1
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Kaplánek R, Kejík Z, Hajduch J, Veselá K, Kučnirová K, Skaličková M, Venhauerová A, Hosnedlová B, Hromádka R, Dytrych P, Novotný P, Abramenko N, Antonyová V, Hoskovec D, Babula P, Masařík M, Martásek P, Jakubek M. TET protein inhibitors: Potential and limitations. Biomed Pharmacother 2023; 166:115324. [PMID: 37598475 DOI: 10.1016/j.biopha.2023.115324] [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: 04/25/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
TET proteins (methylcytosine dioxygenases) play an important role in the regulation of gene expression. Dysregulation of their activity is associated with many serious pathogenic states such as oncological diseases. Regulation of their activity by specific inhibitors could represent a promising therapeutic strategy. Therefore, this review describes various types of TET protein inhibitors in terms of their inhibitory mechanism and possible applicability. The potential and possible limitations of this approach are thoroughly discussed in the context of TET protein functionality in living systems. Furthermore, possible therapeutic strategies based on the inhibition of TET proteins are presented and evaluated, especially in the field of oncological diseases.
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Affiliation(s)
- Robert Kaplánek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Zdeněk Kejík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Jan Hajduch
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Veselá
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Kučnirová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Markéta Skaličková
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Anna Venhauerová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Božena Hosnedlová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Róbert Hromádka
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Petr Dytrych
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Novotný
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Nikita Abramenko
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Veronika Antonyová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - David Hoskovec
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Babula
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michal Masařík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Pavel Martásek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
| | - Milan Jakubek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
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2
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Ashok A, Tai WL, Lennikov A, Chang K, Chen J, Li B, Cho KS, Utheim TP, Chen DF. Electrical stimulation alters DNA methylation and promotes neurite outgrowth. J Cell Biochem 2023; 124:1530-1545. [PMID: 37642194 DOI: 10.1002/jcb.30462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
Electrical stimulation (ES) influences neural regeneration and functionality. We here investigate whether ES regulates DNA demethylation, a critical epigenetic event known to influence nerve regeneration. Retinal ganglion cells (RGCs) have long served as a standard model for central nervous system neurons, whose growth and disease development are reportedly affected by DNA methylation. The current study focuses on the ability of ES to rescue RGCs and preserve vision by modulating DNA demethylation. To evaluate DNA demethylation pattern during development, RGCs from mice at different stages of development, were analyzed using qPCR for ten-eleven translocation (TETs) and immunostained for 5 hydroxymethylcytosine (5hmc) and 5 methylcytosine (5mc). To understand the effect of ES on neurite outgrowth and DNA demethylation, cells were subjected to ES at 75 µAmp biphasic ramp for 20 min and cultured for 5 days. ES increased TETs mediated neurite outgrowth, DNA demethylation, TET1 and growth associated protein 43 levels significantly. Immunostaining of PC12 cells following ES for histone 3 lysine 9 trimethylation showed cells attained an antiheterochromatin configuration. Cultured mouse and human retinal explants stained with β-III tubulin exhibited increased neurite growth following ES. Finally, mice subjected to optic nerve crush injury followed by ES exhibited improved RGCs function and phenotype as validated using electroretinogram and immunohistochemistry. Our results point to a possible therapeutic regulation of DNA demethylation by ES in neurons.
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Affiliation(s)
- Ajay Ashok
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Wai Lydia Tai
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Anton Lennikov
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Karen Chang
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Julie Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Boyuan Li
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Kin-Sang Cho
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Tor Paaske Utheim
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Dong Feng Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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3
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Gorin G, Pachter L. Length biases in single-cell RNA sequencing of pre-mRNA. BIOPHYSICAL REPORTS 2022; 3:100097. [PMID: 36660179 PMCID: PMC9843228 DOI: 10.1016/j.bpr.2022.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Single-cell RNA sequencing data can be modeled using Markov chains to yield genome-wide insights into transcriptional physics. However, quantitative inference with such data requires careful assessment of noise sources. We find that long pre-mRNA transcripts are over-represented in sequencing data. To explain this trend, we propose a length-based model of capture bias, which may produce false-positive observations. We solve this model and use it to find concordant parameter trends as well as systematic, mechanistically interpretable technical and biological differences in paired data sets.
