven translocation 1 mediated-DNA hydroxymethylation is required for myelination and remyelination in the mouse brain. Nat Commun 2021; 12:5091. [PMID: 34429415 PMCID: PMC8385008 DOI: 10.1038/s41467-021-25353-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 08/05/2021] [Indexed: 11/08/2022] Open
Abstract
Ten-eleven translocation (TET) proteins, the dioxygenase for DNA hydroxymethylation, are important players in nervous system development and diseases. However, their role in myelination and remyelination after injury remains elusive. Here, we identify a genome-wide and locus-specific DNA hydroxymethylation landscape shift during differentiation of oligodendrocyte-progenitor cells (OPC). Ablation of Tet1 results in stage-dependent defects in oligodendrocyte (OL) development and myelination in the mouse brain. The mice lacking Tet1 in the oligodendrocyte lineage develop behavioral deficiency. We also show that TET1 is required for remyelination in adulthood. Transcriptomic, genomic occupancy, and 5-hydroxymethylcytosine (5hmC) profiling reveal a critical TET1-regulated epigenetic program for oligodendrocyte differentiation that includes genes associated with myelination, cell division, and calcium transport. Tet1-deficient OPCs exhibit reduced calcium activity, increasing calcium activity rescues the differentiation defects in vitro. Deletion of a TET1-5hmC target gene, Itpr2, impairs the onset of OPC differentiation. Together, our results suggest that stage-specific TET1-mediated epigenetic programming and intracellular signaling are important for proper myelination and remyelination in mice.
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Mehrmohamadi M, Sepehri MH, Nazer N, Norouzi MR. A Comparative Overview of Epigenomic Profiling Methods. Front Cell Dev Biol 2021; 9:714687. [PMID: 34368164 PMCID: PMC8340004 DOI: 10.3389/fcell.2021.714687] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
In the past decade, assays that profile different aspects of the epigenome have grown exponentially in number and variation. However, standard guidelines for researchers to choose between available tools depending on their needs are lacking. Here, we introduce a comprehensive collection of the most commonly used bulk and single-cell epigenomic assays and compare and contrast their strengths and weaknesses. We summarize some of the most important technical and experimental parameters that should be considered for making an appropriate decision when designing epigenomic experiments.
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Affiliation(s)
- Mahya Mehrmohamadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Naghme Nazer
- Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
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22
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Rygiel CA, Goodrich JM, Solano-González M, Mercado-García A, Hu H, Téllez-Rojo MM, Peterson KE, Dolinoy DC. Prenatal Lead (Pb) Exposure and Peripheral Blood DNA Methylation (5mC) and Hydroxymethylation (5hmC) in Mexican Adolescents from the ELEMENT Birth Cohort. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:67002. [PMID: 34152198 PMCID: PMC8216410 DOI: 10.1289/ehp8507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Gestational lead (Pb) exposure can adversely affect offspring health through multiple mechanisms, including epigenomic alterations via DNA methylation (5mC) and hydroxymethylation (5hmC), an intermediate in oxidative demethylation. Most current methods do not distinguish between 5mC and 5hmC, limiting insights into their individual roles. OBJECTIVE Our study sought to identify the association of trimester-specific (T1, T2, T3) prenatal Pb exposure with 5mC and 5hmC levels at multiple cytosine-phosphate-guanine sites within gene regions previously associated with prenatal Pb (HCN2, NINJ2, RAB5A, TPPP) in whole blood leukocytes of children ages 11-18 years of age. METHODS Participants from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) birth cohorts were selected (n=144) for pyrosequencing analysis following oxidative or standard sodium bisulfite treatment. This workflow directly quantifies total methylation (5mC+5hmC) and 5mC only; 5hmC is estimated by subtraction. RESULTS Participants were 51% male, and mean maternal blood lead levels (BLL) were 6.43±5.16μg/dL in Trimester 1 (T1), 5.66±5.21μg/dL in Trimester 2 (T2), and 5.86±4.34μg/dL in Trimester 3 (T3). In addition, 5hmC levels were calculated for HCN2 (mean±standard deviation(SD), 2.08±4.18%), NINJ2 (G/C: 2.01±5.95; GG: 0.90±3.97), RAB5A (0.66±0.80%), and TPPP (1.11±6.67%). Furthermore, 5mC levels were measured in HCN2 (81.3±9.63%), NINJ2 (heterozygotes: 38.6±7.39%; GG homozygotes: 67.3±9.83%), RAB5A (1.41±1.21%), and TPPP (92.5±8.03%). Several significant associations between BLLs and 5mC/5hmC were identified: T1 BLLs with 5mC in HCN2 (β=-0.37, p=0.03) and 5hmC in NINJ2 (β=0.49, p=0.003); T2 BLLs with 5mC in HCN2 (β=0.37, p=0.03) and 5hmC in NINJ2 (β=0.27, p=0.008); and T3 BLLs with 5mC in HCN2 (β=0.50, p=0.01) and NINJ2 (β=-0.35, p=0.004) and 5hmC in NINJ2 (β=0.45, p<0.001). NINJ2 5mC was negatively correlated with gene expression (Pearson r=-0.5, p-value=0.005), whereas 5hmC was positively correlated (r=0.4, p-value=0.04). DISCUSSION These findings suggest there is variable 5hmC in human whole blood and that prenatal Pb exposure is associated with gene-specific 5mC and 5hmC levels at adolescence, providing evidence to consider 5hmC as a regulatory mechanism that is responsive to environmental exposures. https://doi.org/10.1289/EHP8507.
