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Martini D, Digregorio M, Voto IAP, Morabito G, Degl'Innocenti A, Giudetti G, Giannaccini M, Andreazzoli M. Kdm7a expression is spatiotemporally regulated in developing Xenopus laevis embryos, and its overexpression influences late retinal development. Dev Dyn 2024; 253:508-518. [PMID: 37909656 DOI: 10.1002/dvdy.670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Post-translational histone modifications are among the most common epigenetic modifications that orchestrate gene expression, playing a pivotal role during embryonic development and in various pathological conditions. Among histone lysine demethylases, KDM7A, also known as KIAA1718 or JHDM1D, catalyzes the demethylation of H3K9me1/2 and H3K27me1/2, leading to transcriptional regulation. Previous data suggest that KDM7A plays a central role in several biological processes, including cell proliferation, commitment, differentiation, apoptosis, and maintenance. However, information on the expression pattern of KDM7A in whole organisms is limited, and its functional role is still unclear. RESULTS In Xenopus development, kdm7a is expressed early, undergoing spatiotemporal regulation in various organs and tissues, including the central nervous system and the eye. Focusing on retinal development, we found that kdm7a overexpression does not affect the expression of genes critically involved in early neural development and eye-field specification, whereas unbalances the distribution of neural cell subtypes in the mature retina by disfavoring the development of ganglion cells while promoting that of horizontal cells. CONCLUSIONS Kdm7a is dynamically expressed during embryonic development, and its overexpression influences late retinal development, suggesting a potential involvement in the molecular machinery regulating the spatiotemporally ordered generation of retinal neuronal subtypes.
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Pinto TS, Feltran GDS, Fernandes CJDC, de Camargo Andrade AF, Coque ADC, Silva SL, Abuderman AA, Zambuzzi WF, Foganholi da Silva RA. Epigenetic changes in shear-stressed endothelial cells. Cell Biol Int 2024; 48:665-681. [PMID: 38420868 DOI: 10.1002/cbin.12138] [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: 03/19/2023] [Revised: 01/18/2024] [Accepted: 01/28/2024] [Indexed: 03/02/2024]
Abstract
Epigenetic changes, particularly histone compaction modifications, have emerged as critical regulators in the epigenetic pathway driving endothelial cell phenotype under constant exposure to laminar forces induced by blood flow. However, the underlying epigenetic mechanisms governing endothelial cell behavior in this context remain poorly understood. To address this knowledge gap, we conducted in vitro experiments using human umbilical vein endothelial cells subjected to various tensional forces simulating pathophysiological blood flow shear stress conditions, ranging from normotensive to hypertensive forces. Our study uncovers a noteworthy observation wherein endothelial cells exposed to high shear stress demonstrate a decrease in the epigenetic marks H3K4ac and H3K27ac, accompanied by significant alterations in the levels of HDAC (histone deacetylase) proteins. Moreover, we demonstrate a negative regulatory effect of increased shear stress on HOXA13 gene expression and a concomitant increase in the expression of the long noncoding RNA, HOTTIP, suggesting a direct association with the suppression of HOXA13. Collectively, these findings represent the first evidence of the role of histone-related epigenetic modifications in modulating chromatin compaction during mechanosignaling of endothelial cells in response to elevated shear stress forces. Additionally, our results highlight the importance of understanding the physiological role of HOXA13 in vascular biology and hypertensive patients, emphasizing the potential for developing small molecules to modulate its activity. These findings warrant further preclinical investigations and open new avenues for therapeutic interventions targeting epigenetic mechanisms in hypertensive conditions.
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Affiliation(s)
- Thaís Silva Pinto
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Geórgia da Silva Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Célio Júnior da C Fernandes
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Amanda Fantini de Camargo Andrade
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Alex de Camargo Coque
- Epigenetic Study Center and Gene Regulation-CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
| | - Simone L Silva
- School of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
| | - Abdulwahab A Abuderman
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Riyadh, Saudi Arabia
| | - Willian F Zambuzzi
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, Paulista State University-UNESP, Botucatu, São Paulo, Brazil
| | - Rodrigo A Foganholi da Silva
- Epigenetic Study Center and Gene Regulation-CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
- School of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
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3
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Zareifar P, Ahmed HM, Ghaderi P, Farahmand Y, Rahnama N, Esbati R, Moradi A, Yazdani O, Sadeghipour Y. miR-142-3p/5p role in cancer: From epigenetic regulation to immunomodulation. Cell Biochem Funct 2024; 42:e3931. [PMID: 38379239 DOI: 10.1002/cbf.3931] [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: 12/01/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
MicroRNAs (miRNAs) play critical roles in cancer pathobiology, acting as regulators of gene expression and pivotal drivers of tumorigenesis. It is believed that miRNAs act through canonical mechanisms, involving the binding of mature miRNAs to target messenger RNAs (mRNAs) and subsequent repression of protein translation or degradation of target mRNAs. miR-142-3p/5p has been extensively studied and established as a key regulator in various malignancies. Recent discoveries have revealed miR-142-3p/5p serve as either oncogene or tumor suppressor in cancer. By targeting epigenetic factor and cancer-related signaling pathway, miR-142-3p/5p can regulate wide range of downstream genes. The immune modulatory role of miR-142-3p/5p has been shown in various cancers, which provides significant insight into immunosuppression and tumor escape from the immune response. Exosomes with miR-142-3p/5p facilitate cell communication and can affect cancer cell behavior, offering potential therapeutic, and diagnosis applications in cancer therapy. In this review, for the first time, we comprehensively summarize the current knowledge regarding mentioned functions of miR-142-3p/5p in cancer pathobiology.
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Affiliation(s)
- Parisa Zareifar
- Golestan University of Medical Science, Gorgan, Golestan, Iran
| | | | - Pouya Ghaderi
- Department of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Yalda Farahmand
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Negin Rahnama
- Department of Internal Medicine and Health Services, Semnan University of Medical Sciences, Semnan, Iran
| | - Romina Esbati
- Department of Medicine, Shahid Beheshti University, Tehran, Iran
| | - Ali Moradi
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Yazdani
- Department of Medicine, Shahid Beheshti University, Tehran, Iran
| | - Yasin Sadeghipour
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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4
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Bokor S, Csölle I, Felső R, Vass RA, Funke S, Ertl T, Molnár D. Dietary nutrients during gestation cause obesity and related metabolic changes by altering DNA methylation in the offspring. Front Endocrinol (Lausanne) 2024; 15:1287255. [PMID: 38449848 PMCID: PMC10916691 DOI: 10.3389/fendo.2024.1287255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
Growing evidence shows that maternal nutrition from preconception until lactation has an important effect on the development of non-communicable diseases in the offspring. Biological responses to environmental stress during pregnancy, including undernutrition or overnutrition of various nutrients, are transmitted in part by DNA methylation. The aim of the present narrative review is to summarize literature data on altered DNA methylation patterns caused by maternal macronutrient or vitamin intake and its association with offspring's phenotype (obesity and related metabolic changes). With our literature search, we found evidence for the association between alterations in DNA methylation pattern of different genes caused by maternal under- or overnutrition of several nutrients (protein, fructose, fat, vitamin D, methyl-group donor nutrients) during 3 critical periods of programming (preconception, pregnancy, lactation) and the development of obesity or related metabolic changes (glucose, insulin, lipid, leptin, adiponectin levels, blood pressure, non-alcoholic fatty liver disease) in offspring. The review highlights that maternal consumption of several nutrients could individually affect the development of offspring's obesity and related metabolic changes via alterations in DNA methylation.
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Affiliation(s)
- Szilvia Bokor
- Department of Paediatrics, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
| | - Ildikó Csölle
- Department of Paediatrics, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Regina Felső
- Department of Paediatrics, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
| | - Réka A. Vass
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
- Department of Obstetrics and Gynaecology, Medical School, University of Pécs, Pécs, Hungary
- Obstetrics and Gynecology, Magyar Imre Hospital Ajka, Ajka, Hungary
| | - Simone Funke
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
- Department of Obstetrics and Gynaecology, Medical School, University of Pécs, Pécs, Hungary
| | - Tibor Ertl
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
- Department of Obstetrics and Gynaecology, Medical School, University of Pécs, Pécs, Hungary
| | - Dénes Molnár
- Department of Paediatrics, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory on Human Reproduction, University of Pécs, Pécs, Hungary
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Dashti P, Lewallen EA, Gordon JA, Montecino MA, van Leeuwen JP, Stein GS, van der Eerden BC, Davie JR, van Wijnen AJ. Protein arginine methyltransferases PRMT1, PRMT4/CARM1 and PRMT5 have distinct functions in control of osteoblast differentiation. Bone Rep 2023; 19:101704. [PMID: 37593409 PMCID: PMC10430181 DOI: 10.1016/j.bonr.2023.101704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Osteogenic differentiation of mesenchymal cells is controlled by epigenetic enzymes that regulate post-translational modifications of histones. Compared to acetyl or methyltransferases, the physiological functions of protein arginine methyltransferases (PRMTs) in osteoblast differentiation remain minimally understood. Therefore, we surveyed the expression and function of all nine mammalian PRMT members during osteoblast differentiation. RNA-seq gene expression profiling shows that Prmt1, Prmt4/Carm1 and Prmt5 represent the most prominently expressed PRMT subtypes in mouse calvarial bone and MC3T3 osteoblasts as well as human musculoskeletal tissues and mesenchymal stromal cells (MSCs). Based on effects of siRNA depletion, it appears that PRMT members have different functional effects: (i) loss of Prmt1 stimulates and (ii) loss of Prmt5 decreases calcium deposition of mouse MC3T3 osteoblasts, while (iii) loss of Carm1 is inconsequential for calcium deposition. Decreased Prmt5 suppresses expression of multiple genes involved in mineralization (e.g., Alpl, Ibsp, Phospho1) consistent with a positive role in osteogenesis. Depletion of Prmt1, Carm1 and Prmt5 has intricate but modest time-dependent effects on the expression of a panel of osteoblast differentiation and proliferation markers but does not change mRNA levels for select epigenetic regulators (e.g., Ezh1, Ezh2, Brd2 and Brd4). Treatment with the Class I PRMT inhibitor GSK715 enhances extracellular matrix mineralization of MC3T3 cells, while blocking formation of H3R17me2a but not H4R3me2a marks. In sum, Prmt1, Carm1 and Prmt5 have distinct biological roles during osteoblast differentiation, and different types histone H3 and H4 arginine methylation may contribute to the chromatin landscape during osteoblast differentiation.