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Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Lior Pachter
- Division of Biology and Biological Engineering, Pasadena, California
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California
- Corresponding author
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4
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New Insights into TETs in Psychiatric Disorders. Int J Mol Sci 2022; 23:ijms23094909. [PMID: 35563298 PMCID: PMC9103987 DOI: 10.3390/ijms23094909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Psychiatric disorders are complex and heterogeneous disorders arising from the interaction of multiple factors based on neurobiology, genetics, culture, and life experience. Increasing evidence indicates that sustained abnormalities are maintained by epigenetic modifications in specific brain regions. Over the past decade, the critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Here, we review the progress of studies designed to provide a better understanding of how profiles of TET proteins and 5hmC are powerful mechanisms by which to explain neuronal plasticity and long-term behaviors, and impact transcriptional programs operative in the brain that contribute to psychiatric disorders.
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5
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Dusadeemeelap C, Rojasawasthien T, Matsubara T, Kokabu S, Addison WN. Inhibition of TET-mediated DNA demethylation suppresses osteoblast differentiation. FASEB J 2022; 36:e22153. [PMID: 34997955 DOI: 10.1096/fj.202101402r] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 12/26/2022]
Abstract
DNA methylation is an epigenetic modification critical for the regulation of chromatin structure and gene expression during development and disease. The ten-eleven translocation (TET) enzyme family catalyzes the hydroxymethylation and subsequent demethylation of DNA by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Little is known about TET protein function due to a lack of pharmacological tools to manipulate DNA hydroxymethylation levels. In this study, we examined the role of TET-mediated DNA hydroxymethylation during BMP-induced C2C12 osteoblast differentiation using a novel cytosine-based selective TET enzyme inhibitor, Bobcat339 (BC339). Treatment of C2C12 cells with BC339 increased global 5mC and decreased global 5hmC without adversely affecting cell viability, proliferation, or apoptosis. Furthermore, BC339 treatment inhibited osteoblast marker gene expression and decreased alkaline phosphatase activity during differentiation. Methylated DNA immunoprecipitation and bisulfite sequencing showed that inhibition of TET with BC339 led to increased 5mC at specific CpG-rich regions at the promoter of Sp7, a key osteoblast transcription factor. Consistent with promoter 5mC marks being associated with transcriptional repression, luciferase activity of an Sp7-promoter-reporter construct was repressed by in vitro DNA methylation or BC339. Chromatin immunoprecipitation analysis confirmed that TET2 does indeed occupy the promoter region of Sp7. Accordingly, forced overexpression of SP7 rescued the inhibition of osteogenic differentiation by BC339. In conclusion, our data suggest that TET-mediated DNA demethylation of genomic regions, including the Sp7 promoter, plays a role in the initiation of osteoblast differentiation. Furthermore, BC339 is a novel pharmacological tool for the modulation of DNA methylation dynamics for research and therapeutic applications.
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Affiliation(s)
- Chirada Dusadeemeelap
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Japan.,Division of Special Needs and Geriatric Dentistry, Kyushu Dental University, Kitakyushu, Japan
| | - Thira Rojasawasthien
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Japan
| | - Takuma Matsubara
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Japan
| | - Shoichiro Kokabu
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Japan
| | - William N Addison
- Division of Molecular Signaling and Biochemistry, Kyushu Dental University, Kitakyushu, Japan
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6
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The emerging roles of srGAPs in cancer. Mol Biol Rep 2021; 49:755-759. [PMID: 34825319 DOI: 10.1007/s11033-021-06872-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
GTPase activating proteins (GAPs) were initially considered as the inhibitors of cell signaling pathways because of their nature to activate the intrinsic GTPase activity of the RhoGTPases. But recent studies of dysregulated GAPs in many cancers such as glioblastoma, colorectal cancer, breast cancer, and renal cancer have elucidated the important roles of GAPs in carcinogenesis and GAPs have been shown to perform multiple nonconventional functions in different contexts. We have discussed the recent developments in the roles played by different types of srGAPs (SLIT-ROBO Rho GTPase-activating proteins) in cancer.