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Affiliation(s)
- Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | | | | | - Howard Hu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Karen E. Peterson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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23
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Shirai K, Nagae G, Seki M, Kudo Y, Kamio A, Hayashi A, Okabe A, Ota S, Tsutsumi S, Fujita T, Yamamoto S, Nakaki R, Kanki Y, Osawa T, Midorikawa Y, Tateishi K, Ichinose M, Aburatani H. TET1 upregulation drives cancer cell growth through aberrant enhancer hydroxymethylation of HMGA2 in hepatocellular carcinoma. Cancer Sci 2021; 112:2855-2869. [PMID: 33970549 PMCID: PMC8253281 DOI: 10.1111/cas.14897] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
Ten‐eleven translocation 1 (TET1) is an essential methylcytosine dioxygenase of the DNA demethylation pathway. Despite its dysregulation being known to occur in human cancer, the role of TET1 remains poorly understood. In this study, we report that TET1 promotes cell growth in human liver cancer. The transcriptome analysis of 68 clinical liver samples revealed a subgroup of TET1‐upregulated hepatocellular carcinoma (HCC), demonstrating hepatoblast‐like gene expression signatures. We performed comprehensive cytosine methylation and hydroxymethylation (5‐hmC) profiling and found that 5‐hmC was aberrantly deposited preferentially in active enhancers. TET1 knockdown in hepatoma cell lines decreased hmC deposition with cell growth suppression. HMGA2 was highly expressed in a TET1high subgroup of HCC, associated with the hyperhydroxymethylation of its intronic region, marked as histone H3K4–monomethylated, where the H3K27‐acetylated active enhancer chromatin state induced interactions with its promoter. Collectively, our findings point to a novel type of epigenetic dysregulation, methylcytosine dioxygenase TET1, which promotes cell proliferation via the ectopic enhancer of its oncogenic targets, HMGA2, in hepatoblast‐like HCC.
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Affiliation(s)
- Kiyokazu Shirai
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Gastroenterology, Wakayama Medical University, Wakayama, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Motoaki Seki
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yotaro Kudo
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Asuka Kamio
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Akimasa Hayashi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Atsushi Okabe
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Ota
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takanori Fujita
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Ryo Nakaki
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yasuharu Kanki
- Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tsuyoshi Osawa
- Division of Integrative Nutriomics and Oncology, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yutaka Midorikawa
- Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Keisuke Tateishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Ichinose
- Department of Gastroenterology, Wakayama Medical University, Wakayama, Japan.,Faculty of Medicine, Teikyo University, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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TET2 Inhibits PD-L1 Gene Expression in Breast Cancer Cells through Histone Deacetylation. Cancers (Basel) 2021; 13:cancers13092207. [PMID: 34064441 PMCID: PMC8125390 DOI: 10.3390/cancers13092207] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Programmed cell death ligand 1 (PD-L1) is an essential immune checkpoint molecule that helps tumor cells to escape the immune surveillance. The aim of the current study was to investigate the epigenetic mechanisms underlying the aberrant expression of PD-L1 in breast cancer cells. Here, we identified TET2 as a negative regulator of PD-L1 gene transcription in breast cancer cells. Mechanistically, TET2 recruits HDAC1/2 to the PD-L1 promoter and facilitates the deacetylation of H3K27ac, resulting to the suppression of PD-L1 gene transcription. Our work reveals an unanticipated role of TET2-HDAC1/2 complex in the regulation of PD-L1 gene expression, providing new insights into the epigenetic mechanisms that drive immune evasion during breast cancer pathogenesis. Abstract Activation of PD-1/PD-L1 checkpoint is a critical step for the immune evasion of malignant tumors including breast cancer. However, the epigenetic mechanism underlying the aberrant expression of PD-L1 in breast cancer cells remains poorly understood. To investigate the role of TET2 in the regulation of PD-L1 gene expression, quantitative reverse transcription PCR (RT-qPCR), Western blotting, chromatin immunoprecipitation (ChIP) assay and MeDIP/hMeDIP-qPCR were performed on MCF7 and MDA-MB-231 human breast cancer cells. Here, we reported that TET2 depletion upregulated PD-L1 gene expression in MCF7 cells. Conversely, ectopic expression of TET2 inhibited PD-L1 gene expression in MDA-MB-231 cells. Mechanistically, TET2 protein recruits histone deacetylases (HDACs) to PD-L1 gene promoter and orchestrates a repressive chromatin structure to suppress PD-L1 gene transcription, which is likely independent of DNA demethylation. Consistently, treatment with HDAC inhibitors upregulated PD-L1 gene expression in wild-type (WT) but not TET2 KO MCF7 cells. Furthermore, analysis of the CCLE and TCGA data showed a negative correlation between TET2 and PD-L1 expression in breast cancer. Taken together, our results identify a new epigenetic regulatory mechanism of PD-L1 gene transcription, linking the catalytic activity-independent role of TET2 to the anti-tumor immunity in breast cancer.
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25
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Li CC, Chen HY, Dong YH, Luo X, Hu J, Zhang CY. Advances in Detection of Epigenetic Modification—5-Hydroxymethylcytosine. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a20120564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Liu S, de Medeiros MC, Fernandez EM, Zarins KR, Cavalcante RG, Qin T, Wolf GT, Figueroa ME, D'Silva NJ, Rozek LS, Sartor MA. 5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers. Clin Epigenetics 2020; 12:175. [PMID: 33203436 PMCID: PMC7672859 DOI: 10.1186/s13148-020-00965-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.