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Affiliation(s)
- Parisa Dashti
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | | | - Martin A. Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | | | - Gary S. Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Bram C.J. van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands
| | - James R. Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada
| | - Andre J. van Wijnen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
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Mehmood A, Shah S, Guo RY, Haider A, Shi M, Ali H, Ali I, Ullah R, Li B. Methyl-CpG-Binding Protein 2 Emerges as a Central Player in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorders. Cell Mol Neurobiol 2023; 43:4071-4101. [PMID: 37955798 DOI: 10.1007/s10571-023-01432-7] [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: 08/27/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
MECP2 and its product methyl-CpG binding protein 2 (MeCP2) are associated with multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD), which are inflammatory, autoimmune, and demyelinating disorders of the central nervous system (CNS). However, the mechanisms and pathways regulated by MeCP2 in immune activation in favor of MS and NMOSD are not fully understood. We summarize findings that use the binding properties of MeCP2 to identify its targets, particularly the genes recognized by MeCP2 and associated with several neurological disorders. MeCP2 regulates gene expression in neurons, immune cells and during development by modulating various mechanisms and pathways. Dysregulation of the MeCP2 signaling pathway has been associated with several disorders, including neurological and autoimmune diseases. A thorough understanding of the molecular mechanisms underlying MeCP2 function can provide new therapeutic strategies for these conditions. The nervous system is the primary system affected in MeCP2-associated disorders, and other systems may also contribute to MeCP2 action through its target genes. MeCP2 signaling pathways provide promise as potential therapeutic targets in progressive MS and NMOSD. MeCP2 not only increases susceptibility and induces anti-inflammatory responses in immune sites but also leads to a chronic increase in pro-inflammatory cytokines gene expression (IFN-γ, TNF-α, and IL-1β) and downregulates the genes involved in immune regulation (IL-10, FoxP3, and CX3CR1). MeCP2 may modulate similar mechanisms in different pathologies and suggest that treatments for MS and NMOSD disorders may be effective in treating related disorders. MeCP2 regulates gene expression in MS and NMOSD. However, dysregulation of the MeCP2 signaling pathway is implicated in these disorders. MeCP2 plays a role as a therapeutic target for MS and NMOSD and provides pathways and mechanisms that are modulated by MeCP2 in the regulation of gene expression.
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Affiliation(s)
- Arshad Mehmood
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Suleman Shah
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Ruo-Yi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Arsalan Haider
- Key Lab of Health Psychology, Institute of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Mengya Shi
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
| | - Ijaz Ali
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Hawally, 32093, Kuwait
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Center, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China.
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China.
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Chen Y, Wu XL, Hu HB, Yang SN, Zhang ZY, Fu GL, Zhang CT, Li ZM, Wu F, Si KW, Ma YB, Ji SF, Zhou JS, Ren XY, Xiao XL, Liu JX. Neuronal MeCP2 in the dentate gyrus regulates mossy fiber sprouting of mice with temporal lobe epilepsy. Neurobiol Dis 2023; 188:106346. [PMID: 37931884 DOI: 10.1016/j.nbd.2023.106346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023] Open
Abstract
Sprouting of mossy fibers, one of the most consistent findings in tissue from patients with mesial temporal lobe epilepsy, exhibits several uncommon axonal growth features and has been considered a paradigmatic example of circuit plasticity that occurs in the adult brain. Clarifying the mechanisms responsible may provide new insight into epileptogenesis as well as axon misguidance in the central nervous system. Methyl-CpG-binding protein 2 (MeCP2) binds to methylated genomic DNA to regulate a range of physiological functions implicated in neuronal development and adult synaptic plasticity. However, exploring the potential role of MeCP2 in the documented misguidance of axons in the dentate gyrus has not yet been attempted. In this study, a status epilepticus-induced decrease of neuronal MeCP2 was observed in the dentate gyrus (DG). An essential regulatory role of MeCP2 in the development of functional mossy fiber sprouting (MFS) was confirmed through stereotaxic injection of a recombinant adeno-associated virus (AAV) to up- or down-regulate MeCP2 in the dentate neurons. Chromatin immunoprecipitation sequencing (ChIP-seq) was performed to identify the binding profile of native MeCP2 using micro-dissected dentate tissues. In both dentate tissues and HT22 cell lines, we demonstrated that MeCP2 could act as a transcription repressor on miR-682 with the involvement of the DNA methylation mechanism. Further, we found that miR-682 could bind to mRNA of phosphatase and tensin homolog (PTEN) in a sequence specific manner, thus leading to the suppression of PTEN and excessive activation of mTOR. This study therefore presents a novel epigenetic mechanism by identifying MeCP2/miR-682/PTEN/mTOR as an essential signal pathway in regulating the formation of MFS in the temporal lobe epileptic (TLE) mice. SIGNIFICANCE STATEMENT: Understanding the mechanisms that regulate axon guidance is important for a better comprehension of neural disorders. Sprouting of mossy fibers, one of the most consistent findings in patients with mesial temporal lobe epilepsy, has been considered a paradigmatic example of circuit plasticity in the adult brain. Although abnormal regulation of DNA methylation has been observed in both experimental rodents and humans with epilepsy, the potential role of DNA methylation in this well-documented example of sprouting of dentate axon remains elusive. This study demonstrates an essential role of methyl-CpG-binding protein 2 in the formation of mossy fiber sprouting. The underlying signal pathway has been also identified. The data hence provide new insight into epileptogenesis as well as axon misguidance in the central nervous system.
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Affiliation(s)
- Yu Chen
- Institute of Neurobiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City 710061, China
| | - Xiao-Lin Wu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China
| | - Hai-Bo Hu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China
| | - Shu-Nan Yang
- Institute of Neurobiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City 710061, China
| | - Zi-Yi Zhang
- Institute of Neurobiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City 710061, China
| | - Guan-Ling Fu
- Institute of Neurobiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City 710061, China
| | - Chu-Tong Zhang
- Qide College, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Zi-Meng Li
- Zonglian College, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Feng Wu
- Center of Teaching and Experiment for Medical Postgraduates, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an 710061, China
| | - Kai-Wei Si
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an 710061, China
| | - Yan-Bing Ma
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China
| | - Sheng-Feng Ji
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China
| | - Jin-Song Zhou
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China
| | - Xiao-Yong Ren
- Department of Otolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Xin-Li Xiao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China.
| | - Jian-Xin Liu
- Institute of Neurobiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City, 710061, China; Institute of Neuroscience, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an City 710061, China.
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8
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Arshavsky YI. Memory: Synaptic or Cellular, That Is the Question. Neuroscientist 2023; 29:538-553. [PMID: 35713238 DOI: 10.1177/10738584221086488] [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] [Indexed: 11/17/2022]
Abstract
According to the commonly accepted opinion, memory engrams are formed and stored at the level of neural networks due to a change in the strength of synaptic connections between neurons. This hypothesis of synaptic plasticity (HSP), formulated by Donald Hebb in the 1940s, continues to dominate the directions of experimental studies and the interpretations of experimental results in the field. The universal acceptance of the HSP has transformed it from a hypothesis into an incontrovertible theory. In this article, I show that the entire body of experimental and clinical data obtained in studies of long-term memory in mammals and humans is inconsistent with the HSP. Instead, these data suggest that long-term memory is formed and stored at the intracellular level where it is reliably protected from ongoing synaptic activity, including pathological epileptic activity. It seems that the generally accepted HSP became a serious obstacle to understanding the mechanisms of memory and that progress in this field requires rethinking this doctrine and shifting experimental efforts toward exploring the intracellular mechanisms.
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Affiliation(s)
- Yuri I Arshavsky
- BioCircuits Institute, University of California San Diego, La Jolla, CA, USA
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9
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Zhang Y, Yang H, Jiang M, Nie X. Exploring the pathogenesis and treatment of IgA nephropathy based on epigenetics. Epigenomics 2023; 15:1017-1026. [PMID: 37909120 DOI: 10.2217/epi-2023-0318] [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] [Indexed: 11/02/2023] Open
Abstract
IgA nephropathy is the most common primary glomerulonephritis worldwide. However, its exact cause remains unclear, with known genetic factors explaining only 11% of the variation. Recently, researchers have turned their attention to epigenetic abnormalities in immune-related diseases, recognizing their significance in IgA nephropathy's development and progression. This emerging field has revolutionized our understanding of epigenetics in IgA nephropathy research. Though in its early stages, studying IgA nephropathy's epigenetics holds promise for unraveling its pathogenesis and identifying new biomarkers and therapies. This review aims to comprehensively analyze epigenetics' role in IgA nephropathy's development and suggest avenues for potential therapeutic interventions. In the future, assessing and modulating epigenetics may become integral in diagnosing, tailoring treatments and assessing prognoses for IgA nephropathy.
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Affiliation(s)
- Yunfan Zhang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Huanhuan Yang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Ming Jiang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
| | - Xiaojing Nie
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350025, China
- Department of Pediatrics, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, 350025, China
- Department of Pediatrics, Affiliated Dongfang Hospital, Xiamen University, Fuzhou, 350025, China
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10
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Sun D, Ding Z, Hai Y, Cheng Y. Advances in epigenetic research of adolescent idiopathic scoliosis and congenital scoliosis. Front Genet 2023; 14:1211376. [PMID: 37564871 PMCID: PMC10411889 DOI: 10.3389/fgene.2023.1211376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
Scoliosis is a three-dimensional structural deformity of the spine; more than 80% of scoliosis has no specific pathogenesis but is understood to be closely related to genetic, hormonal, and environmental factors. In recent years, the epigenetic alterations observed in scoliosis have been analyzed in numerous studies to determine the pathogenesis and progression of this condition, however, there is currently no comprehensive review of the epigenetic factors to date. We searched PubMed, Embase, and Web of Science databases for relative studies without language and date restrictions in March 2023. Twenty-five studies were included in this review and analyzed from the four main aspects of epigenetic alteration: DNA methylation, non-coding RNAs, histone modifications, and chromatin remodeling. The relationship between DNA methylation, non-coding RNAs, and scoliosis was considerably reported in the literature, and the corresponding related signaling pathways and novel biomarkers observed in scoliosis provide insights into innovative prevention and treatment strategies. However, the role of histone modifications is rarely reported in scoliosis, and few studies have investigated the relationship between scoliosis and chromatin remodeling. Therefore, these related fields need to be further explored to elucidate the overall effects of epigenetics in scoliosis.
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Affiliation(s)
| | | | - Yong Hai
- Department of Orthopedic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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11
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Vuu YM, Kadar Shahib A, Rastegar M. The Potential Therapeutic Application of Simvastatin for Brain Complications and Mechanisms of Action. Pharmaceuticals (Basel) 2023; 16:914. [PMID: 37513826 PMCID: PMC10385015 DOI: 10.3390/ph16070914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Statins are common drugs that are clinically used to reduce elevated plasma cholesterol levels. Based on their solubility, statins are considered to be either hydrophilic or lipophilic. Amongst them, simvastatin has the highest lipophilicity to facilitate its ability to cross the blood-brain barrier. Recent studies have suggested that simvastatin could be a promising therapeutic option for different brain complications and diseases ranging from brain tumors (i.e., medulloblastoma and glioblastoma) to neurological disorders (i.e., Alzheimer's disease, Parkinson's disease, and Huntington's disease). Specific mechanisms of disease amelioration, however, are still unclear. Independent studies suggest that simvastatin may reduce the risk of developing certain neurodegenerative disorders. Meanwhile, other studies point towards inducing cell death in brain tumor cell lines. In this review, we outline the potential therapeutic effects of simvastatin on brain complications and review the clinically relevant molecular mechanisms in different cases.