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7
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Achour M, Ferdousi F, Sasaki K, Isoda H. Luteolin Modulates Neural Stem Cells Fate Determination: In vitro Study on Human Neural Stem Cells, and in vivo Study on LPS-Induced Depression Mice Model. Front Cell Dev Biol 2021; 9:753279. [PMID: 34790666 PMCID: PMC8591246 DOI: 10.3389/fcell.2021.753279] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022] Open
Abstract
Luteolin is a natural flavone with neurotrophic effects observed on different neuronal cell lines. In the present study, we aimed to assess the effect of luteolin on hNSCs fate determination and the LPS-induced neuroinflammation in a mouse model of depression with astrocytogenesis defect. hNSCs were cultured in basal cell culture medium (control) or medium supplemented with luteolin or AICAR, a known inducer of astrogenesis. A whole-genome transcriptomic analysis showed that luteolin upregulated the expressions of genes related to neurotrophin, dopaminergic, hippo, and Wnt signaling pathways, and downregulated the genes involved in p53, TNF, FOXO, and Notch signaling pathways. We also found that astrocyte-specific gene GFAP, as well as other genes of the key signaling pathways involved in astrogenesis such as Wnt, BMP, and JAK-STAT pathways were upregulated in luteolin-treated hNSCs. On the other hand, neurogenesis and oligodendrogenesis-related genes, TUBB3, NEUROD 1 and 6, and MBP, were downregulated in luteolin-treated hNSCs. Furthermore, immunostaining showed that percentages of GFAP+ cells were significantly higher in luteolin- and AICAR-treated hNSCs compared to control hNSCs. Additionally, RT-qPCR results showed that luteolin upregulated the expressions of GFAP, BMP2, and STAT3, whereas the expression of TUBB3 remained unchanged. Next, we evaluated the effects of luteolin in LPS-induced mice model of depression that represents defects in astrocytogenesis. We found that oral administration of luteolin (10 mg/Kg) for eight consecutive days could decrease the immobility time on tail suspension test, a mouse behavioral test measuring depression-like behavior, and attenuate LPS-induced inflammatory responses by significantly decreasing IL-6 production in mice brain-derived astrocytes and serum, and TNFα and corticosterone levels in serum. Luteolin treatment also significantly increased mature BDNF, dopamine, and noradrenaline levels in the hypothalamus of LPS-induced depression mice. Though the behavioral effects of luteolin did not reach statistical significance, global gene expression analyses of mice hippocampus and brain-derived NSCs highlighted the modulatory effects of luteolin on different signaling pathways involved in the pathophysiology of depression. Altogether, our findings suggest an astrocytogenic potential of luteolin and its possible therapeutic benefits in neuroinflammatory and neurodegenerative diseases. However, further studies are required to identify the specific mechanism of action of luteolin.
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Affiliation(s)
- Mariem Achour
- Laboratory of Metabolic Biophysics and Applied Pharmacology, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia.,Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan
| | - Farhana Ferdousi
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology (AIST)-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
| | - Kazunori Sasaki
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology (AIST)-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
| | - Hiroko Isoda
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology (AIST)-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
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8
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Damal Villivalam S, You D, Kim J, Lim HW, Xiao H, Zushin PJH, Oguri Y, Amin P, Kang S. TET1 is a beige adipocyte-selective epigenetic suppressor of thermogenesis. Nat Commun 2020; 11:4313. [PMID: 32855402 PMCID: PMC7453011 DOI: 10.1038/s41467-020-18054-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 07/27/2020] [Indexed: 02/02/2023] Open
Abstract
It has been suggested that beige fat thermogenesis is tightly controlled by epigenetic regulators that sense environmental cues such as temperature. Here, we report that subcutaneous adipose expression of the DNA demethylase TET1 is suppressed by cold and other stimulators of beige adipocyte thermogenesis. TET1 acts as an autonomous repressor of key thermogenic genes, including Ucp1 and Ppargc1a, in beige adipocytes. Adipose-selective Tet1 knockout mice generated by using Fabp4-Cre improves cold tolerance and increases energy expenditure and protects against diet-induced obesity and insulin resistance. Moreover, the suppressive role of TET1 in the thermogenic gene regulation of beige adipocytes is largely DNA demethylase-independent. Rather, TET1 coordinates with HDAC1 to mediate the epigenetic changes to suppress thermogenic gene transcription. Taken together, TET1 is a potent beige-selective epigenetic breaker of the thermogenic gene program. Our findings may lead to a therapeutic strategy to increase energy expenditure in obesity and related metabolic disorders. Epigenetic regulators contribute to the modulation of adipose thermogenesis by sensing environmental cues and regulating gene expression in response. Here the authors report that a DNA demethylase TET1 mediates epigenetic changes to repress thermogenic genes in mouse adipose tissue.
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Affiliation(s)
- Sneha Damal Villivalam
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Dongjoo You
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Jinse Kim
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Hee Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center Department of Pediatrics & Biomedical Informatics, University of Cincinnati, 3333 Burnet Ave. MLC 7024, Cincinnati, OH, 45229, USA
| | - Han Xiao
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Pete-James H Zushin
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Yasuo Oguri
- UCSF Diabetes Center, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Cell and Tissue Biology, University of California, San Francisco, CA, 94143, USA
| | - Pouya Amin
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sona Kang
- Nutritional Sciences and Toxicology Department, University of California Berkeley, Berkeley, CA, 94720, USA.