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Affiliation(s)
- Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | | | - Evan M Fernandez
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA
| | - Gregory T Wolf
- Department of Otolaryngology-Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Maria E Figueroa
- Department of Human Genetics and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Nisha J D'Silva
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI, 48109-2218, USA. .,Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
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27
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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28
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Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L, Branco MR, Marques CJ. Tet3 regulates cellular identity and DNA methylation in neural progenitor cells. Cell Mol Life Sci 2020; 77:2871-2883. [PMID: 31646359 PMCID: PMC7326798 DOI: 10.1007/s00018-019-03335-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/26/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
TET enzymes oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), a process thought to be intermediary in an active DNA demethylation mechanism. Notably, 5hmC is highly abundant in the brain and in neuronal cells. Here, we interrogated the function of Tet3 in neural precursor cells (NPCs), using a stable and inducible knockdown system and an in vitro neural differentiation protocol. We show that Tet3 is upregulated during neural differentiation, whereas Tet1 is downregulated. Surprisingly, Tet3 knockdown led to a de-repression of pluripotency-associated genes such as Oct4, Nanog or Tcl1, with concomitant hypomethylation. Moreover, in Tet3 knockdown NPCs, we observed the appearance of OCT4-positive cells forming cellular aggregates, suggesting de-differentiation of the cells. Notably, Tet3 KD led to a genome-scale loss of DNA methylation and hypermethylation of a smaller number of CpGs that are located at neurogenesis-related genes and at imprinting control regions (ICRs) of Peg10, Zrsr1 and Mcts2 imprinted genes. Overall, our results suggest that TET3 is necessary to maintain silencing of pluripotency genes and consequently neural stem cell identity, possibly through regulation of DNA methylation levels in neural precursor cells.
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Affiliation(s)
- Mafalda Santiago
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Claudia Antunes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Marta Guedes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Michelina Iacovino
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Medical Genetics, Department of Pediatrics, Harbor UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA, 90502, USA
| | - Michael Kyba
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Luísa Pinto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - C Joana Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, 4710-057, Braga/Guimarães, Portugal.
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
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Kochmanski J, Bernstein AI. The Impact of Environmental Factors on 5-Hydroxymethylcytosine in the Brain. Curr Environ Health Rep 2020; 7:109-120. [PMID: 32020534 PMCID: PMC7809708 DOI: 10.1007/s40572-020-00268-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW The aims of this review are to evaluate the methods used to measure 5-hydroxymethylcytosine (5-hmC), and then summarize the available data investigating the impact of environmental factors on 5-hydroxymethylcytosine (5-hmC) in the brain. RECENT FINDINGS Recent research has shown that some environmental factors, including exposure to exogenous chemicals, stress, altered diet, and exercise, are all associated with 5-hmC variation in the brain. However, due to a lack of specificity in the methods used to generate a majority of the available data, it cannot be determined whether environment-induced changes in 5-hmC occur in specific biological pathways. Environment appears to shape 5-hmC levels in the brain, but the available literature is hampered by limitations in measurement methods. The field of neuroepigenetics needs to adopt new tools to increase the specificity of its data and enhance biological interpretation of exposure-related changes in 5-hmC. This will help improve understanding of the potential roles for environmental factors and 5-hmC in neurological disease.
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Affiliation(s)
- Joseph Kochmanski
- Department of Translational Neuroscience, Grand Rapids Research Center, Michigan State University College of Human Medicine, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - Alison I Bernstein
- Department of Translational Neuroscience, Grand Rapids Research Center, Michigan State University College of Human Medicine, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA.
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Rao VK, Swarnaseetha A, Tham GH, Lin WQ, Han BB, Benoukraf T, Xu GL, Ong CT. Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation. Nucleic Acids Res 2020; 48:1225-1238. [PMID: 31807777 PMCID: PMC7026633 DOI: 10.1093/nar/gkz1144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tet3 regulates the dynamic balance between 5-methylcyotsine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA during brain development and homeostasis. However, it remains unclear how its functions are modulated in a context-dependent manner during neuronal differentiation. Here, we show that cyclin-dependent kinase 5 (cdk5) phosphorylates Tet3 at the highly conserved serine 1310 and 1379 residues within its catalytic domain, changing its in vitro dioxygenase activity. Interestingly, when stably expressed in Tet1, 2, 3 triple-knockout mouse embryonic stem cells (ESCs), wild-type Tet3 induces higher level of 5hmC and concomitant expression of genes associated with neurogenesis whereas phosphor-mutant (S1310A/S1379A) Tet3 causes elevated 5hmC and expression of genes that are linked to metabolic processes. Consistent with this observation, Tet3-knockout mouse ESCs rescued with wild-type Tet3 have higher level of 5hmC at the promoter of neuron-specific gene BRN2 when compared to cells that expressed phosphor-mutant Tet3. Wild-type and phosphor-mutant Tet3 also exhibit differential binding affinity to histone variant H2A.Z. The differential 5hmC enrichment and H2A.Z occupancy at BRN2 promoter is correlated with higher gene expression and more efficient neuronal differentiation of ESCs that expressed wild-type Tet3. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 is required for robust activation of neuronal differentiation program.
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Affiliation(s)
- Vinay Kumar Rao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Adusumalli Swarnaseetha
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Guo-Hong Tham
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Wei-Qi Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Bin-Bin Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chin-Tong Ong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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31
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Uribe-Lewis S, Carroll T, Menon S, Nicholson A, Manasterski PJ, Winton DJ, Buczacki SJA, Murrell A. 5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation. Sci Rep 2020; 10:546. [PMID: 31953501 PMCID: PMC6969059 DOI: 10.1038/s41598-019-57214-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Cytosine hydroxymethylation (5hmC) in mammalian DNA is the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. While it has been shown that the TETs influence 5mC metabolism, pluripotency and differentiation during early embryonic development, the functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is still unknown. Here we report that 5hmC levels undergo highly dynamic changes during adult stem cell differentiation from intestinal progenitors to differentiated intestinal epithelium. We profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny to identify 43425 differentially hydroxymethylated regions and 5325 differentially expressed genes. These differentially marked regions showed both losses and gains of 5hmC after differentiation, despite lower global levels of 5hmC in progenitor cells. In progenitors, 5hmC did not correlate with gene transcript levels, however, upon differentiation the global increase in 5hmC content showed an overall positive correlation with gene expression level as well as prominent associations with histone modifications that typify active genes and enhancer elements. Our data support a gene regulatory role for 5hmC that is predominant over its role in controlling DNA methylation states.