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Affiliation(s)
| | | | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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12
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Sattarifard H, Safaei A, Khazeeva E, Rastegar M, Davie JR. Mitogen- and stress-activated protein kinase (MSK1/2) regulated gene expression in normal and disease states. Biochem Cell Biol 2023; 101:204-219. [PMID: 36812480 DOI: 10.1139/bcb-2022-0371] [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] [Indexed: 02/24/2023] Open
Abstract
The mitogen- and stress-activated protein kinases (MSK) are epigenetic modifiers that regulate gene expression in normal and disease cell states. MSK1 and 2 are involved in a chain of signal transduction events bringing signals from the external environment of a cell to specific sites in the genome. MSK1/2 phosphorylate histone H3 at multiple sites, resulting in chromatin remodeling at regulatory elements of target genes and the induction of gene expression. Several transcription factors (RELA of NF-κB and CREB) are also phosphorylated by MSK1/2 and contribute to induction of gene expression. In response to signal transduction pathways, MSK1/2 can stimulate genes involved in cell proliferation, inflammation, innate immunity, neuronal function, and neoplastic transformation. Abrogation of the MSK-involved signaling pathway is among the mechanisms by which pathogenic bacteria subdue the host's innate immunity. Depending on the signal transduction pathways in play and the MSK-targeted genes, MSK may promote or hinder metastasis. Thus, depending on the type of cancer and genes involved, MSK overexpression may be a good or poor prognostic factor. In this review, we focus on mechanisms by which MSK1/2 regulate gene expression, and recent studies on their roles in normal and diseased cells.
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Affiliation(s)
- Hedieh Sattarifard
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Akram Safaei
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Enzhe Khazeeva
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
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13
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Nguyen-Vo TH, Trinh QH, Nguyen L, Nguyen-Hoang PU, Rahardja S, Nguyen BP. i4mC-GRU: Identifying DNA N 4-Methylcytosine sites in mouse genomes using bidirectional gated recurrent unit and sequence-embedded features. Comput Struct Biotechnol J 2023; 21:3045-3053. [PMID: 37273848 PMCID: PMC10238585 DOI: 10.1016/j.csbj.2023.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 06/06/2023] Open
Abstract
N4-methylcytosine (4mC) is one of the most common DNA methylation modifications found in both prokaryotic and eukaryotic genomes. Since the 4mC has various essential biological roles, determining its location helps reveal unexplored physiological and pathological pathways. In this study, we propose an effective computational method called i4mC-GRU using a gated recurrent unit and duplet sequence-embedded features to predict potential 4mC sites in mouse (Mus musculus) genomes. To fairly assess the performance of the model, we compared our method with several state-of-the-art methods using two different benchmark datasets. Our results showed that i4mC-GRU achieved area under the receiver operating characteristic curve values of 0.97 and 0.89 and area under the precision-recall curve values of 0.98 and 0.90 on the first and second benchmark datasets, respectively. Briefly, our method outperformed existing methods in predicting 4mC sites in mouse genomes. Also, we deployed i4mC-GRU as an online web server, supporting users in genomics studies.
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Affiliation(s)
- Thanh-Hoang Nguyen-Vo
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
- School of Innovation, Design and Technology, Wellington Institute of Technology, Wellington 5012, New Zealand
| | - Quang H. Trinh
- School of Information and Communication Technology, Hanoi University of Science and Technology, Hanoi 100000, Vietnam
| | - Loc Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Phuong-Uyen Nguyen-Hoang
- Computational Biology Center, International University - VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Susanto Rahardja
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi’an 710072, China
- Infocomm Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore
| | - Binh P. Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
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14
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Nejati-Koshki K, Roberts CT, Babaei G, Rastegar M. The Epigenetic Reader Methyl-CpG-Binding Protein 2 (MeCP2) Is an Emerging Oncogene in Cancer Biology. Cancers (Basel) 2023; 15:2683. [PMID: 37345019 DOI: 10.3390/cancers15102683] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic mechanisms are gene regulatory processes that control gene expression and cellular identity. Epigenetic factors include the "writers", "readers", and "erasers" of epigenetic modifications such as DNA methylation. Accordingly, the nuclear protein Methyl-CpG-Binding Protein 2 (MeCP2) is a reader of DNA methylation with key roles in cellular identity and function. Research studies have linked altered DNA methylation, deregulation of MeCP2 levels, or MECP2 gene mutations to different types of human disease. Due to the high expression level of MeCP2 in the brain, many studies have focused on its role in neurological and neurodevelopmental disorders. However, it is becoming increasingly apparent that MeCP2 also participates in the tumorigenesis of different types of human cancer, with potential oncogenic properties. It is well documented that aberrant epigenetic regulation such as altered DNA methylation may lead to cancer and the process of tumorigenesis. However, direct involvement of MeCP2 with that of human cancer was not fully investigated until lately. In recent years, a multitude of research studies from independent groups have explored the molecular mechanisms involving MeCP2 in a vast array of human cancers that focus on the oncogenic characteristics of MeCP2. Here, we provide an overview of the proposed role of MeCP2 as an emerging oncogene in different types of human cancer.
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Affiliation(s)
- Kazem Nejati-Koshki
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil 85991-56189, Iran
| | - Chris-Tiann Roberts
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Ghader Babaei
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia 57157-89400, Iran
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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15
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Serirukchutarungsee S, Watari I, Narukawa M, Podyma-Inoue KA, Sangsuriyothai P, Ono T. Two-generation exposure to a high-fat diet induces the change of salty taste preference in rats. Sci Rep 2023; 13:5742. [PMID: 37029190 PMCID: PMC10082214 DOI: 10.1038/s41598-023-31662-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/15/2023] [Indexed: 04/09/2023] Open
Abstract
High-fat diet (HFD) leads to multiple complications, including taste alteration. This study observed the effect of a two-generation exposure to an HFD on the peripheral taste system in offspring. Ten pregnant Wistar rats were assigned a standard diet (SD) (n = 5) or HFD (n = 5) from day 7 of pregnancy through the lactation. Thirty-six male and female 3-week-old offspring were measured for body weight and blood glucose level, and the circumvallate papillae were collected. The other twenty-four 3-week-old offspring were weaned on the same diet as their mothers and raised individually. The taste preference behaviors were studied using the two-bottle taste preference test and analyzed five basic tastes (sweet, bitter, umami, sour, and salty). The expressions of epithelial sodium channel alpha subunit (ENaCα) and angiotensin II receptor type 1 (AT1) in the circumvallate papilla were analyzed by immunohistochemical staining and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We found increased body weight and salty taste preference of offspring from the HFD group in both sexes. Correspondingly, the AT1 level of the taste bud cells significantly increased in 3-week-old female offspring from the HFD group. An increase in AT1 levels may be a risk factor for changes in salty taste preference.
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Affiliation(s)
- Saranya Serirukchutarungsee
- Department of Orthodontic Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo City, Tokyo, 113-8510, Japan
- Department of Pedodontics and Preventive Dentistry, Faculty of Dentistry, Srinakharinwirot University, Bangkok, Thailand
| | - Ippei Watari
- Department of Orthodontic Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo City, Tokyo, 113-8510, Japan.
| | - Masataka Narukawa
- Department of Food and Nutrition, Kyoto Women's University, Kyoto, Japan
| | - Katarzyna Anna Podyma-Inoue
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Pornchanok Sangsuriyothai
- Department of Orthodontic Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo City, Tokyo, 113-8510, Japan
- Department of Orthodontics, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Takashi Ono
- Department of Orthodontic Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo City, Tokyo, 113-8510, Japan
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16
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Kohestani H, Wereszczynski J. The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics. Biophys J 2023; 122:1229-1239. [PMID: 36798026 PMCID: PMC10111275 DOI: 10.1016/j.bpj.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 01/22/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Noncoding RNAs (ncRNAs) are an emerging epigenetic factor and have been recognized as playing a key role in many gene expression pathways. Structurally, binding of ncRNAs to isolated DNA is strongly dependent on sequence complementary and results in the formation of an RNA.DNA-DNA (RDD) triple helix. However, in vivo DNA is not isolated but is rather packed in chromatin fibers, the fundamental unit of which is the nucleosome. Biochemical experiments have shown that ncRNA binding to nucleosomal DNA is elevated at DNA entry and exit sites and is dependent on the presence of the H3 N-terminal tails. However, the structural and dynamical bases for these mechanisms remain unknown. Here, we have examined the mechanisms and effects of RDD formation in the context of the nucleosome using a series of all-atom molecular dynamics simulations. Results highlight the importance of DNA sequence on complex stability, elucidate the effects of the H3 tails on RDD structures, show how RDD formation impacts the structure and dynamics of the H3 tails, and show how RNA alters the local and global DNA double-helical structure. Together, our results suggest ncRNAs can modify nucleosome, and potentially higher-order chromatin, structures and dynamics as a means of exerting epigenetic control.
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Affiliation(s)
- Havva Kohestani
- Department of Biology, Illinois Institute of Technology, Chicago, Illinois
| | - Jeff Wereszczynski
- Departments of Physics & Biology, Illinois Institute of Technology, Chicago, Illinois.
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17
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Lo JO, D’Mello RJ, Watch L, Schust DJ, Murphy SK. An epigenetic synopsis of parental substance use. Epigenomics 2023; 15:453-473. [PMID: 37282544 PMCID: PMC10308258 DOI: 10.2217/epi-2023-0064] [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: 02/21/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023] Open
Abstract
The rate of substance use is rising, especially among reproductive-age individuals. Emerging evidence suggests that paternal pre-conception and maternal prenatal substance use may alter offspring epigenetic regulation (changes to gene expression without modifying DNA) and outcomes later in life, including neurodevelopment and mental health. However, relatively little is known due to the complexities and limitations of existing studies, making causal interpretations challenging. This review examines the contributions and influence of parental substance use on the gametes and potential transmissibility to the offspring's epigenome as possible areas to target public health warnings and healthcare provider counseling of individuals or couples in the pre-conception and prenatal periods to ultimately mitigate short- and long-term offspring morbidity and mortality.
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Affiliation(s)
- Jamie O Lo
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; Department of Obstetrics & Gynecology, Maternal Fetal Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rahul J D’Mello
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; Department of Obstetrics & Gynecology, Maternal Fetal Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lester Watch
- Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Danny J Schust
- Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
- Division of Reproductive Endocrinology & Infertility, Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Susan K Murphy
- Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27710, USA
- Division of Reproductive Sciences, Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC 27701, USA; Division of Environmental Sciences & Policy, Duke Nicholas School of the Environment, Duke University, Durham, NC 27708, USA; Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
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18
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Chauhan J, Yoshioka M, Pogash S, Strovel JW, Fletcher S. Discovery and anti-tumor activity of 4-(benzylamino)-6-(3,5-dimethylisoxazol-4-yl)quinoline-2(1H)-one (CG13250), a potent, selective and orally bioavailable BET bromodomain inhibitor. Bioorg Med Chem Lett 2023; 86:129220. [PMID: 36905966 DOI: 10.1016/j.bmcl.2023.129220] [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: 01/14/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
The bromodomain and extra-terminal domain (BET) proteins are epigenetic readers involved in the regulation of gene transcription. Inhibitors of the BET proteins, in particular BRD4, have demonstrated anti-tumour activities and efficacies in clinical trials. Herein, we describe the discovery of potent and selective inhibitors of BRD4, and demonstrate that the lead compound CG13250 is orally bioavailable and efficacious in a mouse xenograft model of leukemia.