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9
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Perrier JP, Kenny DA, Chaulot-Talmon A, Byrne CJ, Sellem E, Jouneau L, Aubert-Frambourg A, Schibler L, Jammes H, Lonergan P, Fair S, Kiefer H. Accelerating Onset of Puberty Through Modification of Early Life Nutrition Induces Modest but Persistent Changes in Bull Sperm DNA Methylation Profiles Post-puberty. Front Genet 2020; 11:945. [PMID: 33005172 PMCID: PMC7479244 DOI: 10.3389/fgene.2020.00945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
In humans and model species, alterations of sperm DNA methylation patterns have been reported in cases of spermatogenesis defects, male infertility and exposure to toxins or nutritional challenges, suggesting that a memory of environmental or physiological changes is recorded in the sperm methylome. The objective of this study was to ascertain if early life plane of nutrition could have a latent effect on DNA methylation patterns in sperm produced post-puberty. Holstein-Friesian calves were assigned to either a high (H) or moderate (M) plane of nutrition for the first 24 weeks of age, then reassigned to the M diet until puberty, resulting in HM and MM groups. Sperm DNA methylation patterns from contrasted subgroups of bulls in the HM (ejaculates recovered at 15 months of age; n = 9) and in the MM (15 and 16 months of age; n = 7 and 9, respectively) were obtained using Reduced Representation Bisulfite Sequencing. Both 15 and 16 months were selected in the MM treatment as these bulls reached puberty approximately 1 month after the HM bulls. Hierarchical clustering demonstrated that inter-individual variability unrelated to diet or age dominated DNA methylation profiles. While the comparison between 15 and 16 months of age revealed almost no change, 580 differentially methylated CpGs (DMCs) were identified between the HM and MM groups. Differentially methylated CpGs were mostly hypermethylated in the HM group, and enriched in endogenous retrotransposons, introns, intergenic regions, and shores and shelves of CpG islands. Furthermore, genes involved in spermatogenesis, Sertoli cell function, and the hypothalamic-pituitary-gonadal axis were targeted by differential methylation when HM and MM groups were compared at 15 months of age, reflecting the earlier timing of puberty onset in the HM bulls. In contrast, the genes still differentially methylated in MM bulls at 16 months of age were enriched for ATP-binding molecular function, suggesting that changes to the sperm methylome could persist even after the HM and MM bulls reached a similar level of sexual maturity. Together, results demonstrate that enhanced plane of nutrition in pre-pubertal calves associated with advanced puberty induced modest but persistent changes in sperm DNA methylation profiles after puberty.
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Affiliation(s)
- Jean-Philippe Perrier
- Laboratory of Animal Reproduction, Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Aurélie Chaulot-Talmon
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Colin J Byrne
- Laboratory of Animal Reproduction, Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, University of Limerick, Limerick, Ireland.,Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | | | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Anne Aubert-Frambourg
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | | | - Hélène Jammes
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sean Fair
- Laboratory of Animal Reproduction, Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
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10
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Cervantes-Ayalc A, Ruiz Esparza-Garrido R, Velázquez-Flores MÁ. Long Interspersed Nuclear Elements 1 (LINE1): The chimeric transcript L1-MET and its involvement in cancer. Cancer Genet 2020; 241:1-11. [PMID: 31918342 DOI: 10.1016/j.cancergen.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022]
Abstract
Long interspersed nuclear elements 1 (LINE1) are non-LTR retrotransposons that represent the greatest remodeling force of the human genome during evolution. Genomically, LINE1 are constituted by a 5´ untranslated region (UTR), where the promoter regions are located, three open reading frames (ORF0, ORF1, and ORF2) and one 3´UTR, which has a poly(A) tail that harbors the short interspersed nuclear elements (SINEs) Alu and SVA. Although the intrinsic nature of LINE1 is to be copied and inserted into the genome, an increase in their mobility produces genomic instability. In response to this, the cell has "designed" many mechanisms controlling the retrotransposition levels of LINE1; however, alterations in these regulation systems can increase LINE1 mobility and the formation of chimeric genes. Evidence indicates that 988 human genes have LINE1 inserted in their sequence, resulting in the transcriptional control of genes by their own promoters, as well as by the LINE1 antisense promoter (ASP). To date, very little is known about the biologic impact of this and the L1-MET chimera is a more or less studied case. ASP hypomethylation has been observed in all studied cancer types, leading to increased L1-MET expression. In specific types of cancer, this L1-MET increase controls both low and high MET protein levels. It remains to be clarified if this protein product is a chimeric protein.