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Affiliation(s)
- Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University New York, New York, NY, 10065, USA
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anna Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Piotr J Manasterski
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Douglas J Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Simon J A Buczacki
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Addenbrookes Biomedical Campus, Cambridge, CB2 0AF, UK
| | - Adele Murrell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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32
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Yang J, Bashkenova N, Zang R, Huang X, Wang J. The roles of TET family proteins in development and stem cells. Development 2020; 147:147/2/dev183129. [PMID: 31941705 DOI: 10.1242/dev.183129] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ten-eleven translocation (TET) methylcytosine dioxygenases are enzymes that catalyze the demethylation of 5-methylcytosine on DNA. Through global and site-specific demethylation, they regulate cell fate decisions during development and in embryonic stem cells by maintaining pluripotency or by regulating differentiation. In this Primer, we provide an updated overview of TET functions in development and stem cells. We discuss the catalytic and non-catalytic activities of TETs, and their roles as epigenetic regulators of both DNA and RNA hydroxymethylation, highlighting how TET proteins function in regulating gene expression at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nazym Bashkenova
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ruge Zang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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33
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Rauluseviciute I, Drabløs F, Rye MB. DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis. Clin Epigenetics 2019; 11:193. [PMID: 31831061 PMCID: PMC6909609 DOI: 10.1186/s13148-019-0795-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/04/2019] [Indexed: 02/06/2023] Open
Abstract
Sequencing technologies have changed not only our approaches to classical genetics, but also the field of epigenetics. Specific methods allow scientists to identify novel genome-wide epigenetic patterns of DNA methylation down to single-nucleotide resolution. DNA methylation is the most researched epigenetic mark involved in various processes in the human cell, including gene regulation and development of diseases, such as cancer. Increasing numbers of DNA methylation sequencing datasets from human genome are produced using various platforms-from methylated DNA precipitation to the whole genome bisulfite sequencing. Many of those datasets are fully accessible for repeated analyses. Sequencing experiments have become routine in laboratories around the world, while analysis of outcoming data is still a challenge among the majority of scientists, since in many cases it requires advanced computational skills. Even though various tools are being created and published, guidelines for their selection are often not clear, especially to non-bioinformaticians with limited experience in computational analyses. Separate tools are often used for individual steps in the analysis, and these can be challenging to manage and integrate. However, in some instances, tools are combined into pipelines that are capable to complete all the essential steps to achieve the result. In the case of DNA methylation sequencing analysis, the goal of such pipeline is to map sequencing reads, calculate methylation levels, and distinguish differentially methylated positions and/or regions. The objective of this review is to describe basic principles and steps in the analysis of DNA methylation sequencing data that in particular have been used for mammalian genomes, and more importantly to present and discuss the most pronounced computational pipelines that can be used to analyze such data. We aim to provide a good starting point for scientists with limited experience in computational analyses of DNA methylation and hydroxymethylation data, and recommend a few tools that are powerful, but still easy enough to use for their own data analysis.
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Affiliation(s)
- Ieva Rauluseviciute
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, NO-7491, Trondheim, Norway.
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, NO-7491, Trondheim, Norway
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, NO-7491, Trondheim, Norway.,Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, NO-7030, Trondheim, Norway
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34
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Wang X. Stem cells in tissues, organoids, and cancers. Cell Mol Life Sci 2019; 76:4043-4070. [PMID: 31317205 PMCID: PMC6785598 DOI: 10.1007/s00018-019-03199-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022]
Abstract
Stem cells give rise to all cells and build the tissue structures in our body, and heterogeneity and plasticity are the hallmarks of stem cells. Epigenetic modification, which is associated with niche signals, determines stem cell differentiation and somatic cell reprogramming. Stem cells play a critical role in the development of tumors and are capable of generating 3D organoids. Understanding the properties of stem cells will improve our capacity to maintain tissue homeostasis. Dissecting epigenetic regulation could be helpful for achieving efficient cell reprograming and for developing new drugs for cancer treatment. Stem cell-derived organoids open up new avenues for modeling human diseases and for regenerative medicine. Nevertheless, in addition to the achievements in stem cell research, many challenges still need to be overcome for stem cells to have versatile application in clinics.
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Affiliation(s)
- Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, 510275, China.
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35
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Morris-Blanco KC, Kim T, Lopez MS, Bertogliat MJ, Chelluboina B, Vemuganti R. Induction of DNA Hydroxymethylation Protects the Brain After Stroke. Stroke 2019; 50:2513-2521. [PMID: 31327315 DOI: 10.1161/strokeaha.119.025665] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background and Purpose- Epigenetics play a significant role in brain pathologies. We currently evaluated the role of a recently discovered brain-enriched epigenetic modification known as 5-hydroxymethylcytosine (5hmC) in regulating transcriptomic and pathogenic mechanisms after focal ischemic injury. Methods- Young and aged male and female mice were subjected to transient middle cerebral artery occlusion, and the peri-infarct region was analyzed at various times of reperfusion. Two days before middle cerebral artery occlusion, short-interfering RNA against an isoform of the 5hmC producing enzyme TET (ten-eleven translocase) was injected intracerebrally. Ascorbate was injected intraperitoneally at 5 minutes, 30 minutes, or 2 hours of reperfusion. Motor function was tested with rotarod and beam-walk test. Results- Focal ischemia rapidly induced the activity of TET, the enzyme that catalyzes the formation of 5hmC and preferentially increased expression of the TET3 isoform in the peri-infarct region of the ischemic cortex. Levels of 5hmC were increased in a TET3-dependent manner, and inhibition of TET3 led to wide-scale reductions in the postischemic expression of neuroprotective genes involved in antioxidant defense and DNA repair. TET3 knockdown in adult male and female mice further increased brain degeneration after focal ischemia, demonstrating a role for TET3 and 5hmC in endogenous protection against stroke. Ascorbate treatment after focal ischemia enhanced TET3 activity and 5hmC enrichment in the peri-infarct region. TET3 activation by ascorbate provided robust protection against ischemic injury in young and aged mice of both sexes. Moreover, ascorbate treatment improved motor function recovery in both male and female mice. Conclusions- Collectively, these results indicate the potential of TET3 and 5hmC as novel stroke therapeutic targets. Visual Overview- An online visual overview is available for this article.