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Affiliation(s)
- Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA
| | - Makoto Yoshioka
- ConverGene LLC, 4800 Montgomery Lane, c/o Dreyfuss 10th Floor, Bethesda, MD 20814, USA
| | - Sarah Pogash
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA
| | - Jeffrey W Strovel
- ConverGene LLC, 4800 Montgomery Lane, c/o Dreyfuss 10th Floor, Bethesda, MD 20814, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA; University of Maryland Greenebaum Cancer Center, Baltimore, MD 21201, USA.
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19
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Epigenetic Differences Arise in Endothelial Cells Responding to Cobalt–Chromium. J Funct Biomater 2023; 14:jfb14030127. [PMID: 36976051 PMCID: PMC10052026 DOI: 10.3390/jfb14030127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
Cobalt–chromium (Co-Cr)-based alloys are emerging with important characteristics for use in dentistry, but the knowledge of epigenetic mechanisms in endothelial cells has barely been achieved. In order to address this issue, we have prepared a previously Co-Cr-enriched medium to further treat endothelial cells (HUVEC) for up to 72 h. Our data show there is important involvement with epigenetic machinery. Based on the data, it is believed that methylation balance in response to Co-Cr is finely modulated by DNMTs (DNA methyltransferases) and TETs (Tet methylcytosine dioxygenases), especially DNMT3B and both TET1 and TET2. Additionally, histone compaction HDAC6 (histone deacetylase 6) seems to develop a significant effect in endothelial cells. The requirement of SIRT1 seems to have a crucial role in this scenario. SIRT1 is associated with a capacity to modulate the expression of HIF-1α in response to hypoxia microenvironments, thus presenting a protective effect. As mentioned previously, cobalt is able to prevent HIF1A degradation and maintain hypoxia-related signaling in eukaryotic cells. Together, our results show, for the first time, a descriptive study reporting the relevance of epigenetic machinery in endothelial cells responding to cobalt–chromium, and it opens new perspectives to better understand their repercussions as prerequisites for driving cell adhesion, cell cycle progression, and angiogenesis surrounding this Co-Cr-based implantable device.
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20
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MeCP2 Is an Epigenetic Factor That Links DNA Methylation with Brain Metabolism. Int J Mol Sci 2023; 24:ijms24044218. [PMID: 36835623 PMCID: PMC9966807 DOI: 10.3390/ijms24044218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
DNA methylation, one of the most well-studied epigenetic modifications, is involved in a wide spectrum of biological processes. Epigenetic mechanisms control cellular morphology and function. Such regulatory mechanisms involve histone modifications, chromatin remodeling, DNA methylation, non-coding regulatory RNA molecules, and RNA modifications. One of the most well-studied epigenetic modifications is DNA methylation that plays key roles in development, health, and disease. Our brain is probably the most complex part of our body, with a high level of DNA methylation. A key protein that binds to different types of methylated DNA in the brain is the methyl-CpG binding protein 2 (MeCP2). MeCP2 acts in a dose-dependent manner and its abnormally high or low expression level, deregulation, and/or genetic mutations lead to neurodevelopmental disorders and aberrant brain function. Recently, some of MeCP2-associated neurodevelopmental disorders have emerged as neurometabolic disorders, suggesting a role for MeCP2 in brain metabolism. Of note, MECP2 loss-of-function mutation in Rett Syndrome is reported to cause impairment of glucose and cholesterol metabolism in human patients and/or mouse models of disease. The purpose of this review is to outline the metabolic abnormalities in MeCP2-associated neurodevelopmental disorders that currently have no available cure. We aim to provide an updated overview into the role of metabolic defects associated with MeCP2-mediated cellular function for consideration of future therapeutic strategies.
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21
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Idriss S, Hallal M, El-Kurdi A, Zalzali H, El-Rassi I, Ehli EA, Davis CM, Chung PED, Gendoo DMA, Zacksenhaus E, Saab R, Khoueiry P. A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements. Genome Res 2023; 33:269-282. [PMID: 36650051 PMCID: PMC10069464 DOI: 10.1101/gr.277037.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Pediatric pineoblastomas (PBs) are rare and aggressive tumors of grade IV histology. Although some oncogenic drivers are characterized, including germline mutations in RB1 and DICER1, the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated genome-wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible genome dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac signal become enriched for repressive state elements and harbor motifs of repressor transcription factors like HINFP, GLI2, and YY1. Copy number variant analysis identified deletion events specific to the tumorigenic stage, affecting, among others, the histone gene cluster and Gas1, the growth arrest specific gene. Gene set enrichment analysis and gene expression signatures positioned the model used here close to human PB samples, showing the potential of our findings for exploring new avenues in PB management and therapy. Overall, this study reports the first temporal and in vivo cis-regulatory, expression, and accessibility maps in PB.
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Affiliation(s)
- Salam Idriss
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mohammad Hallal
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Hasan Zalzali
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Inaam El-Rassi
- Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Christel M Davis
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Philip E D Chung
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, United Kingdom
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Raya Saab
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; .,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
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22
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Epigenetics and Metabolism Reprogramming Interplay into Glioblastoma: Novel Insights on Immunosuppressive Mechanisms. Antioxidants (Basel) 2023; 12:antiox12020220. [PMID: 36829778 PMCID: PMC9952003 DOI: 10.3390/antiox12020220] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
The central nervous system represents a complex environment in which glioblastoma adapts skillfully, unleashing a series of mechanisms suitable for its efficient development and diffusion. In particular, changes in gene expression and mutational events that fall within the domain of epigenetics interact complexly with metabolic reprogramming and stress responses enacted in the tumor microenvironment, which in turn fuel genomic instability by providing substrates for DNA modifications. The aim of this review is to analyze this complex interaction that consolidates several conditions that confer a state of immunosuppression and immunoevasion, making glioblastoma capable of escaping attack and elimination by immune cells and therefore invincible against current therapies. The progressive knowledge of the cellular mechanisms that underlie the resistance of the glioblastoma represents, in fact, the only weapon to unmask its weak points to be exploited to plan successful therapeutic strategies.
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Mishra S, Raval M, Kachhawaha AS, Tiwari BS, Tiwari AK. Aging: Epigenetic modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:171-209. [PMID: 37019592 DOI: 10.1016/bs.pmbts.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Aging is one of the most complex and irreversible health conditions characterized by continuous decline in physical/mental activities that eventually poses an increased risk of several diseases and ultimately death. These conditions cannot be ignored by anyone but there are evidences that suggest that exercise, healthy diet and good routines may delay the Aging process significantly. Several studies have demonstrated that Epigenetics plays a key role in Aging and Aging-associated diseases through methylation of DNA, histone modification and non-coding RNA (ncRNA). Comprehension and relevant alterations in these epigenetic modifications can lead to new therapeutic avenues of age-delaying contrivances. These processes affect gene transcription, DNA replication and DNA repair, comprehending epigenetics as a key factor in understanding Aging and developing new avenues for delaying Aging, clinical advancements in ameliorating aging-related diseases and rejuvenating health. In the present article, we have described and advocated the epigenetic role in Aging and associated diseases.
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Shevkoplyas D, Vuu YM, Davie JR, Rastegar M. The Chromatin Structure at the MECP2 Gene and In Silico Prediction of Potential Coding and Non-Coding MECP2 Splice Variants. Int J Mol Sci 2022; 23:ijms232415643. [PMID: 36555295 PMCID: PMC9779294 DOI: 10.3390/ijms232415643] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) is an epigenetic reader that binds to methylated CpG dinucleotides and regulates gene transcription. Mecp2/MECP2 gene has 4 exons, encoding for protein isoforms MeCP2E1 and MeCP2E2. MeCP2 plays key roles in neurodevelopment, therefore, its gain- and loss-of-function mutations lead to neurodevelopmental disorders including Rett Syndrome. Here, we describe the structure, functional domains, and evidence support for potential additional alternatively spliced MECP2 transcripts and protein isoforms. We conclude that NCBI MeCP2 isoforms 3 and 4 contain certain MeCP2 functional domains. Our in silico analysis led to identification of histone modification and accessibility profiles at the MECP2 gene and its cis-regulatory elements. We conclude that the human MECP2 gene associated histone post-translational modifications exhibit high similarity between males and females. Between brain regions, histone modifications were found to be less conserved and enriched within larger genomic segments named as "S1-S11". We also identified highly conserved DNA accessibility regions in different tissues and brain regions, named as "A1-A9" and "B1-B9". DNA methylation profile was similar between mid-frontal gyrus of donors 35 days-25 years of age. Based on ATAC-seq data, the identified hypomethylated regions "H1-H8" intersected with most regions of the accessible chromatin (A regions).
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Anderson EM, Taniguchi M. Epigenetic Effects of Addictive Drugs in the Nucleus Accumbens. Front Mol Neurosci 2022; 15:828055. [PMID: 35813068 PMCID: PMC9260254 DOI: 10.3389/fnmol.2022.828055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/30/2022] [Indexed: 12/28/2022] Open
Abstract
Substance use induces long-lasting behavioral changes and drug craving. Increasing evidence suggests that epigenetic gene regulation contributes to the development and expression of these long-lasting behavioral alterations. Here we systematically review extensive evidence from rodent models of drug-induced changes in epigenetic regulation and epigenetic regulator proteins. We focus on histone acetylation and histone methylation in a brain region important for drug-related behaviors: the nucleus accumbens. We also discuss how experimentally altering these epigenetic regulators via systemically administered compounds or nucleus accumbens-specific manipulations demonstrate the importance of these proteins in the behavioral effects of drugs and suggest potential therapeutic value to treat people with substance use disorder. Finally, we discuss limitations and future directions for the field of epigenetic studies in the behavioral effects of addictive drugs and suggest how to use these insights to develop efficacious treatments.
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Orozco G, Gupta M, Gedaly R, Marti F. Untangling the Knots of Regulatory T Cell Therapy in Solid Organ Transplantation. Front Immunol 2022; 13:883855. [PMID: 35720387 PMCID: PMC9198594 DOI: 10.3389/fimmu.2022.883855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 12/16/2022] Open
Abstract
Numerous preclinical studies have provided solid evidence supporting adoptive transfer of regulatory T cells (Tregs) to induce organ tolerance. As a result, there are 7 currently active Treg cell-based clinical trials in solid organ transplantation worldwide, all of which are early phase I or phase I/II trials. Although the results of these trials are optimistic and support both safety and feasibility, many experimental and clinical unanswered questions are slowing the progression of this new therapeutic alternative. In this review, we bring to the forefront the major challenges that Treg cell transplant investigators are currently facing, including the phenotypic and functional diversity of Treg cells, lineage stability, non-standardized ex vivo Treg cell manufacturing process, adequacy of administration route, inability of monitoring and tracking infused cells, and lack of biomarkers or validated surrogate endpoints of efficacy in clinical trials. With this plethora of interrogation marks, we are at a challenging and exciting crossroad where properly addressing these questions will determine the successful implementation of Treg cell-based immunotherapy in clinical transplantation.
