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Chen Z, Choi ER, Encarnacion AM, Yao H, Ding M, Park YH, Choi SM, An YJ, Hong E, Choi HJ, Kim SK, Nam YE, Kim GJ, Park SW, Kim JS, Kim E, Lee S, Cho JH, Lee TH. Discovery of TCP-(MP)-caffeic acid analogs as a new class of agents for treatment of osteoclastic bone loss. Bioorg Chem 2024; 150:107603. [PMID: 38968905 DOI: 10.1016/j.bioorg.2024.107603] [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: 02/28/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Inhibition of LSD1 was proposed as promising and attractive therapies for treating osteoporosis. Here, we synthesized a series of novel TCP-(MP)-Caffeic acid analogs as potential LSD1 inhibitors to assess their inhibitory effects on osteoclastogenesis by using TRAP-staining assay and try to explore the preliminary SAR. Among them, TCP-MP-CA (11a) demonstrated osteoclastic bone loss both in vitro and in vivo, showing a significant improvement in the in vivo effects compared to the LSD1 inhibitor GSK-LSD1. Additionally, we elucidated a mechanism that 11a and its precursor that 11e directly bind to LSD1/CoREST complex through FAD to inhibit LSD1 demethylation activity and influence its downstream IκB/NF-κB signaling pathway, and thus regulate osteoclastic bone loss. These findings suggested 11a or 11e as potential novel candidates for treating osteoclastic bone loss, and a concept for further development of TCP-(MP)-Caffeic acid analogs for therapeutic use in osteoporosis clinics.
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Affiliation(s)
- Zhihao Chen
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Eun Rang Choi
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Alessandra Marie Encarnacion
- Department of Interdisciplinary Program of Biomedical Engineering, Graduate School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hongyuan Yao
- Department of Interdisciplinary Program of Biomedical Engineering, Graduate School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Mina Ding
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Young-Hoon Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Se Myeong Choi
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Yeon Jin An
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Hye-Ji Choi
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang Kyoon Kim
- Preclinical Research Center (PRC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
| | - Ye Eun Nam
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang-Wook Park
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Eunae Kim
- Department of Pharmacy, College of Pharmacy, Chosun University, Gwangju 61452, Republic of Korea
| | - Sunwoo Lee
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jong Hyun Cho
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea; Department of Translational Biomedical Sciences, Graduate School of Dong-A University, Busan 49201, Republic of Korea.
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea; Department of Interdisciplinary Program of Biomedical Engineering, Graduate School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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2
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Yu J, Yu C, Bayliss G, Zhuang S. Protein arginine methyltransferases in renal development, injury, repair, and fibrosis. Front Pharmacol 2023; 14:1123415. [PMID: 36817133 PMCID: PMC9935595 DOI: 10.3389/fphar.2023.1123415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Protein arginine methyltransferases (PRMTs) methylate a range of histone and non-histone substrates and participate in multiple biological processes by regulating gene transcription and post-translational modifications. To date, most studies on PRMTs have focused on their roles in tumors and in the physiological and pathological conditions of other organs. Emerging evidence indicates that PRMTs are expressed in the kidney and contribute to renal development, injury, repair, and fibrosis. In this review, we summarize the role and the mechanisms of PRMTs in regulating these renal processes and provide a perspective for future clinical applications.
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Affiliation(s)
- Jianjun Yu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chao Yu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Georgia Bayliss
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, RI, United States
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, RI, United States
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3
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Epigenetic Regulation of Methylation in Determining the Fate of Dental Mesenchymal Stem Cells. Stem Cells Int 2022; 2022:5015856. [PMID: 36187229 PMCID: PMC9522499 DOI: 10.1155/2022/5015856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Dental mesenchymal stem cells (DMSCs) are crucial in tooth development and periodontal health, and their multipotential differentiation and self-renewal ability play a critical role in tissue engineering and regenerative medicine. Methylation modifications could promote the appropriate biological behavior by postsynthetic modification of DNA or protein and make the organism adapt to developmental and environmental prompts by regulating gene expression without changing the DNA sequence. Methylation modifications involved in DMSC fate include DNA methylation, RNA methylation, and histone modifications, which have been proven to exert a significant effect on the regulation of the fate of DMSCs, such as proliferation, self-renewal, and differentiation potential. Understanding the regulation of methylation modifications on the behavior and the immunoinflammatory responses involved in DMSCs contributes to further study of the mechanism of methylation on tissue regeneration and inflammation. In this review, we briefly summarize the key functions of histone methylation, RNA methylation, and DNA methylation in the differentiation potential and self-renewal of DMSCs as well as the opportunities and challenges for their application in tissue regeneration and disease therapy.