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Affiliation(s)
- Kahlilia C Morris-Blanco
- From the Department of Neurological Surgery (K.C.M.-B., T.K., M.S.L., M.J.B., B.C., R.V.), University of Wisconsin-Madison, Madison, WI.,William S. Middleton Veterans Administration Hospital, Madison, WI, (K.C.M.-B., T.K., R.V.)
| | - TaeHee Kim
- From the Department of Neurological Surgery (K.C.M.-B., T.K., M.S.L., M.J.B., B.C., R.V.), University of Wisconsin-Madison, Madison, WI.,William S. Middleton Veterans Administration Hospital, Madison, WI, (K.C.M.-B., T.K., R.V.)
| | - Mary S Lopez
- From the Department of Neurological Surgery (K.C.M.-B., T.K., M.S.L., M.J.B., B.C., R.V.), University of Wisconsin-Madison, Madison, WI.,Cellular and Molecular Pathology Training Program (M.S.L., R.V.), University of Wisconsin-Madison, Madison, WI
| | - Mario J Bertogliat
- From the Department of Neurological Surgery (K.C.M.-B., T.K., M.S.L., M.J.B., B.C., R.V.), University of Wisconsin-Madison, Madison, WI
| | - Bharath Chelluboina
- From the Department of Neurological Surgery (K.C.M.-B., T.K., M.S.L., M.J.B., B.C., R.V.), University of Wisconsin-Madison, Madison, WI
| | - Raghu Vemuganti
- From the Department of Neurological Surgery (K.C.M.-B., T.K., M.S.L., M.J.B., B.C., R.V.), University of Wisconsin-Madison, Madison, WI.,Cellular and Molecular Pathology Training Program (M.S.L., R.V.), University of Wisconsin-Madison, Madison, WI.,William S. Middleton Veterans Administration Hospital, Madison, WI, (K.C.M.-B., T.K., R.V.)
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36
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Noack F, Pataskar A, Schneider M, Buchholz F, Tiwari VK, Calegari F. Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis. Life Sci Alliance 2019; 2:2/2/e201900331. [PMID: 30814272 PMCID: PMC6394126 DOI: 10.26508/lsa.201900331] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/17/2022] Open
Abstract
This work describes the dynamics of DNA modifications in specific cell types of the developing mammalian cortex. By providing a new method to manipulate this process in vivo, it is shown how this process can influence brain formation. Dynamic changes in DNA (hydroxy-)methylation are fundamental for stem cell differentiation. However, the signature of these epigenetic marks in specific cell types during corticogenesis is unknown. Moreover, site-specific manipulation of cytosine modifications is needed to reveal the significance and function of these changes. Here, we report the first assessment of (hydroxy-)methylation in neural stem cells, neurogenic progenitors, and newborn neurons during mammalian corticogenesis. We found that gain in hydroxymethylation and loss in methylation occur sequentially at specific cellular transitions during neurogenic commitment. We also found that these changes predominantly occur within enhancers of neurogenic genes up-regulated during neurogenesis and target of pioneer transcription factors. We further optimized the use of dCas9-Tet1 manipulation of (hydroxy-)methylation, locus-specifically, in vivo, showing the biological relevance of our observations for Dchs1, a regulator of corticogenesis involved in developmental malformations and cognitive impairment. Together, our data reveal the dynamics of cytosine modifications in lineage-related cell types, whereby methylation is reduced and hydroxymethylation gained during the neurogenic lineage concurrently with up-regulation of pioneer transcription factors and activation of enhancers for neurogenic genes.
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Affiliation(s)
- Florian Noack
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
| | | | - Martin Schneider
- Medical Systems Biology, School of Medicine, Technische Universität Dresden and Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, School of Medicine, Technische Universität Dresden and Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Federico Calegari
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
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37
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Li G, Qian H. Hydroxymethylation of protein-encoding genes in the testes involved in precocious puberty of Eriocheir sinensis. Gene 2019; 683:18-27. [PMID: 30315924 DOI: 10.1016/j.gene.2018.10.019] [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: 06/10/2018] [Revised: 09/04/2018] [Accepted: 10/09/2018] [Indexed: 10/28/2022]
Abstract
To investigate the possible effects of epigenetic modification of testis protein-encoding genes on precocious puberty of Eriocheir sinensis, we used MeDIP-seq and hMeDIP-seq techniques to compare the methylation and hydroxymethylation of 263 E. sinensis protein-encoding genes known in the NCBI database in precocious testes with those in normally developing testes. The results showed that total methylation level of those genes was lower than their total hydroxymethylation level. Moreover, their total hydroxymethylation level in precocious testes was significantly lower than that in normal testes. In addition, no methylated genes had significant difference, but there were 37 different hydroxymethylated genes (DhMGs) in the precocious testes compared to the normal ones. Among the DhMGs, 21 were hypo-hydroxymethylated and 16 were hyper-hydroxymethylated. The hypo-hydroxymethylated DhMGs were associated with development, cell structural and cytoskeletal proteins, and response to stress. However, the hyper-hydroxymethylated DhMGs included immune-related genes, free radicals removement-related genes, protein folding-related genes, and so on. In addition, some DhMGs were hyper-hydroxymethylated while their homologous DhMGs were hypo-hydroxymethylated. The results of a qRT-PCR assay showed that the expression levels of 5 DhMGs randomly chosen presented a positive correlation with their hydroxymethylation levels. It can be seen that hydroxymethylation might regulate the expression of genes and be involved in precocious puberty to cause high mortality of crabs. Therefore, the hydroxymethylation level of DhMGs may be used as an evaluation index with economically meaningful growth and breeding traits.