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Affiliation(s)
- Andrea Cervantes-Ayalc
- Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX 06720, México.
| | - Ruth Ruiz Esparza-Garrido
- Catedrática CONACyT, Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX 06720, México; Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX 06720, México.
| | - Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX 06720, México; Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico.
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11
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Mahajan V, Farquhar C, Ponnampalam AP. Could DNA hydroxymethylation be crucial in influencing steroid hormone signaling in endometrial biology and endometriosis? Mol Reprod Dev 2019; 87:7-16. [PMID: 31749216 DOI: 10.1002/mrd.23299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Endometriosis affects 10% of reproductive-aged women. It is characterized by the growth of the endometrium, outside the uterus and is associated with infertility and chronic abdominal pain. Lack of noninvasive diagnostic tools and early screening tests results in delayed treatment and subsequently increased disease severity. Endometriosis is a disease associated with a deregulated hormonal response, therefore, understanding the molecular mechanisms that govern this hormonal interplay is of paramount importance. DNA methylation is an epigenetic mark that regulates gene expression and is often associated with genes that code for steroid receptors and enzymes associated with estrogen synthesis and metabolism in endometriosis. DNA hydroxymethylation, which is structurally similar to methylation but functionally different, is a biologically critical mechanism that is also known to regulate gene expression. Ten Eleven Translocation (TET) proteins mediate hydroxymethylation. However, the role of DNA hydroxymethylation or TETs in the endometrium remains relatively unexplored. Currently, the "gold standard" technique used to study methylation patterns is bisulfite genomic sequencing. This technique also detects hydroxymethylation but fails to distinguish between the two, thereby limiting our understanding of these two processes. The presence of TETs in the male and female reproductive tract and its contribution to endometrial cancer makes it an important factor to study in endometriosis. This review summarizes the role of DNA methylation in aberrant steroid hormone signaling and hypothesizes that hydroxymethylation could be a factor influencing hormonal instability seen in endometriosis.
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Affiliation(s)
- Vishakha Mahajan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Cynthia Farquhar
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Anna P Ponnampalam
- The Liggins Institute, The University of Auckland, Auckland, New Zealand.,Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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12
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He H, Li W, Shen B, Zhao H, Liu J, Qin J, Shi J, Yi X, Peng M, Huo R, Jin G. Gene expression changes induced by valproate in the process of rat hippocampal neural stem cells differentiation. Cell Biol Int 2019; 44:536-548. [PMID: 31642547 DOI: 10.1002/cbin.11254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 10/19/2019] [Indexed: 12/14/2022]
Abstract
Valproate (VPA), an effective clinical approved anti-epileptic drug and mood stabilizer, has been believed to induce neuronal differentiation at the expense of inhibiting astrocytic and oligodendrocytic differentiation. Nevertheless, the involving mechanisms of it remain unclear yet. In the present study, we explored the global gene expression changes of fetus rat hippocampal neural stem cells following VPA treatment by high-throughput microarray. We obtained 874 significantly upregulated genes and 258 obviously downregulated genes (fold change > 2 and P < 0.05). Then, we performed gene ontology and pathway analyses of these differentially expressed genes and chose several genes associated with nervous system according to gene ontology analysis to conduct expression analysis to validate the reliability of the array results as well as reveal possible mechanisms of VPA. To get a better comprehension of the differentially regulated genes by VPA, we conducted protein-protein association analysis of these genes, which offered a source for further studies. In addition, we made the overlap between the VPA-downregulated genes and the predicted target genes of VPA-upregulated microRNAs (miRNAs), which were previously demonstrated. These overlapped genes may provide a source to find functional VPA/miRNA/mRNA axes during neuronal differentiation. This study first constructed a comprehensive potential downstream gene map of VPA in the process of neuronal differentiation.
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Affiliation(s)
- Hui He
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Wen Li
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Beilei Shen
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Heyan Zhao
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Juan Liu
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Jianbing Qin
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Jinhong Shi
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Xin Yi
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Min Peng
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
| | - Ran Huo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangning District, 211166, PR China
| | - Guohua Jin
- Department of Human Anatomy, Medical School, Nantong University, 19 Qixiu Road, Nantong, Chongchuan District, 226001, PR China
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Liu D, Li G, Zuo Y. Function determinants of TET proteins: the arrangements of sequence motifs with specific codes. Brief Bioinform 2019; 20:1826-1835. [DOI: 10.1093/bib/bby053] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/23/2018] [Indexed: 12/11/2022] Open
Abstract
Abstract
The ten-eleven translocation (TET) proteins play a crucial role in promoting locus-specific reversal of DNA methylation, a type of chromatin modification. Considerable evidences have demonstrated that the sequence motifs with specific codes are important to determine the functions of domains and active sites. Here, we surveyed major studies and reviews regarding the multiple functions of the TET proteins and established the patterns of the motif arrangements that determine the functions of TET proteins. First, we summarized the functional sequence basis of TET proteins and identified the new functional motifs based on the phylogenetic relationship. Next, we described the sequence characteristics of the functional motifs in detail and provided an overview of the relationship between the sequence motifs and the functions of TET proteins, including known functions and potential functions. Finally, we highlighted that sequence motifs with diverse post-translational modifications perform unique functions, and different selection pressures lead to different arrangements of sequence motifs, resulting in different paralogs and isoforms.