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Affiliation(s)
- Gabriel Orozco
- Department of Surgery - Transplant Division, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Meera Gupta
- Department of Surgery - Transplant Division, College of Medicine, University of Kentucky, Lexington, KY, United States.,Alliance Research Initiative [Treg cells to Induce Liver Tolerance (TILT) Alliance], University of Kentucky College of Medicine, Lexington, KY, United States
| | - Roberto Gedaly
- Department of Surgery - Transplant Division, College of Medicine, University of Kentucky, Lexington, KY, United States.,Alliance Research Initiative [Treg cells to Induce Liver Tolerance (TILT) Alliance], University of Kentucky College of Medicine, Lexington, KY, United States.,Lucille Parker Markey Cancer Center, University of Kentucky, College of Medicine, Lexington, KY, United States
| | - Francesc Marti
- Department of Surgery - Transplant Division, College of Medicine, University of Kentucky, Lexington, KY, United States.,Alliance Research Initiative [Treg cells to Induce Liver Tolerance (TILT) Alliance], University of Kentucky College of Medicine, Lexington, KY, United States.,Lucille Parker Markey Cancer Center, University of Kentucky, College of Medicine, Lexington, KY, United States
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MeCP2 and transcriptional control of eukaryotic gene expression. Eur J Cell Biol 2022; 101:151237. [DOI: 10.1016/j.ejcb.2022.151237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
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Differential Sensitivity of the Protein Translation Initiation Machinery and mTOR Signaling to MECP2 Gain- and Loss-of-Function Involves MeCP2 Isoform-Specific Homeostasis in the Brain. Cells 2022; 11:cells11091442. [PMID: 35563748 PMCID: PMC9105805 DOI: 10.3390/cells11091442] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic gene expression is controlled at multiple levels, including gene transcription and protein translation initiation. One molecule with key roles in both regulatory mechanisms is methyl CpG binding protein 2 (MeCP2). MECP2 gain- and loss-of-function mutations lead to Rett Syndrome and MECP2 Duplication Syndrome, respectively. To study MECP2 gain-of-function, we generated stably transduced human brain cells using lentiviral vectors for both MECP2E1 and MECP2E2 isoforms. Stable overexpression was confirmed by Western blot and immunofluorescence. We assessed the impact of MeCP2E1-E2 gain-of-function on the MeCP2 homeostasis regulatory network (MECP2E1/E2-BDNF/BDNF-miR-132), mTOR-AKT signaling, ribosome biogenesis, markers of chromatin structure, and protein translation initiation. We observed that combined co-transduction of MeCP2 isoforms led to protein degradation of MeCP2E1. Proteosome inhibition by MG132 treatment recovered MeCP2E1 protein within an hour, suggesting its induced degradation through the proteosome pathway. No significant change was detected for translation initiation factors as a result of MeCP2E1, MeCP2E2, or combined overexpression of both isoforms. In contrast, analysis of human Rett Syndrome brains tissues compared with controls indicated impaired protein translation initiation, suggesting that such mechanisms may have differential sensitivity to MECP2 gain- and loss-of-function. Collectively, our results provide further insight towards the dose-dependent functional role of MeCP2 isoforms in the human brain.
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Abstract
Although tumourigenesis occurs due to genetic mutations, the role of epigenetic dysregulations in cancer is also well established. Epigenetic dysregulations in cancer may occur as a result of mutations in genes encoding histone/DNA-modifying enzymes and chromatin remodellers or mutations in histone protein itself. It is also true that misregulated gene expression without genetic mutations in these factors could also support tumour initiation and progression. Interestingly, metabolic rewiring has emerged as a hallmark of cancer due to gene mutations in specific metabolic enzymes or dietary/environmental factors. Recent studies report an intricate cross-talk between epigenetic and metabolic reprogramming in cancer. This review discusses the role of epigenetic and metabolic dysregulations and their cross-talk in tumourigenesis with a special focus on gliomagenesis. We also discuss the role of recently developed human embryonic stem cells/induced pluripotent stem cells-derived organoid models of gliomas and how these models are proving instrumental in uncovering human-specific cellular and molecular complexities of gliomagenesis.
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Affiliation(s)
- Bismi Phasaludeen
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Suraiya Anjum Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
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Paul S, Goswami L, Pegu R, Kumar Chatterjee S, Sundar Bhattacharya S. Epigenetic regulations enhance adaptability and valorization efficiency in Eisenia fetida and Eudrilus eugeniae during vermicomposting of textile sludge: Insights on repair mechanisms of metal-induced genetic damage and oxidative stress. BIORESOURCE TECHNOLOGY 2022; 345:126493. [PMID: 34883193 DOI: 10.1016/j.biortech.2021.126493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Genotoxicity-based assessments of vermitechnology for textile-sludge valorization have rarely been attempted. Therefore, waste sanitization and epigenetic stress-regulation efficiency of Eisenia fetida and Eudrilus eugeniae were evaluated in silk (DSPS) and cotton (CPWS) processing sludge-based vermibeds. Vermicomposting resulted in greater C, N, and P recovery than composting. Earthworm population reduced by 6-50% in DSPS/CPWS, while it significantly increased in cow dung (CD) mixed DSPS/CPWS. The Cr, Cd, Pb, and Zn accumulation efficiency of earthworms was higher in DSPS-based feedstocks than CPWS. However, metal-rich sludge elevated oxidative stress, causing greater inhibition of cell viability and DNA damage in Eudrilus than in Eisenia. Although histo-architecture of chloragogenous tissues was perturbed, earthworms combatted metal-induced lipid peroxidation via the activation of catalase, superoxide-dismutase, and reduced-glutathione. Correlation statistics revealed that genetic integrity in earthworms was restored through DNA-methyltransferase activity, especially in DSPS/CPWS + CD vermibeds. Overall, Eisenia was a healthier choice than Eudrilus for sustainable valorization of textile-sludge.
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Affiliation(s)
- Sarmistha Paul
- Soil and Agro Bio-engineering Lab, Department of Environmental Science, Tezpur University, Tezpur 784 028, India
| | - Linee Goswami
- Department of Botany, Visva-Bharati Santiniketan, West Bengal 731235, India
| | - Ratul Pegu
- Soil and Agro Bio-engineering Lab, Department of Environmental Science, Tezpur University, Tezpur 784 028, India
| | - Subhendu Kumar Chatterjee
- Department of Biological Science, Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal 741246, India
| | - Satya Sundar Bhattacharya
- Soil and Agro Bio-engineering Lab, Department of Environmental Science, Tezpur University, Tezpur 784 028, India.
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Li C, Cao M, Zhou X. Role of epigenetics in parturition and preterm birth. Biol Rev Camb Philos Soc 2021; 97:851-873. [PMID: 34939297 DOI: 10.1111/brv.12825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022]
Abstract
Preterm birth occurs worldwide and is associated with high morbidity, mortality, and economic cost. Although several risk factors associated with parturition and preterm birth have been identified, mechanisms underlying this syndrome remain unclear, thereby limiting the implementation of interventions for prevention and management. Known triggers of preterm birth include conditions related to inflammatory and immunological pathways, as well as genetics and maternal history. Importantly, epigenetics, which is the study of heritable phenotypic changes that occur without alterations in the DNA sequence, may play a role in linking social and environmental risk factors for preterm birth. Epigenetic approaches to the study of preterm birth, including analyses of the effects of microRNAs, long non-coding RNAs, DNA methylation, and histone modification, have contributed to an improved understanding of the molecular bases of both term and preterm birth. Additionally, epigenetic modifications have been linked to factors already associated with preterm birth, including obesity and smoking. The prevention and management of preterm birth remains a challenge worldwide. Although epigenetic analysis provides valuable insights into the causes and risk factors associated with this syndrome, further studies are necessary to determine whether epigenetic approaches can be used routinely for the diagnosis, prevention, and management of preterm birth.
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Affiliation(s)
- Chunjin Li
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Maosheng Cao
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
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Gandhirajan A, Roychowdhury S, Vachharajani V. Sirtuins and Sepsis: Cross Talk between Redox and Epigenetic Pathways. Antioxidants (Basel) 2021; 11:antiox11010003. [PMID: 35052507 PMCID: PMC8772830 DOI: 10.3390/antiox11010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 12/19/2022] Open
Abstract
Sepsis and septic shock are the leading causes of death among hospitalized patients in the US. The immune response in sepsis transitions from a pro-inflammatory and pro-oxidant hyper-inflammation to an anti-inflammatory and cytoprotective hypo-inflammatory phase. While 1/3rd sepsis-related deaths occur during hyper-, a vast majority of sepsis-mortality occurs during the hypo-inflammation. Hyper-inflammation is cytotoxic for the immune cells and cannot be sustained. As a compensatory mechanism, the immune cells transition from cytotoxic hyper-inflammation to a cytoprotective hypo-inflammation with anti-inflammatory/immunosuppressive phase. However, the hypo-inflammation is associated with an inability to clear invading pathogens, leaving the host susceptible to secondary infections. Thus, the maladaptive immune response leads to a marked departure from homeostasis during sepsis-phases. The transition from hyper- to hypo-inflammation occurs via epigenetic programming. Sirtuins, a highly conserved family of histone deacetylators and guardians of homeostasis, are integral to the epigenetic programming in sepsis. Through their anti-inflammatory and anti-oxidant properties, the sirtuins modulate the immune response in sepsis. We review the role of sirtuins in orchestrating the interplay between the oxidative stress and epigenetic programming during sepsis.
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Affiliation(s)
- Anugraha Gandhirajan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (A.G.); (S.R.)
| | - Sanjoy Roychowdhury
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (A.G.); (S.R.)
| | - Vidula Vachharajani
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (A.G.); (S.R.)
- Department of Critical Care Medicine, Respiratory Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Correspondence:
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Zhou J, Li Z, Hu J, Wang C, Liu R, Lv Y. HOGG1-assisted DNA methylation analysis via a sensitive lanthanide labelling strategy. Talanta 2021; 239:123136. [PMID: 34920255 DOI: 10.1016/j.talanta.2021.123136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 01/09/2023]
Abstract
The assessment of DNA methylation level is an important indicator for the diagnosis and treatment of some diseases. DNA methylation assays are usually based on nucleic acid amplification strategies, which are time-consuming and complicated in operation procedures. Herein, we proposed a sensitive lanthanide-labelled ICP-MS method for DNA methylation analysis that exploited the feature of Human 8-oxoGuanine DNA Glycosylase (hOGG1), which specifically recognizes 8-oxo-G/5mC base pairs to effectively distinguish methylated DNA. A low limit of detection of 84 pM was achieved, and a 0.1% methylation level can be discriminated in the mixture, without any amplification procedure. Compared with commonly used nucleic acid amplification strategies, this proposed method is time-saving and low probability of false positive. Moreover, this work has been successfully validated in human serum samples, the recovery rates is between 96.7% and 105%, and the relative standard deviation (RSD) is in the range of 3.0%-3.5%, indicating that this method has the potential to be applied in clinical and biological samples quantitative analysis.