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Affiliation(s)
- Genliang Li
- Youjiang Medical University for Nationalities, Baise 533000, Guangxi, People's Republic of China.
| | - Hui Qian
- Youjiang Medical University for Nationalities, Baise 533000, Guangxi, People's Republic of China
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38
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Bonvin E, Radaelli E, Bizet M, Luciani F, Calonne E, Putmans P, Nittner D, Singh NK, Santagostino SF, Petit V, Larue L, Marine JC, Fuks F. TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression. Cancer Res 2018; 79:482-494. [PMID: 30538121 DOI: 10.1158/0008-5472.can-18-1214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/03/2018] [Accepted: 12/06/2018] [Indexed: 11/16/2022]
Abstract
Although numerous epigenetic aberrancies accumulate in melanoma, their contribution to initiation and progression remain unclear. The epigenetic mark 5-hydroxymethylcytosine (5hmC), generated through TET-mediated DNA modification, is now referred to as the sixth base of DNA and has recently been reported as a potential biomarker for multiple types of cancer. Loss of 5hmC is an epigenetic hallmark of melanoma, but whether a decrease in 5hmc levels contributes directly to pathogenesis or whether it merely results from disease progression-associated epigenetic remodeling remains to be established. Here, we show that NRAS-driven melanomagenesis in mice is accompanied by an overall decrease in 5hmC and specific 5hmC gains in selected gene bodies. Strikingly, genetic ablation of Tet2 in mice cooperated with oncogenic NRASQ61K to promote melanoma initiation while suppressing specific gains in 5hmC. We conclude that TET2 acts as a barrier to melanoma initiation and progression, partly by promoting 5hmC gains in specific gene bodies. SIGNIFICANCE: This work emphasizes the importance of epigenome plasticity in cancer development and highlights the involvement of druggable epigenetic factors in cancer.
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Affiliation(s)
- Elise Bonvin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Enrico Radaelli
- Mouse Histopathology Core Facility, VIB Center for Brain & Disease Research, Leuven, Belgium.,Comparative Pathology Core, University of Pennsylvania, School of Veterinary Medicine, Department of Pathobiology, Philadelphia, Pennsylvania
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Flavie Luciani
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - David Nittner
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium.,Histopathology Expertise Center, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Nitesh Kumar Singh
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sara Francesca Santagostino
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, New York.,Department of Safety Assessment, Genentech, Inc., South San Francisco, California
| | - Valérie Petit
- Normal and Pathological Development of Melanocytes, CNRS UMR3347, INSERM U1021, Institut Curie, Orsay, France
| | - Lionel Larue
- Normal and Pathological Development of Melanocytes, CNRS UMR3347, INSERM U1021, Institut Curie, Orsay, France
| | - Jean Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.
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39
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Wu X, Li G, Xie R. Decoding the role of TET family dioxygenases in lineage specification. Epigenetics Chromatin 2018; 11:58. [PMID: 30290828 PMCID: PMC6172806 DOI: 10.1186/s13072-018-0228-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of methylcytosine oxidase ten-eleven translocation (TET) proteins, we have witnessed an exponential increase in studies examining their roles in epigenetic regulation. TET family proteins catalyze the sequential oxidation of 5-methylcytosine (5mC) to oxidized methylcytosines including 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine. TETs contribute to the regulation of lineage-specific gene expression via modulating DNA 5mC/5hmC balances at the proximal and distal regulatory elements of cell identity genes, and therefore enhance chromatin accessibility and gene transcription. Emerging evidence suggests that TET dioxygenases participate in the establishment and/or maintenance of hypomethylated bivalent domains at multiple differentiation-associated genes, and thus ensure developmental plasticity. Here, we review the current state of knowledge concerning TET family proteins, DNA hydroxymethylation, their distribution, and function in endoderm, mesoderm, and neuroectoderm specification. We will summarize the evidence pertaining to their crucial regulatory roles in lineage commitment and development.
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Affiliation(s)
- Xinwei Wu
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Gang Li
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Ruiyu Xie
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.
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40
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Kochmanski J, Marchlewicz EH, Cavalcante RG, Sartor MA, Dolinoy DC. Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood. Epigenetics 2018; 13:779-792. [PMID: 30079798 PMCID: PMC6224215 DOI: 10.1080/15592294.2018.1507198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/25/2018] [Indexed: 01/10/2023] Open
Abstract
DNA methylation at cytosine-phosphate-guanine (CpG) dinucleotides changes as a function of age in humans and animal models, a process that may contribute to chronic disease development. Recent studies have investigated the role of an oxidized form of DNA methylation - 5-hydroxymethylcytosine (5hmC) - in the epigenome, but its contribution to age-related DNA methylation remains unclear. We tested the hypothesis that 5hmC changes with age, but in a direction opposite to 5-methylcytosine (5mC), potentially playing a distinct role in aging. To characterize epigenetic aging, genome-wide 5mC and 5hmC were measured in longitudinal blood samples (2, 4, and 10 months of age) from isogenic mice using two sequencing methods - enhanced reduced representation bisulfite sequencing and hydroxymethylated DNA immunoprecipitation sequencing. Examining the epigenome by age, we identified 28,196 unique differentially methylated CpGs (DMCs) and 8,613 differentially hydroxymethylated regions (DHMRs). Mouse blood showed a general pattern of epigenome-wide hypermethylation and hypo-hydroxymethylation with age. Comparing age-related DMCs and DHMRs, 1,854 annotated genes showed both differential 5mC and 5hmC, including one gene - Nfic - at five CpGs in the same 250 bp chromosomal region. At this region, 5mC and 5hmC levels both decreased with age. Reflecting these age-related epigenetic changes, Nfic RNA expression in blood decreased with age, suggesting that age-related regulation of this gene may be driven by 5hmC, not canonical DNA methylation. Combined, our genome-wide results show age-related differential 5mC and 5hmC, as well as some evidence that changes in 5hmC may drive age-related DNA methylation and gene expression.
