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Liu J, Sun Q, Liu D, Liang H, Chen Y, Ye F, Zhang Q. Epigenome-850K-wide profiling reveals peripheral blood differential methylation in term low birth weight. Epigenomics 2024; 16:821-833. [PMID: 38957889 PMCID: PMC11370964 DOI: 10.1080/17501911.2024.2358744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/20/2024] [Indexed: 07/04/2024] Open
Abstract
Aim: We investigate the genome-wide DNA methylation (DNAm) patterns of term low birth weight (TLBW) neonates.Methods: In the discovery phase, we assayed 32 samples (TLBW/control:16/16) using the EPIC 850k BeadChip Array. Targeted pyrosequencing of in 60 samples (TLBW/control:28/32) using targeted pyrosequencing during the replication phase.Results: The 850K array identified TLBW-associated 144 differentially methylated positions (DMPs) and 149 DMRs. Nearly 77% DMPs exhibited hypomethylation, located in the opensea and gene body regions. The most significantly enriched pathway in KEGG is sphingolipid metabolism (hsa00600), and the genes GALC and SGMS1 related to this pathway both show hypomethylation.Conclusion: Our analysis provides evidence of genome-wide DNAm alterations in TLBW. Further investigations are needed to elucidate the functional significance of these DNAm changes.
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Affiliation(s)
- Jing Liu
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qi Sun
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Die Liu
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Haixiao Liang
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Yuanmei Chen
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Fang Ye
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Qi Zhang
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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2
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Divyajanani S, Harithpriya K, Ganesan K, Ramkumar KM. Dietary Polyphenols Remodel DNA Methylation Patterns of NRF2 in Chronic Disease. Nutrients 2023; 15:3347. [PMID: 37571283 PMCID: PMC10420661 DOI: 10.3390/nu15153347] [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: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor crucial in regulating cellular homeostasis and apoptosis. The NRF2 gene has been implicated in various biological activities, including antioxidant, anti-inflammatory, and anticancer properties. NRF2 can be regulated genetically and epigenetically at the transcriptional, post-transcriptional, and translational levels. Although DNA methylation is one of the critical biological processes vital for gene expression, sometimes, anomalous methylation patterns result in the dysregulation of genes and consequent diseases and disorders. Several studies have reported promoter hypermethylation downregulated NRF2 expression and its downstream targets. In contrast to the unalterable nature of genetic patterns, epigenetic changes can be reversed, opening up new possibilities in developing therapies for various metabolic disorders and diseases. This review discusses the current state of the NRF2-mediated antioxidative and chemopreventive activities of several natural phytochemicals, including sulforaphane, resveratrol, curcumin, luteolin, corosolic acid, apigenin, and most other compounds that have been found to activate NRF2. This epigenetic reversal of hypermethylated NRF2 states provides new opportunities for research into dietary phytochemistry that affects the human epigenome and the possibility for cutting-edge approaches to target NRF2-mediated signaling to prevent chronic disorders.
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Affiliation(s)
- Srinivasaragavan Divyajanani
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603210, Tamil Nadu, India; (S.D.); (K.H.)
| | - Kannan Harithpriya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603210, Tamil Nadu, India; (S.D.); (K.H.)
| | - Kumar Ganesan
- School of Chinese Medicine, LKS Faculty of Medicine, University of Hong Kong, 3 Sassoon Road, Hong Kong, China;
| | - Kunka Mohanram Ramkumar
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603210, Tamil Nadu, India; (S.D.); (K.H.)
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3
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Sibley LA, Broda N, Gross WR, Menezes AF, Embry RB, Swaroop VT, Chambers HG, Schipma MJ, Lieber RL, Domenighetti AA. Differential DNA methylation and transcriptional signatures characterize impairment of muscle stem cells in pediatric human muscle contractures after brain injury. FASEB J 2021; 35:e21928. [PMID: 34559924 DOI: 10.1096/fj.202100649r] [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: 04/17/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
Limb contractures are a debilitating and progressive consequence of a wide range of upper motor neuron injuries that affect skeletal muscle function. One type of perinatal brain injury causes cerebral palsy (CP), which affects a child's ability to move and is often painful. While several rehabilitation therapies are used to treat contractures, their long-term effectiveness is marginal since such therapies do not change muscle biological properties. Therefore, new therapies based on a biological understanding of contracture development are needed. Here, we show that myoblast progenitors from contractured muscle in children with CP are hyperproliferative. This phenotype is associated with DNA hypermethylation and specific gene expression patterns that favor cell proliferation over quiescence. Treatment of CP myoblasts with 5-azacytidine, a DNA hypomethylating agent, reduced this epigenetic imprint to TD levels, promoting exit from mitosis and molecular mechanisms of cellular quiescence. Together with previous studies demonstrating reduction in myoblast differentiation, this suggests a mechanism of contracture formation that is due to epigenetic modifications that alter the myogenic program of muscle-generating stem cells. We suggest that normalization of DNA methylation levels could rescue myogenesis and promote regulated muscle growth in muscle contracture and thus may represent a new nonsurgical approach to treating this devastating neuromuscular condition.