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Affiliation(s)
- Jing Zhou
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Ziyan Li
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Jianyu Hu
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Chaoqun Wang
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Rui Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 WangJiang Road, Chengdu, 610064, PR China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu, 610064, PR China; Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 WangJiang Road, Chengdu, 610064, PR China.
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Suarez-Bregua P, Rosendo S, Comesaña P, Sánchez-Ruiloba L, Morán P, Planas M, Rotllant J. Dynamic changes in DNA methylation during seahorse (Hippocampus reidi) postnatal development and settlement. Front Zool 2021; 18:52. [PMID: 34627317 PMCID: PMC8502395 DOI: 10.1186/s12983-021-00436-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/22/2021] [Indexed: 11/30/2022] Open
Abstract
Introduction Most living marine organisms have a biphasic life cycle dependent on metamorphosis and settlement. These critical life-history events mean that a developmentally competent larva undergoes a range of coordinated morphological and physiological changes that are in synchrony with the ecological transition from a pelagic to a benthonic lifestyle. Therefore, transition from a pelagic to a benthonic habitat requires multiple adaptations, however, the underlying mechanisms regulating this process still remains unclear. Epigenetic regulation and specifically DNA methylation, has been suggested to be particularly important for organisms to adapt to new environments. Seahorses (Family Syngnathidae, Genus Hippocampus) are a fascinating group of fish, distinguished by their unique anatomical features, reproductive strategy and behavior. They are unique among vertebrate species due to their “male pregnancy”, where males nourish developing embryos and larvae in a brood pouch until hatching and parturition occurs. After birth, free-swimming offspring are pelagic and subsequently they change into a demersal lifestyle. Therefore, to begin to address the question whether epigenetic processes could be involved in the transition from a planktonic to a benthonic lifestyle observed in seahorses, we studied global DNA methylation profiles in a tropical seahorse species (Hippocampus reidi) during postnatal development and settlement. Results We performed methylation-sensitive amplified polymorphism (MSAP) along with quantitative expression analysis for genes suggested to be involved in the methylation machinery at six age groups: 1, 5, 10, 20, 30 and 40 days after male’s pouch release (DAR). Results revealed that the H. reidi genome has a significantly different DNA methylation profile during postnatal development and settlement on demersal habitats. Moreover, gene expression analysis showed up- and down-regulation of specific DNA methyltransferases (DNMTs) encoding genes. Conclusion Our data show that the differences in the DNA methylation patterns seen among developmental stages and during the transition from a pelagic to a benthonic lifestyle suggest a potential for epigenetic regulation of gene expression (through DNA methylation) in this species. Therefore, epigenetic mechanisms could be necessary for seahorse settlement. Nevertheless, if these epigenetic mechanisms come from internal or if they are initiated via external environmental cues should be further investigated.
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Affiliation(s)
- Paula Suarez-Bregua
- Acuatic Biotechnology-ACUABIOTEC Lab, Department of Biotechnology and Aquaculture, Marine Research Institute IIM-CSIC, Vigo, Pontevedra, Spain.
| | - Sofia Rosendo
- Acuatic Biotechnology-ACUABIOTEC Lab, Department of Biotechnology and Aquaculture, Marine Research Institute IIM-CSIC, Vigo, Pontevedra, Spain
| | - Pilar Comesaña
- Acuatic Biotechnology-ACUABIOTEC Lab, Department of Biotechnology and Aquaculture, Marine Research Institute IIM-CSIC, Vigo, Pontevedra, Spain
| | - Lucia Sánchez-Ruiloba
- Acuatic Biotechnology-ACUABIOTEC Lab, Department of Biotechnology and Aquaculture, Marine Research Institute IIM-CSIC, Vigo, Pontevedra, Spain
| | - Paloma Morán
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Pontevedra, Spain
| | - Miquel Planas
- Department of Ecology and Marine Resources, Marine Research Institute IIM-CSIC, Vigo, Pontevedra, Spain
| | - Josep Rotllant
- Acuatic Biotechnology-ACUABIOTEC Lab, Department of Biotechnology and Aquaculture, Marine Research Institute IIM-CSIC, Vigo, Pontevedra, Spain.
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Buist M, Fuss D, Rastegar M. Transcriptional Regulation of MECP2E1-E2 Isoforms and BDNF by Metformin and Simvastatin through Analyzing Nascent RNA Synthesis in a Human Brain Cell Line. Biomolecules 2021; 11:biom11081253. [PMID: 34439919 PMCID: PMC8391797 DOI: 10.3390/biom11081253] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 12/25/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) is the main DNA methyl-binding protein in the brain that binds to 5-methylcytosine and 5-hydroxymethyl cytosine. MECP2 gene mutations are the main origin of Rett Syndrome (RTT), a neurodevelopmental disorder in young females. The disease has no existing cure, however, metabolic drugs such as metformin and statins have recently emerged as potential therapeutic candidates. In addition, induced MECP2-BDNF homeostasis regulation has been suggested as a therapy avenue. Here, we analyzed nascent RNA synthesis versus steady state total cellular RNA to study the transcriptional effects of metformin (an anti-diabetic drug) on MECP2 isoforms (E1 and E2) and BNDF in a human brain cell line. Additionally, we investigated the impact of simvastatin (a cholesterol lowering drug) on transcriptional regulation of MECP2E1/E2-BDNF. Metformin was capable of post-transcriptionally inducing BDNF and/or MECP2E1, while transcriptionally inhibiting MECP2E2. In contrast simvastatin significantly inhibited BDNF transcription without significantly impacting MECP2E2 transcripts. Further analysis of ribosomal RNA transcripts confirmed that the drug neither individually nor in combination affected these fundamentally important transcripts. Experimental analysis was completed in conditions of the presence or absence of serum starvation that showed minimal impact for serum deprival, although significant inhibition of steady state MECP2E1 by simvastatin was only detected in non-serum starved cells. Taken together, our results suggest that metformin controls MECP2E1/E2-BDNF transcriptionally and/or post-transcriptionally, and that simvastatin is a potent transcriptional inhibitor of BDNF. The transcriptional effect of these drugs on MECP2E1/E2-BDNF were not additive under these tested conditions, however, either drug may have potential application for related disorders.
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Affiliation(s)
| | | | - Mojgan Rastegar
- Correspondence: ; Tel.: +1-(204)-272-3108; Fax: +1-(204)-789-3900
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The molecular pathway triggered by zirconia in endothelial cells involves epigenetic control. Tissue Cell 2021; 73:101627. [PMID: 34425516 DOI: 10.1016/j.tice.2021.101627] [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: 09/03/2020] [Revised: 07/14/2021] [Accepted: 08/14/2021] [Indexed: 11/24/2022]
Abstract
The requirement to achieve natural looking restorations is one of the most challenging aspects in dentistry. Although zirconia has provided new opportunities for achieving superior aesthetics and physicochemical outcomes, very little has been achieved for its cellular and molecular performance, especially considering angiogenesis and osteogenesis. As angiogenesis is a secondary event and concomitant to osteogenesis, an indirect effect of dental implant on endothelial cells could be the release of active molecules such as those already reported affecting osteoblasts. To better address this issue, we challenged human endothelial cells (HUVECs) with zirconia-conditioned medium up to 72 h to allow analysis specific gene expression and protein pattern of mediators of epigenetic machinery in full. Our data shows involvement of zirconia in triggering intracellular signaling through MAPK-ERK activation, leading the signal to activate histone deacetylase HDAC6 likely with concomitant well-modulated DNA methylation profile by DNMTs and TETs. These signaling pathways seem to culminate in cytoskeleton rearrangement of endothelial cells, an important prerequisite to cell migration expected in angiogenesis. Collectively, this study demonstrates for the first time epigenetic-related molecular mechanism involved in endothelial cells responding to zirconia, revealing a repertoire of signaling molecules capable of executing the reprogramming process of gene expression, which are necessary to drive cell proliferation, migration, and consequently angiogenesis. This set of data can further studies using gene editing approaches to better elucidate functional roles.
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Chan DW, Lam WY, Chen F, Yung MMH, Chan YS, Chan WS, He F, Liu SS, Chan KKL, Li B, Ngan HYS. Genome-wide DNA methylome analysis identifies methylation signatures associated with survival and drug resistance of ovarian cancers. Clin Epigenetics 2021; 13:142. [PMID: 34294135 PMCID: PMC8296615 DOI: 10.1186/s13148-021-01130-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND In contrast to stable genetic events, epigenetic changes are highly plastic and play crucial roles in tumor evolution and development. Epithelial ovarian cancer (EOC) is a highly heterogeneous disease that is generally associated with poor prognosis and treatment failure. Profiling epigenome-wide DNA methylation status is therefore essential to better characterize the impact of epigenetic alterations on the heterogeneity of EOC. METHODS An epigenome-wide association study was conducted to evaluate global DNA methylation in a retrospective cohort of 80 mixed subtypes of primary ovarian cancers and 30 patients with high-grade serous ovarian carcinoma (HGSOC). Three demethylating agents, azacytidine, decitabine, and thioguanine, were tested their anti-cancer and anti-chemoresistant effects on HGSOC cells. RESULTS Global DNA hypermethylation was significantly associated with high-grade tumors, platinum resistance, and poor prognosis. We determined that 9313 differentially methylated probes (DMPs) were enriched in their relative gene regions of 4938 genes involved in small GTPases and were significantly correlated with the PI3K-AKT, MAPK, RAS, and WNT oncogenic pathways. On the other hand, global DNA hypermethylation was preferentially associated with recurrent HGSOC. A total of 2969 DMPs corresponding to 1471 genes were involved in olfactory transduction, and calcium and cAMP signaling. Co-treatment with demethylating agents showed significant growth retardation in ovarian cancer cells through differential inductions, such as cell apoptosis by azacytidine or G2/M cell cycle arrest by decitabine and thioguanine. Notably, azacytidine and decitabine, though not thioguanine, synergistically enhanced cisplatin-mediated cytotoxicity in HGSOC cells. CONCLUSIONS This study demonstrates the significant association of global hypermethylation with poor prognosis and drug resistance in high-grade EOC and highlights the potential of demethylating agents in cancer treatment.
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Affiliation(s)
- David W Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China.
| | - Wai-Yip Lam
- Lee's Pharmaceutical (HK) Ltd, 1/F Building 20E, Phase 3, Hong Kong Science Park, Shatin, Hong Kong, People's Republic of China
| | - Fushun Chen
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Mingo M H Yung
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Yau-Sang Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Wai-Sun Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Fangfang He
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Stephanie S Liu
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Karen K L Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Benjamin Li
- Lee's Pharmaceutical (HK) Ltd, 1/F Building 20E, Phase 3, Hong Kong Science Park, Shatin, Hong Kong, People's Republic of China
| | - Hextan Y S Ngan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China. .,Department of Obstetrics and Gynaecology, 6/F Professorial Block, Queen Mary Hospital, Pokfulam, Hong Kong, People's Republic of China.