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Affiliation(s)
- Dongyang Liu
- The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Guangpeng Li
- The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yongchun Zuo
- The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
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14
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Exploring the Drug Repurposing Versatility of Valproic Acid as a Multifunctional Regulator of Innate and Adaptive Immune Cells. J Immunol Res 2019; 2019:9678098. [PMID: 31001564 PMCID: PMC6437734 DOI: 10.1155/2019/9678098] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/30/2018] [Accepted: 01/02/2019] [Indexed: 12/11/2022] Open
Abstract
Valproic acid (VPA) is widely recognized for its use in the control of epilepsy and other neurological disorders in the past 50 years. Recent evidence has shown the potential of VPA in the control of certain cancers, owed in part to its role in modulating epigenetic changes through the inhibition of histone deacetylases, affecting the expression of genes involved in the cell cycle, differentiation, and apoptosis. The direct impact of VPA in cells of the immune system has only been explored recently. In this review, we discuss the effects of VPA in the suppression of some activation mechanisms in several immune cells that lead to an anti-inflammatory response. As expected, immune cells are not exempt from the effect of VPA, as it also affects the expression of genes of the cell cycle and apoptosis through epigenetic modifications. In addition to inhibiting histone deacetylases, VPA promotes RNA interference, activates histone methyltransferases, or represses the activation of transcription factors. However, during the infectious process, the effectiveness of VPA is subject to the biological nature of the pathogen and the associated immune response; this is because VPA can promote the control or the progression of the infection. Due to its various effects, VPA is a promising alternative for the control of autoimmune diseases and hypersensitivity and needs to be further explored.
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15
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Noack F, Pataskar A, Schneider M, Buchholz F, Tiwari VK, Calegari F. Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis. Life Sci Alliance 2019; 2:2/2/e201900331. [PMID: 30814272 PMCID: PMC6394126 DOI: 10.26508/lsa.201900331] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/17/2022] Open
Abstract
This work describes the dynamics of DNA modifications in specific cell types of the developing mammalian cortex. By providing a new method to manipulate this process in vivo, it is shown how this process can influence brain formation. Dynamic changes in DNA (hydroxy-)methylation are fundamental for stem cell differentiation. However, the signature of these epigenetic marks in specific cell types during corticogenesis is unknown. Moreover, site-specific manipulation of cytosine modifications is needed to reveal the significance and function of these changes. Here, we report the first assessment of (hydroxy-)methylation in neural stem cells, neurogenic progenitors, and newborn neurons during mammalian corticogenesis. We found that gain in hydroxymethylation and loss in methylation occur sequentially at specific cellular transitions during neurogenic commitment. We also found that these changes predominantly occur within enhancers of neurogenic genes up-regulated during neurogenesis and target of pioneer transcription factors. We further optimized the use of dCas9-Tet1 manipulation of (hydroxy-)methylation, locus-specifically, in vivo, showing the biological relevance of our observations for Dchs1, a regulator of corticogenesis involved in developmental malformations and cognitive impairment. Together, our data reveal the dynamics of cytosine modifications in lineage-related cell types, whereby methylation is reduced and hydroxymethylation gained during the neurogenic lineage concurrently with up-regulation of pioneer transcription factors and activation of enhancers for neurogenic genes.