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Affiliation(s)
| | | | | | | | - Ryan B Embry
- NUseq Core, Northwestern University, Chicago, Illinois, USA
| | - Vineeta T Swaroop
- Shirley Ryan AbilityLab, Chicago, Illinois, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Henry G Chambers
- Rady Children's Hospital and Health Center, San Diego, California, USA
| | - Matthew J Schipma
- Rady Children's Hospital and Health Center, San Diego, California, USA
| | - Richard L Lieber
- Shirley Ryan AbilityLab, Chicago, Illinois, USA.,Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, Illinois, USA.,Hines VA Medical Center, Maywood, Illinois, USA
| | - Andrea A Domenighetti
- Shirley Ryan AbilityLab, Chicago, Illinois, USA.,Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, Illinois, USA
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4
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Diddens J, Coussement L, Frankl-Vilches C, Majumdar G, Steyaert S, Ter Haar SM, Galle J, De Meester E, De Keulenaer S, Van Criekinge W, Cornil CA, Balthazart J, Van Der Linden A, De Meyer T, Vanden Berghe W. DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon. Front Cell Dev Biol 2021; 9:583555. [PMID: 33816458 PMCID: PMC8017237 DOI: 10.3389/fcell.2021.583555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Song learning in zebra finches (Taeniopygia guttata) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2, AR, and FOS) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.
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Affiliation(s)
- Jolien Diddens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Louis Coussement
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gaurav Majumdar
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sandra Steyaert
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Sita M Ter Haar
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jeroen Galle
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sarah De Keulenaer
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Charlotte A Cornil
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jacques Balthazart
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Annemie Van Der Linden
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim De Meyer
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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5
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Wang J, Xiao M, Wang J, Wang S, Zhang J, Guo Y, Tang Y, Gu J. NRF2-Related Epigenetic Modifications in Cardiac and Vascular Complications of Diabetes Mellitus. Front Endocrinol (Lausanne) 2021; 12:598005. [PMID: 34248833 PMCID: PMC8269153 DOI: 10.3389/fendo.2021.598005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
Diabetes mellitus (DM) is a highly prevalent chronic disease that is accompanied with serious complications, especially cardiac and vascular complications. Thus, there is an urgent need to identify new strategies to treat diabetic cardiac and vascular complications. Nuclear factor erythroid 2-related factor 2 (NRF2) has been verified as a crucial target for the prevention and treatment of diabetic complications. The function of NRF2 in the treatment of diabetic complications has been widely reported, but the role of NRF2-related epigenetic modifications remains unclear. The purpose of this review is to summarize the recent advances in targeting NRF2-related epigenetic modifications in the treatment of cardiac and vascular complications associated with DM. We also discuss agonists that could potentially regulate NRF2-associated epigenetic mechanisms. This review provides a better understanding of strategies to target NRF2 to protect against DM-related cardiac and vascular complications.
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Affiliation(s)
- Jie Wang
- School of Nursing, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Mengjie Xiao
- School of Nursing, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Wang
- School of Nursing, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shudong Wang
- Department of Cardiology, The First Hospital of Jilin University, Changchun, China
| | - Jingjing Zhang
- Department of Cardiology, The First Hospital of China Medical University, and Department of Cardiology at the People’s Hospital of Liaoning Province, Shenyang, China
| | - Yuanfang Guo
- School of Nursing, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yufeng Tang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Junlian Gu
- School of Nursing, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Junlian Gu,
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6
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Yin L, Banerjee S, Fan J, He J, Lu X, Xie H. Epigenetic regulation of neuronal cell specification inferred with single cell "Omics" data. Comput Struct Biotechnol J 2020; 18:942-952. [PMID: 32368329 PMCID: PMC7184133 DOI: 10.1016/j.csbj.2020.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
The brain is a highly complex organ consisting of numerous types of cells with ample diversity at the epigenetic level to achieve distinct gene expression profiles. During neuronal cell specification, transcription factors (TFs) form regulatory modules with chromatin remodeling proteins to initiate the cascade of epigenetic changes. Currently, little is known about brain epigenetic regulatory modules and how they regulate gene expression in a cell-type specific manner. To infer TFs involved in neuronal specification, we applied a recursive motif search approach on the differentially methylated regions identified from single-cell methylomes. The epigenetic transcription regulatory modules (ETRM), including EGR1 and MEF2C, were predicted and the co-expression of TFs in ETRMs were examined with RNA-seq data from single or sorted brain cells using a conditional probability matrix. Lastly, computational predications were validated with EGR1 ChIP-seq data. In addition, methylome and RNA-seq data generated from Egr1 knockout mice supported the essential role of EGR1 in brain epigenome programming, in particular for excitatory neurons. In summary, we demonstrated that brain single cell methylome and RNA-seq data can be integrated to gain a better understanding of how ETRMs control cell specification. The analytical pipeline implemented in this study is freely accessible in the Github repository (https://github.com/Gavin-Yinld/brain_TF).
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Affiliation(s)
- Liduo Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Sharmi Banerjee
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA 24061, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jiayi Fan
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jianlin He
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Hehuang Xie
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA.,School of Neuroscience, Blacksburg, VA, 24061, USA
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