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Romero-Pimentel AL, Almeida D, Muñoz-Montero S, Rangel C, Mendoza-Morales R, Gonzalez-Saenz EE, Nagy C, Chen G, Aouabed Z, Theroux JF, Turecki G, Martinez-Levy G, Walss-Bass C, Monroy-Jaramillo N, Fernández-Figueroa EA, Gómez-Cotero A, García-Dolores F, Morales-Marin ME, Nicolini H. Integrative DNA Methylation and Gene Expression Analysis in the Prefrontal Cortex of Mexicans Who Died by Suicide. Int J Neuropsychopharmacol 2021; 24:935-947. [PMID: 34214149 PMCID: PMC8653872 DOI: 10.1093/ijnp/pyab042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/04/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Suicide represents a major health concern, especially in developing countries. While many demographic risk factors have been proposed, the underlying molecular pathology of suicide remains poorly understood. A body of evidence suggests that aberrant DNA methylation and expression is involved. In this study, we examined DNA methylation profiles and concordant gene expression changes in the prefrontal cortex of Mexicans who died by suicide. METHODS In collaboration with the coroner's office in Mexico City, brain samples of males who died by suicide (n = 35) and age-matched sudden death controls (n = 13) were collected. DNA and RNA were extracted from prefrontal cortex tissue and analyzed with the Infinium Methylation480k and the HumanHT-12 v4 Expression Beadchips, respectively. RESULTS We report evidence of altered DNA methylation profiles at 4430 genomic regions together with 622 genes characterized by differential expression in cases vs controls. Seventy genes were found to have concordant methylation and expression changes. Metacore-enriched analysis identified 10 genes with biological relevance to psychiatric phenotypes and suicide (ADCY9, CRH, NFATC4, ABCC8, HMGA1, KAT2A, EPHA2, TRRAP, CD22, and CBLN1) and highlighted the association that ADCY9 has with various pathways, including signal transduction regulated by the cAMP-responsive element modulator, neurophysiological process regulated by the corticotrophin-releasing hormone, and synaptic plasticity. We therefore went on to validate the observed hypomethylation of ADCY9 in cases vs control through targeted bisulfite sequencing. CONCLUSION Our study represents the first, to our knowledge, analysis of DNA methylation and gene expression associated with suicide in a Mexican population using postmortem brain, providing novel insights for convergent molecular alterations associated with suicide.
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Affiliation(s)
- Ana L Romero-Pimentel
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico,McGill Group of Suicide Studies, Montreal,Canada
| | - Daniel Almeida
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Said Muñoz-Montero
- Facultad de Psicología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Claudia Rangel
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Roberto Mendoza-Morales
- Instituto de Ciencias Forenses del Tribunal Superior de Justicia de la CDMX, Mexico City, Mexico
| | - Eli E Gonzalez-Saenz
- Instituto de Ciencias Forenses del Tribunal Superior de Justicia de la CDMX, Mexico City, Mexico
| | - Corina Nagy
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gary Chen
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Zahia Aouabed
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Gustavo Turecki
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gabriela Martinez-Levy
- Psychiatric Genetics Department, Clinical Research Branch, National Institute of Psychiatry Ramón de la Fuente, Mexico City, Mexico
| | - Consuelo Walss-Bass
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas,USA
| | - Nancy Monroy-Jaramillo
- Department of Neurogenetics, National Institute of Neurology and Neurosurgery, Manuel Velasco Suarez, Mexico City, Mexico
| | | | - Amalia Gómez-Cotero
- Centro Interdisciplinario de Ciencias de la Salud, Instituto Politécnico Nacional, Unidad Santo Tomás, Mexico City, Mexico
| | - Fernando García-Dolores
- Instituto de Ciencias Forenses del Tribunal Superior de Justicia de la CDMX, Mexico City, Mexico
| | | | - Humberto Nicolini
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico,Correspondence: José Humberto Nicolini Sánchez, MD, PhD, Laboratorio de Genómica de Enfermedades Psiquiátricas y neurodegenerativas, Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Ciudad de México, CDMX, México ()
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Cai S, Quan S, Yang G, Chen M, Ye Q, Wang G, Yu H, Wang Y, Qiao S, Zeng X. Nutritional Status Impacts Epigenetic Regulation in Early Embryo Development: A Scoping Review. Adv Nutr 2021; 12:1877-1892. [PMID: 33873200 PMCID: PMC8483970 DOI: 10.1093/advances/nmab038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/03/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
With the increasing maternal age and the use of assisted reproductive technology in various countries worldwide, the influence of epigenetic modification on embryonic development is increasingly notable and prominent. Epigenetic modification disorders caused by various nutritional imbalance would cause embryonic development abnormalities and even have an indelible impact on health in adulthood. In this scoping review, we summarize the main epigenetic modifications in mammals and the synergies among different epigenetic modifications, especially DNA methylation, histone acetylation, and histone methylation. We performed an in-depth analysis of the regulation of various epigenetic modifications on mammals from zygote formation to cleavage stage and blastocyst stage, and reviewed the modifications of key sites and their potential molecular mechanisms. In addition, we discuss the effects of nutrition (protein, lipids, and one-carbon metabolism) on epigenetic modification in embryos and emphasize the importance of various nutrients in embryonic development and epigenetics during pregnancy. Failures in epigenetic regulation have been implicated in mammalian and human early embryo loss and disease. With the use of reproductive technologies, it is becoming even more important to establish developmentally competent embryos. Therefore, it is essential to evaluate the extent to which embryos are sensitive to these epigenetic modifications and nutrition status. Understanding the epigenetic regulation of early embryo development will help us make better use of reproductive technologies and nutrition regulation to improve reproductive health in mammals.
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Affiliation(s)
- Shuang Cai
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Shuang Quan
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Guangxin Yang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Qianhong Ye
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Gang Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Yuming Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
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Role of DNA Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome Pathobiology and Mechanism of Disease. Biomolecules 2021; 11:biom11010075. [PMID: 33429932 PMCID: PMC7827577 DOI: 10.3390/biom11010075] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/16/2022] Open
Abstract
Rett Syndrome (RTT) is a severe, rare, and progressive developmental disorder with patients displaying neurological regression and autism spectrum features. The affected individuals are primarily young females, and more than 95% of patients carry de novo mutation(s) in the Methyl-CpG-Binding Protein 2 (MECP2) gene. While the majority of RTT patients have MECP2 mutations (classical RTT), a small fraction of the patients (atypical RTT) may carry genetic mutations in other genes such as the cyclin-dependent kinase-like 5 (CDKL5) and FOXG1. Due to the neurological basis of RTT symptoms, MeCP2 function was originally studied in nerve cells (neurons). However, later research highlighted its importance in other cell types of the brain including glia. In this regard, scientists benefitted from modeling the disease using many different cellular systems and transgenic mice with loss- or gain-of-function mutations. Additionally, limited research in human postmortem brain tissues provided invaluable findings in RTT pathobiology and disease mechanism. MeCP2 expression in the brain is tightly regulated, and its altered expression leads to abnormal brain function, implicating MeCP2 in some cases of autism spectrum disorders. In certain disease conditions, MeCP2 homeostasis control is impaired, the regulation of which in rodents involves a regulatory microRNA (miR132) and brain-derived neurotrophic factor (BDNF). Here, we will provide an overview of recent advances in understanding the underlying mechanism of disease in RTT and the associated genetic mutations in the MECP2 gene along with the pathobiology of the disease, the role of the two most studied protein variants (MeCP2E1 and MeCP2E2 isoforms), and the regulatory mechanisms that control MeCP2 homeostasis network in the brain, including BDNF and miR132.
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41
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Gendoping und molekulares Doping. Rechtsmedizin (Berl) 2020. [DOI: 10.1007/s00194-020-00431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Beacon TH, Delcuve GP, Davie JR. Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus 1. Genome 2020; 64:386-399. [PMID: 33086021 DOI: 10.1139/gen-2020-0124] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The angiotensin-converting enzyme 2 (ACE2) is the receptor for the three coronaviruses HCoV-NL63, SARS-CoV, and SARS-CoV-2. ACE2 is involved in the regulation of the renin-angiotensin system and blood pressure. ACE2 is also involved in the regulation of several signaling pathways, including integrin signaling. ACE2 expression is regulated transcriptionally and post-transcriptionally. The expression of the gene is regulated by two promoters, with usage varying among tissues. ACE2 expression is greatest in the small intestine, kidney, and heart and detectable in a variety of tissues and cell types. Herein we review the chemical and mechanical signal transduction pathways regulating the expression of the ACE2 gene and the epigenetic/chromatin features of the expressed gene.
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Affiliation(s)
- Tasnim H Beacon
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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Beacon TH, Su RC, Lakowski TM, Delcuve GP, Davie JR. SARS-CoV-2 multifaceted interaction with the human host. Part II: Innate immunity response, immunopathology, and epigenetics. IUBMB Life 2020; 72:2331-2354. [PMID: 32936531 DOI: 10.1002/iub.2379] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 makes its way into the cell via the ACE2 receptor and the proteolytic action of TMPRSS2. In response to the SARS-CoV-2 infection, the innate immune response is the first line of defense, triggering multiple signaling pathways to produce interferons, pro-inflammatory cytokines and chemokines, and initiating the adaptive immune response against the virus. Unsurprisingly, the virus has developed strategies to evade detection, which can result in delayed, excessive activation of the innate immune system. The response elicited by the host depends on multiple factors, including health status, age, and sex. An overactive innate immune response can lead to a cytokine storm, inflammation, and vascular disruption, leading to the vast array of symptoms exhibited by COVID-19 patients. What is known about the expression and epigenetic regulation of the ACE2 gene and the various players in the host response are explored in this review.
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Affiliation(s)
- Tasnim H Beacon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ruey-Chyi Su
- National HIV and Retrovirology Laboratory, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada
| | - Ted M Lakowski
- College of Pharmacy, Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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Pejhan S, Del Bigio MR, Rastegar M. The MeCP2E1/E2-BDNF- miR132 Homeostasis Regulatory Network Is Region-Dependent in the Human Brain and Is Impaired in Rett Syndrome Patients. Front Cell Dev Biol 2020; 8:763. [PMID: 32974336 PMCID: PMC7471663 DOI: 10.3389/fcell.2020.00763] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Abstract
Rett Syndrome (RTT) is a rare and progressive neurodevelopmental disorder that is caused by de novo mutations in the X-linked Methyl CpG binding protein 2 (MECP2) gene and is subjected to X-chromosome inactivation. RTT is commonly associated with neurological regression, autistic features, motor control impairment, seizures, loss of speech and purposeful hand movements, mainly affecting females. Different animal and cellular model systems have tremendously contributed to our current knowledge about MeCP2 and RTT. However, the majority of these findings remain unexamined in the brain of RTT patients. Based on previous studies in rodent brains, the highly conserved neuronal microRNA “miR132” was suggested to be an inhibitor of MeCP2 expression. The neuronal miR132 itself is induced by Brain Derived Neurotrophic Factor (BDNF), a neurotransmitter modulator, which in turn is controlled by MeCP2. This makes the basis of the MECP2-BDNF-miR132 feedback regulatory loop in the brain. Here, we studied the components of this feedback regulatory network in humans, and its possible impairment in the brain of RTT patients. In this regard, we evaluated the transcript and protein levels of MECP2/MeCP2E1 and E2 isoforms, BDNF/BDNF, and miR132 (both 3p and 5p strands) by real time RT-PCR, Western blot, and ELISA in four different regions of the human RTT brains and their age-, post-mortem delay-, and sex-matched controls. The transcript level of the studied elements was significantly compromised in RTT patients, even though the change was not identical in different parts of the brain. Our data indicates that MeCP2E1/E2-BDNF protein levels did not follow their corresponding transcript trends. Correlational studies suggested that the MECP2E1/E2-BDNF-miR132 homeostasis regulation might not be similarly controlled in different parts of the human brain. Despite challenges in evaluating autopsy samples in rare diseases, our findings would help to shed some light on RTT pathobiology, and obscurities caused by limited studies on MeCP2 regulation in the human brain.