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Affiliation(s)
- Joseph Kochmanski
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth H. Marchlewicz
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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41
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Kochmanski JJ, Marchlewicz EH, Cavalcante RG, Perera BPU, Sartor MA, Dolinoy DC. Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:077006. [PMID: 30044229 PMCID: PMC6108846 DOI: 10.1289/ehp3441] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic machinery plays an important role in genomic imprinting, a developmental process that establishes parent-of-origin-specific monoallelic gene expression. Although a number of studies have investigated the role of 5-methylcytosine in imprinting control, the contribution of 5-hydroxymethylcytosine (5-hmC) to this epigenetic phenomenon remains unclear. OBJECTIVES Using matched mouse blood samples (from mice at 2, 4, and 10 months of age), our objective was to examine the effects of perinatal bisphenol A (BPA) exposure (50 μg/kg diet) on longitudinal 5-hmC patterns at imprinted regions. We also aimed to test the hypothesis that 5-hmC would show defined patterns at imprinted genes that persist across the life course. METHODS Genome-wide 5-hmC levels were measured using hydroxymethylated DNA immunoprecipitation sequencing (HMeDIP-seq). Modeling of differential hydroxymethylation by BPA exposure was performed using a pipeline of bioinformatics tools, including the csaw R package. RESULTS Based on BPA exposure, we identified 5,950 differentially hydroxymethylated regions (DHMRs), including 12 DHMRs that were annotated to murine imprinted genes—Gnas, Grb10, Plagl1, Klf14, Pde10a, Snrpn, Airn, Cmah, Ppp1r9a, Kcnq1, Phactr2, and Pde4d. When visualized, these imprinted gene DHMRs showed clear, consistent patterns of differential 5-hmC by developmental BPA exposure that persisted throughout adulthood. CONCLUSIONS These data show long-term establishment of 5-hmC marks at imprinted loci during development. Further, the effect of perinatal BPA exposure on 5-hmC at specific imprinted loci indicates that developmental exposure to environmental toxicants may alter long-term imprinted gene regulation via an epigenetic mechanism. https://doi.org/10.1289/EHP3441.
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Affiliation(s)
- Joseph J Kochmanski
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elizabeth H Marchlewicz
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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42
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Pavlovic M, Ray P, Pavlovic K, Kotamarti A, Chen M, Zhang MQ. DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. Bioinformatics 2018; 33:2986-2994. [PMID: 28505334 DOI: 10.1093/bioinformatics/btx316] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/11/2017] [Indexed: 12/15/2022] Open
Abstract
Motivation 5-Methylcytosine and 5-Hydroxymethylcytosine in DNA are major epigenetic modifications known to significantly alter mammalian gene expression. High-throughput assays to detect these modifications are expensive, labor-intensive, unfeasible in some contexts and leave a portion of the genome unqueried. Hence, we devised a novel, supervised, integrative learning framework to perform whole-genome methylation and hydroxymethylation predictions in CpG dinucleotides. Our framework can also perform imputation of missing or low quality data in existing sequencing datasets. Additionally, we developed infrastructure to perform in silico, high-throughput hypotheses testing on such predicted methylation or hydroxymethylation maps. Results We test our approach on H1 human embryonic stem cells and H1-derived neural progenitor cells. Our predictive model is comparable in accuracy to other state-of-the-art DNA methylation prediction algorithms. We are the first to predict hydroxymethylation in silico with high whole-genome accuracy, paving the way for large-scale reconstruction of hydroxymethylation maps in mammalian model systems. We designed a novel, beam-search driven feature selection algorithm to identify the most discriminative predictor variables, and developed a platform for performing integrative analysis and reconstruction of the epigenome. Our toolkit DIRECTION provides predictions at single nucleotide resolution and identifies relevant features based on resource availability. This offers enhanced biological interpretability of results potentially leading to a better understanding of epigenetic gene regulation. Availability and implementation http://www.pradiptaray.com/direction, under CC-by-SA license. Contacts pradiptaray@gmail.com or mchen@utdallas.edu or michael.zhang@utdallas.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Milos Pavlovic
- Department of Biological Sciences, Center for Systems Biology
| | - Pradipta Ray
- Department of Biological Sciences, Center for Systems Biology.,School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | | | - Aaron Kotamarti
- Department of Biological Sciences, Center for Systems Biology
| | - Min Chen
- Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology.,TNLIST, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
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43
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Masser DR, Hadad N, Porter H, Stout MB, Unnikrishnan A, Stanford DR, Freeman WM. Analysis of DNA modifications in aging research. GeroScience 2018; 40:11-29. [PMID: 29327208 PMCID: PMC5832665 DOI: 10.1007/s11357-018-0005-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging. With recent methodological advances, such as whole genome bisulfite sequencing (WGBS), bisulfite oligonucleotide capture sequencing (BOCS), and bisulfite amplicon sequencing (BSAS), cytosine modifications can now be readily analyzed with base-specific, absolute quantitation at both cytosine-guanine dinucleotide (CG) and non-CG sites throughout the genome or within specific regions of interest by next-generation sequencing. Additional advances, such as oxidative bisulfite conversion to differentiate methylation from hydroxymethylation and analysis of limited input/single-cells, have great promise for continuing to expand epigenomic capabilities. This review provides a background on DNA modifications, the current state-of-the-art for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.