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Affiliation(s)
- Florian Noack
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
| | | | - Martin Schneider
- Medical Systems Biology, School of Medicine, Technische Universität Dresden and Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, School of Medicine, Technische Universität Dresden and Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Federico Calegari
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
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Cakouros D, Hemming S, Gronthos K, Liu R, Zannettino A, Shi S, Gronthos S. Specific functions of TET1 and TET2 in regulating mesenchymal cell lineage determination. Epigenetics Chromatin 2019; 12:3. [PMID: 30606231 PMCID: PMC6317244 DOI: 10.1186/s13072-018-0247-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
Background The 5 hydroxymethylation (5hmC) mark and TET DNA dioxygenases play a pivotal role in embryonic stem cell differentiation and animal development. However, very little is known about TET enzymes in lineage determination of human bone marrow-derived mesenchymal stem/stromal cells (BMSC). We examined the function of all three TET DNA dioxygenases, responsible for DNA hydroxymethylation, in human BMSC cell osteogenic and adipogenic differentiation. Results We used siRNA knockdown and retroviral mediated enforced expression of TET molecules and discovered TET1 to be a repressor of both osteogenesis and adipogenesis. TET1 was found to recruit the co-repressor proteins, SIN3A and the histone lysine methyltransferase, EZH2 to osteogenic genes. Conversely, TET2 was found to be a promoter of both osteogenesis and adipogenesis. The data showed that TET2 was directly responsible for 5hmC levels on osteogenic and adipogenic lineage-associated genes, whereas TET1 also played a role in this process. Interestingly, TET3 showed no functional effect in BMSC osteo-/adipogenic differentiation. Finally, in a mouse model of ovariectomy-induced osteoporosis, the numbers of clonogenic BMSC were dramatically diminished corresponding to lower trabecular bone volume and reduced levels of TET1, TET2 and 5hmC. Conclusion The present study has discovered an epigenetic mechanism mediated through changes in DNA hydroxymethylation status regulating the activation of key genes involved in the lineage determination of skeletal stem cells, which may have implications in BMSC function during normal bone regulation. Targeting TET molecules or their downstream targets may offer new therapeutic strategies to help prevent bone loss and repair following trauma or disease. Electronic supplementary material The online version of this article (10.1186/s13072-018-0247-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dimitrios Cakouros
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Sarah Hemming
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Kahlia Gronthos
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Renjing Liu
- Agnes Ginges Laboratory for Diseases of the Aorta, Centenary Institute for Cancer Medicine and Cell Biology, University of Sydney, Sydney, NSW, 2042, Australia
| | - Andrew Zannettino
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.,Multiple Myeloma Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Songtao Shi
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stan Gronthos
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia. .,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
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17
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The emerging insights into catalytic or non-catalytic roles of TET proteins in tumors and neural development. Oncotarget 2018; 7:64512-64525. [PMID: 27557497 PMCID: PMC5325459 DOI: 10.18632/oncotarget.11412] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/10/2016] [Indexed: 12/29/2022] Open
Abstract
The Ten-eleven translocation (TET) proteins have been recently identified as critical regulators in epigenetic modification, especially in the methylation of cytosine in DNA. TET-mediated DNA oxidation plays prominent roles in a wide variety of physiological and pathological processes, especially in tumor and neural development. TET proteins execute stepwise enzymatic conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). In addition to the more proverbial enzymatic role of TET proteins, TET proteins also possess non-enzymatic activity, through interacting with some epigenetic modifiers. In this review article, we focus on TET proteins dual activities (catalytic or non-catalytic) in tumor and neural development. Hence, the clarification of TET proteins dual activities will contribute to our further understanding of neural development and may open the possibility of new therapeutic avenues to human tumors.
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18
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Abstract
The Slit-Robo GTPase-activating proteins (srGAPs) were first identified as potential Slit-Robo effectors that influence growth cone guidance. Given their N-terminal F-BAR, central GAP and C-terminal SH3 domains, srGAPs have the potential to affect membrane dynamics, Rho family GTPase activity and other binding partners. Recent research has clarified how srGAP family members act in distinct ways at the cell membrane, and has expanded our understanding of the roles of srGAPs in neuronal and non-neuronal cells. Gene duplication of the human-specific paralog of srGAP2 has resulted in srGAP2 family proteins that may have increased the density of dendritic spines and promoted neoteny of the human brain during crucial periods of human evolution, underscoring the importance of srGAPs in the unique sculpting of the human brain. Importantly, srGAPs also play roles outside of the nervous system, including during contact inhibition of cell movement and in establishing and maintaining cell adhesions in epithelia. Changes in srGAP expression may contribute to neurodevelopmental disorders, cancer metastasis and inflammation. As discussed in this Review, much remains to be discovered about how this interesting family of proteins functions in a diverse set of processes in metazoans and the functional roles srGAPs play in human disease.