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Affiliation(s)
- Shervin Pejhan
- Regenerative Medicine Program, Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Marc R Del Bigio
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Mojgan Rastegar
- Regenerative Medicine Program, Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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Kavianpour P, Gemmell MCM, Kahlert JU, Rendina LM. Histone Deacetylase 2 (HDAC2) Inhibitors Containing Boron. Chembiochem 2020; 21:2786-2791. [DOI: 10.1002/cbic.202000131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/30/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Poya Kavianpour
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
| | - Madeleine C. M. Gemmell
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
| | - Jan U. Kahlert
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
| | - Louis M. Rendina
- School of Chemistry, The University of Sydney The University of Sydney F11, Eastern Avenue Sydney NSW 2006 Australia
- The University of Sydney Nano Institute Camperdown NSW 2050 Sydney NSW 2006 Australia
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Pejhan S, Siu VM, Ang LC, Del Bigio MR, Rastegar M. Differential brain region-specific expression of MeCP2 and BDNF in Rett Syndrome patients: a distinct grey-white matter variation. Neuropathol Appl Neurobiol 2020; 46:735-750. [PMID: 32246495 DOI: 10.1111/nan.12619] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/03/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022]
Abstract
INTRODUCTION AND OBJECTIVES Rett Syndrome (RTT) is a neurodevelopmental disorder caused by Methyl CpG Binding Protein 2 (MECP2) gene mutations. Previous studies of MeCP2 in the human brain showed variable and inconsistent mosaic-pattern immunolabelling, which has been interpreted as a reflection of activation-state variability. We aimed to study post mortem MeCP2 and BDNF (MeCP2 target) degradation and brain region-specific detection in relation to RTT pathophysiology. METHODS We investigated MeCP2 and BDNF stabilities in non-RTT human brains by immunohistochemical labelling and compared them in three brain regions of RTT and controls. RESULTS In surgically excised samples of human hippocampus and cerebellum, MeCP2 was universally detected. There was no significantly obvious difference between males and females. However, post mortem delay in autopsy samples had substantial influence on MeCP2 detection. Immunohistochemistry studies in RTT patients showed lower MeCP2 detection in glial cells of the white matter. Glial fibrillary acidic protein (GFAP) expression was also reduced in RTT brain samples without obvious change in myelin basic protein (MBP). Neurons did not show any noticeable decrease in MeCP2 detection. BDNF immunohistochemical detection showed an astroglial/endothelial pattern without noticeable difference between RTT and controls. CONCLUSIONS Our findings indicate that MeCP2 protein is widely expressed in mature human brain cells at all ages. However, our data points towards a possible white matter abnormality in RTT and highlights the importance of studying human RTT brain tissues in parallel with research on animal and cell models of RTT.
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Affiliation(s)
- S Pejhan
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - V M Siu
- Division of Medical Genetics, Department of Paediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - L C Ang
- Department of Pathology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - M R Del Bigio
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - M Rastegar
- Regenerative Medicine Program, and Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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Li J, Xiao H, Luo H, Tan Y, Ni Q, He C, Magdalou J, Chen L, Wang H. GR/HDAC2/TGFβR1 pathway contributes to prenatal caffeine induced-osteoarthritis susceptibility in male adult offspring rats. Food Chem Toxicol 2020; 140:111279. [PMID: 32199975 DOI: 10.1016/j.fct.2020.111279] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 03/05/2020] [Accepted: 03/15/2020] [Indexed: 12/25/2022]
Abstract
Prenatal caffeine exposure (PCE) induces developmental toxicity of multi-organ and susceptibility to multi-disease in offspring. However, the effects of PCE on osteoarthritis susceptibility in adult offspring and its intrauterine programming mechanism remain to be further investigated. Here, we found that PCE induced susceptibility to osteoarthritis in male adult offspring rats, which was related to the inhibited function of cartilage matrix synthesis from fetuses to adults. Meanwhile, PCE consistently downregulated the H3K9ac and expression levels of transforming growth factor β receptor 1 (TGFβR1), and then blocked TGFβ signaling pathway, which contributed to the suppressed cartilage matrix synthesis. Moreover, the high level of corticosterone caused by PCE reduced the H3K9ac level on TGFβR1 promoter region through acting on glucocorticoids receptor (GR) and recruiting histone deacetylase 2 (HDAC2) into the nucleus of fetal chondrocytes. Taken together, PCE induced osteoarthritis susceptibility in male adult offspring rats, which was attributed to the low-functional programming of TGFβR1 induced by corticosterone via GR/HDAC2 signaling.
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Affiliation(s)
- Jing Li
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Hao Xiao
- Department of Orthopedic Surgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Hanwen Luo
- Department of Orthopedic Surgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Yang Tan
- Department of Orthopedic Surgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Qubo Ni
- Department of Orthopedic Surgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Chunjiang He
- Department of Medical Genetics, Basic Medical School of Wuhan University, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | | | - Liaobin Chen
- Department of Orthopedic Surgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
| | - Hui Wang
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
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Suarez-Bregua P, Pérez-Figueroa A, Hernández-Urcera J, Morán P, Rotllant J. Temperature-independent genome-wide DNA methylation profile in turbot post-embryonic development. J Therm Biol 2020; 88:102483. [PMID: 32125973 DOI: 10.1016/j.jtherbio.2019.102483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/29/2019] [Accepted: 12/17/2019] [Indexed: 11/19/2022]
Abstract
The morphological and biological characteristics of ectothermic vertebrates are known to be strongly influenced by environmental conditions, particularly temperature. Epigenetic mechanisms such as DNA methylation have been reported to contribute to the phenotypic plasticity observed in vertebrates in response to environmental changes. Additionally, DNA methylation is a dynamic process that occurs throughout vertebrate ontogeny and it has been associated with the activation and silencing of gene expression during post-embryonic development and metamorphosis. In this study, we investigated genome-wide DNA methylation profiles during turbot metamorphosis, as well as the epigenetic effects of temperature on turbot post-embryonic development. Fish growth and rates of development were greatly affected by rearing temperature. Thus, turbot raised at ambient temperature (18 °C) achieved greater body weights and progressed through development more quickly than those reared at a colder temperature (14 °C). Genome-wide DNA methylation dynamics analyzed via a methylation-sensitive amplified polymorphism (MSAP) technique were not significantly different between animals reared within the two different thermal environments. Furthermore, comparisons between phenotypically similar fish revealed that genome-wide DNA methylation profiles do not necessarily correlate with specific developmental stages in turbot.
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Affiliation(s)
- P Suarez-Bregua
- Department of Biotechnology and Aquaculture, Institute of Marine Research (IIM-CSIC), Vigo, Spain.
| | - A Pérez-Figueroa
- Dep. Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, Spain; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal
| | - J Hernández-Urcera
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografia, Vigo, Spain
| | - P Morán
- Dep. Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, Spain
| | - J Rotllant
- Department of Biotechnology and Aquaculture, Institute of Marine Research (IIM-CSIC), Vigo, Spain.
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Amiri S, Davie JR, Rastegar M. Chronic Ethanol Exposure Alters DNA Methylation in Neural Stem Cells: Role of Mouse Strain and Sex. Mol Neurobiol 2020; 57:650-667. [PMID: 31414368 DOI: 10.1007/s12035-019-01728-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022]
Abstract
Prenatal alcohol exposure (PAE) is considered as a risk factor for the development of fetal alcohol spectrum disorders (FASD). Evidence indicates that PAE affects epigenetic mechanisms (such as DNA methylation) and alters the normal differentiation and development of neural stem cells (NSC) in the fetal brain. However, PAE effects depend on several factors such as sex and strain of the studied subjects. Here, we investigated whether murine sex and strain contribute to the effects of chronic ethanol exposure on DNA methylation machinery of differentiating NSC. Further, the effects of PAE on glial lineage (including both astrocytes and oligodendrocytes) in a sex- and strain-dependent manner have not been studied yet. To examine the effects of chronic ethanol exposure on gliogenesis, we exposed differentiating NSC to glio-inductive culture conditions. Applying a standard in vitro model system, we treated male and female differentiating NSC (obtained from the forebrain of CD1 and C57BL/6 embryos at embryonic day 14.5) with chronic ethanol exposure (70 mM) for 8 days. We show that ethanol induces global DNA hypomethylation, while altering the expression of DNA methylation-related genes in a sex- and strain-specific manner. The observed change in cellular DNA methylation levels was associated with altered expression of glial markers CNPASE, GFAP, and OLIG2 in CD1 (but not C57BL/6) cells. We conclude that the impact of ethanol effect on DNA methylation is dependent on cellular sex and strain. Also, ethanol impact on neural stem cell fate commitment was only detected in cells isolated from CD1 mouse strain, but not in C57BL/6 cells. The results of the current study provide evidence that sex and strain of rodents (C57BL/6 and CD1) during gestation are important factors, which affect alcohol effects on NSC differentiation and DNA methylation. Results of this study may also help in interpreting data on the developmental toxicity of many compounds during the gestational period.
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Affiliation(s)
- Shayan Amiri
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
- Regenerative Medicine Program, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
- Regenerative Medicine Program, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
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Kong S, Zhou C, Bao H, Ni Z, Liu M, He B, Huang L, Sun Y, Wang H, Lu J. Epigenetic control of embryo-uterine crosstalk at peri-implantation. Cell Mol Life Sci 2019; 76:4813-4828. [PMID: 31352535 PMCID: PMC11105790 DOI: 10.1007/s00018-019-03245-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/28/2019] [Accepted: 07/23/2019] [Indexed: 01/05/2023]
Abstract
Embryo implantation is one of the pivotal steps during mammalian pregnancy, since the quality of embryo implantation determines the outcome of ongoing pregnancy and fetal development. A large number of factors, including transcription factors, signalling transduction components, and lipids, have been shown to be indispensable for embryo implantation. Increasing evidence also suggests the important roles of epigenetic factors in this critical event. This review focuses on recent findings about the involvement of epigenetic regulators during embryo implantation.
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Affiliation(s)
- Shuangbo Kong
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Chan Zhou
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Haili Bao
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Zhangli Ni
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Mengying Liu
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Bo He
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Lin Huang
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Yang Sun
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Haibin Wang
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China.
| | - Jinhua Lu
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China.
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