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Affiliation(s)
- Dustin R Masser
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hunter Porter
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael B Stout
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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Sharifi-Zarchi A, Gerovska D, Adachi K, Totonchi M, Pezeshk H, Taft RJ, Schöler HR, Chitsaz H, Sadeghi M, Baharvand H, Araúzo-Bravo MJ. DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. BMC Genomics 2017; 18:964. [PMID: 29233090 PMCID: PMC5727985 DOI: 10.1186/s12864-017-4353-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. Results We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized “seesaw” dynamics between H3K4me1 and H3K4me3 in the low and intermediate DNA methylation range, in which DNA methylation discriminates between enhancers and promoters, marked by H3K4me1 and H3K4me3, respectively. Low methylated regions are H3K4me3 enriched, while those with intermediate DNA methylation levels are progressively H3K4me1 enriched. Additionally, the enrichment of H3K27ac, distinguishing active from primed enhancers, follows a plateau in the lower range of the intermediate DNA methylation level, corresponding to active enhancers, and decreases linearly in the higher range of the intermediate DNA methylation. Thus, the decrease of the DNA methylation switches smoothly the state of the enhancers from a primed to an active state. We summarize these observations into a rule of thumb of one-out-of-three methylation marks: “In each genomic region only one out of these three methylation marks {DNA methylation, H3K4me1, H3K4me3} is high. If it is the DNA methylation, the region is inactive. If it is H3K4me1, the region is an enhancer, and if it is H3K4me3, the region is a promoter”. To test our model, we used available genome-wide datasets of H3K4 methyltransferases knockouts. Our analysis suggests that CXXC proteins, as readers of non-methylated CpGs would regulate the “seesaw” mechanism that focuses H3K4me3 to unmethylated sites, while being repulsed from H3K4me1 decorated enhancers and CpG island shores. Conclusions Our results show that DNA methylation discriminates promoters from enhancers through H3K4me1-H3K4me3 seesaw mechanism, and suggest its possible function in the inheritance of chromatin marks after cell division. Our analyses suggest aberrant formation of promoter-like regions and ectopic transcription of hypomethylated regions of DNA. Such mechanism process can have important implications in biological process in where it has been reported abnormal DNA methylation status such as cancer and aging. Electronic supplementary material The online version of this article (10.1186/s12864-017-4353-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Sharifi-Zarchi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Computer Science Department, Colorado State University, Fort Collins, CO, USA.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Mehdi Totonchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hamid Pezeshk
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | | | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Münster, Germany
| | - Hamidreza Chitsaz
- Computer Science Department, Colorado State University, Fort Collins, CO, USA
| | - Mehdi Sadeghi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.,National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran. .,Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain. .,Computational Biology and Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany. .,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain.
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Hypo-hydroxymethylation of rRNA genes in the precocious Eriocheir sinensis testes revealed using hMeDIP-seq. Sci Rep 2017; 7:11237. [PMID: 28894189 PMCID: PMC5593943 DOI: 10.1038/s41598-017-11517-1] [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: 02/21/2017] [Accepted: 08/25/2017] [Indexed: 11/30/2022] Open
Abstract
Precocious puberty is a common phenomenon in crab breeding that seriously reduces the economic benefits for crab farmers. To address this problem, this study aimed to explore the potential functions of both methylation and hydroxymethylation of testis rRNA genes with respect to precocious puberty in Eriocheir sinensis. The results showed that the rRNA genes in normally developing testes of E. sinensis had low levels of methylation and high levels of hydroxymethylation; however, although methylation levels were similar, the level of hydroxymethylation in precocious testes was lower than normal. Highly significant differences (P < 0.01) in the hydroxymethylation of the 18S and 28S rRNA genes were found between precocious and normal testes. Our results suggested that both the 18S and 28S rRNA genes, which are normally downregulated by hypo-hydroxymethylation, might be involved in the process of precocious puberty. Our results also implied that hydroxymethylation of the 18S and 28S rRNA genes might be used as an important epigenetic molecular marker to evaluate economically significant potential for growth and breeding in this species.
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López V, Fernández A, Fraga M. The role of 5-hydroxymethylcytosine in development, aging and age-related diseases. Ageing Res Rev 2017; 37:28-38. [PMID: 28499883 DOI: 10.1016/j.arr.2017.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/24/2022]
Abstract
DNA methylation at the fifth position of cytosines (5mC) represents a major epigenetic modification in mammals. The recent discovery of 5-hydroxymethylcytosine (5hmC), resulting from 5mC oxidation, is redefining our view of the epigenome, as multiple studies indicate that 5hmC is not simply an intermediate of DNA demethylation, but a genuine epigenetic mark that may play an important functional role in gene regulation. Currently, the availability of platforms that discriminates between the presence of 5mC and 5hmC at single-base resolution is starting to shed light on the functions of 5hmC. In this review, we provide an overview of the genomic distribution of 5hmC, and examine recent findings on the role of this mark and the potential consequences of its misregulation during three fundamental biological processes: cell differentiation, cancer and aging.
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47
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Shi DQ, Ali I, Tang J, Yang WC. New Insights into 5hmC DNA Modification: Generation, Distribution and Function. Front Genet 2017; 8:100. [PMID: 28769976 PMCID: PMC5515870 DOI: 10.3389/fgene.2017.00100] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/05/2017] [Indexed: 01/10/2023] Open
Abstract
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals. Here, we review recent advances on the generation, distribution, and function of 5hmC modification in mammals and discuss its potential roles in plants.
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Affiliation(s)
- Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Iftikhar Ali
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jun Tang
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
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48
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CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function. Genes (Basel) 2017; 8:genes8060148. [PMID: 28545252 PMCID: PMC5485512 DOI: 10.3390/genes8060148] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/18/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Thus, accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Here, we provide an overview of CpG and non-CpG methylation and their roles in neurological diseases.
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49
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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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50
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Qing Y, Tian Z, Bi Y, Wang Y, Long J, Song CX, Diao J. Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine. Bioessays 2017; 39. [DOI: 10.1002/bies.201700010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ying Qing
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
| | - Zhiqi Tian
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
- Center for Mitochondrial Biology and Medicine; The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology Xi'an Jiaotong University; Xi'an China
| | - Ying Bi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Yongyao Wang
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
- Center for Mitochondrial Biology and Medicine; The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology Xi'an Jiaotong University; Xi'an China
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine; The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology Xi'an Jiaotong University; Xi'an China
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine; University of Oxford; Oxford UK
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Jiajie Diao
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
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