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Affiliation(s)
- Bethany Lucas
- Program in Genetics, University of Wisconsin-Madison, 1117 W. Johnson St., Madison, WI 53706, USA
| | - Jeff Hardin
- Program in Genetics, University of Wisconsin-Madison, 1117 W. Johnson St., Madison, WI 53706, USA
- Department of Integrative Biology, University of Wisconsin-Madison, 1117 W. Johnson St., Madison, WI 53706, USA
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Zhao J, Ma XL, Ma JX, Sun L, Lu B, Wang Y, Xing GS, Wang Y, Dong BC, Xu LY, Kuang MJ, Fu L, Bai HH, Ma Y, Jin WL. TET3 Mediates Alterations in the Epigenetic Marker 5hmC and Akt pathway in Steroid-Associated Osteonecrosis. J Bone Miner Res 2017; 32:319-332. [PMID: 27627619 DOI: 10.1002/jbmr.2992] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/01/2016] [Accepted: 09/09/2016] [Indexed: 01/10/2023]
Abstract
Steroid-associated osteonecrosis (SAON) is one of the common complications of clinical glucocorticoid (GC) administration, with osteocyte apoptosis appearing as the primary histopathological lesion. However, the precise mechanism underlying SAON remains unknown. Epigenetic modification may be a major cause of SAON. Recently, cumulative research revealed that Ten-Eleven Translocation (TET) proteins can catalyze the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and then alter the epigenetic state of DNA. Here, we report that TET3-5hmC was upregulated in the femoral head tissues of SAON patients and MLO-Y4 cells with dexamethasone (Dex) treatment. Knockdown of TET3 in MLO-Y4 cells decreased 5hmC enrichment and rescued Dex-induced apoptosis. Meanwhile, the local intramedullary injection of TET3 siRNA in Sprague-Dawley rats abrogated GC-induced osteocyte apoptosis, histopathological changes, abnormal MRI signals, and bone microstructure declines in the femoral head in vivo. Moreover, a hydroxymethylated DNA immunoprecipitation (hMeDIP)-chip analysis of Dex-treated osteocytes revealed 456 different 5hmC-enriched genes. The Akt pathway was found to mediate the functional effect of Dex-induced dynamic 5hmC change; this was further verified in clinical samples. The loss of TET3 in MLO-Y4 cells abrogated Dex-induced Akt signaling pathway inhibition. Therefore, our data for the first time identify the effect of TET3-5hmC on the Akt pathway and the necessity of this signaling cascade in SAON, identifying a new potential therapeutic target. © 2016 American Society for Bone and Mineral Research.
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Affiliation(s)
- Jie Zhao
- Tianjin Medical University General Hospital, Tianjin, China.,Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Xin-Long Ma
- Tianjin Medical University General Hospital, Tianjin, China.,Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Jian-Xiong Ma
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Lei Sun
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Bin Lu
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Ying Wang
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Guo-Sheng Xing
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Yan Wang
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Ben-Chao Dong
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Li-Yan Xu
- Tianjin Medical University General Hospital, Tianjin, China.,Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Ming-Jie Kuang
- Tianjin Medical University General Hospital, Tianjin, China.,Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Lin Fu
- Tianjin Medical University General Hospital, Tianjin, China.,Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Hao-Hao Bai
- Institute of Orthopedics, Tianjin Hospital, Tianjin, China
| | - Yue Ma
- Department of Instrument Science and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai, China.,National Centers for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Lin Jin
- Department of Instrument Science and Engineering, Key Lab. for Thin Film and Microfabrication Technology of Ministry of Education, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong University, Shanghai, China.,National Centers for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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20
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Hack LM, Dick AL, Provençal N. Epigenetic mechanisms involved in the effects of stress exposure: focus on 5-hydroxymethylcytosine. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw016. [PMID: 29492296 PMCID: PMC5804530 DOI: 10.1093/eep/dvw016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/03/2016] [Accepted: 06/11/2016] [Indexed: 05/31/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is a recently re-discovered transient intermediate in the active demethylation pathway that also appears to play an independent role in modulating gene function. Epigenetic marks, particularly 5-methylcytosine, have been widely studied in relation to stress-related disorders given the long-lasting effect that stress has on these marks. 5hmC is a good candidate for involvement in the etiology of these disorders given its elevated concentration in mammalian neurons, its dynamic regulation during development of the central nervous system, and its high variability among individuals. Although we are unaware of any studies published to date examining 5 hmC profiles in human subjects who have developed a psychiatric disorder after a life stressor, there is emerging evidence from the animal literature that 5hmC profiles are altered in the context of fear-conditioning paradigms and stress exposure, suggesting a possible role for 5hmC in the biological underpinnings of stress-related disorders. In this review, the authors examine the available approaches for profiling 5hmC and describe their advantages and disadvantages as well as discuss the studies published thus far investigating 5hmC in the context of fear-related learning and stress exposure in animals. The authors also highlight the global versus locus-specific regulation of 5hmC in these studies. Finally, the limitations of the current studies and their implications are discussed.
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Affiliation(s)
- Laura M. Hack
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA
| | - Alec L.W. Dick
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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