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4
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Zuo ZY, Yang GH, Wang HY, Liu SY, Zhang YJ, Cai Y, Chen F, Dai H, Xiao Y, Cheng MB, Huang Y, Zhang Y. Klf4 methylated by Prmt1 restrains the commitment of primitive endoderm. Nucleic Acids Res 2022; 50:2005-2018. [PMID: 35137179 PMCID: PMC8887470 DOI: 10.1093/nar/gkac054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
The second cell fate decision in the early stage of mammalian embryonic development is pivotal; however, the underlying molecular mechanism is largely unexplored. Here, we report that Prmt1 acts as an important regulator in primitive endoderm (PrE) formation. First, Prmt1 depletion promotes PrE gene expression in mouse embryonic stem cells (ESCs). Single-cell RNA sequencing and flow cytometry assays demonstrated that Prmt1 depletion in mESCs contributes to an emerging cluster, where PrE genes are upregulated significantly. Furthermore, the efficiency of extraembryonic endoderm stem cell induction increased in Prmt1-depleted ESCs. Second, the pluripotency factor Klf4 methylated at Arg396 by Prmt1 is required for recruitment of the repressive mSin3a/HDAC complex to silence PrE genes. Most importantly, an embryonic chimeric assay showed that Prmt1 inhibition and mutated Klf4 at Arg 396 induce the integration of mouse ESCs into the PrE lineage. Therefore, we reveal a regulatory mechanism for cell fate decisions centered on Prmt1-mediated Klf4 methylation.
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Affiliation(s)
- Zhen-yu Zuo
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Guang-hui Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hai-yu Wang
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Shu-yu Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Yan-jun Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Yun Cai
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Fei Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hui Dai
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Yi Xiao
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Mo-bin Cheng
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Ye Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
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5
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Yao T, Xu Z, Hao Z, Yu Y, Liang B, Wang S. KDM5B promotes cell migration by regulating the noncanonical Wnt/PCP pathway in Hirschsprung's disease. Pediatr Surg Int 2022; 38:99-107. [PMID: 34455465 DOI: 10.1007/s00383-021-05005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE We measured the expression of the histone demethylase lysine-specific demethylase 5B (KDM5B) in the bowels of patients with Hirschsprung's disease (HSCR) and investigated the molecular mechanism by which KDM5B promotes the migration of neuronal PC12 cells. METHODS KDM5B expression was detected in the ganglionic and aganglionic colon of patients with HSCR (n = 10) and controls (n = 10). The expression and localization of KDM5B were assessed using immunohistochemical and immunofluorescence staining. Real-time PCR and Western blotting were performed to quantify KDM5B expression. The migration was determined using Transwell and wound-healing assays. G-LISA, GTPase pulldown and luciferase-based reporter gene assays were performed to evaluate the key components of Wnt/planar cell polarity (PCP) signaling in vitro. RESULTS Our current study showed that KDM5B colocalized with neurons. KDM5B expression was reduced in HSCR specimens, while the aganglionic segments showed the greatest reduction. KDM5B knockdown inhibited the migration of PC12 cells. Moreover, inhibition of KDM5B decreased the expression of key genes in the Wnt/PCP pathway, and its inhibitory effect on PC12 cell migration was reversed by Wnt5a treatment. CONCLUSIONS KDM5B promotes neuronal migration via the Wnt/PCP pathway. A potential role for KDM5B in altered enteric nervous system development in HSCR warrants further investigation.
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Affiliation(s)
- Ting Yao
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Zhilin Xu
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Zenghui Hao
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - You Yu
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Bingxue Liang
- Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Shuyu Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China.
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6
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Liu S, Qin D, Yan Y, Wu J, Meng L, Huang W, Wang L, Chen X, Zhang L. Metabolic nuclear receptors coordinate energy metabolism to regulate Sox9 + hepatocyte fate. iScience 2021; 24:103003. [PMID: 34505013 PMCID: PMC8417399 DOI: 10.1016/j.isci.2021.103003] [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: 03/25/2021] [Revised: 04/13/2021] [Accepted: 08/16/2021] [Indexed: 11/26/2022] Open
Abstract
Recent research has indicated the adult liver Sox9+ cells located in the portal triads contribute to the physiological maintenance of liver mass and injury repair. However, the physiology and pathology regulation mechanisms of adult liver Sox9+ cells remain unknown. Here, PPARα and FXR bound to the shared site in Sox9 promoter with opposite transcriptional outputs. PPARα activation enhanced the fatty acid β-oxidation, oxidative phosphorylation (OXPHOS), and adenosine triphosphate (ATP) production, thus promoting proliferation and differentiation of Sox9+ hepatocytes along periportal (PP)-perivenous (PV) axis. However, FXR activation increased glycolysis but decreased OXPHOS and ATP production, therefore preventing proliferation of Sox9+ hepatocytes along PP-PV axis by promoting Sox9+ hepatocyte self-renewal. Our research indicates that metabolic nuclear receptors play critical roles in liver progenitor Sox9+ hepatocyte homeostasis to initiate or terminate liver injury-induced cell proliferation and differentiation, suggesting that PPARα and FXR are potential therapeutic targets for modulating liver regeneration. PPARα promotes Sox9 expression and FXR inhibits Sox9 expression PPARα promotes proliferation and differentiation of Sox9+ hepatocytes FXR promotes Sox9+ hepatocyte self-renewal PPARα and FXR coordinate energy metabolism to regulate Sox9+ hepatocyte fate
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Affiliation(s)
- Shenghui Liu
- College of Veterinary Medicine/Bio-medical Center, Huazhong Agricultural University, Wuhan, Hu Bei 430070, China
| | - Dan Qin
- College of Veterinary Medicine/Bio-medical Center, Huazhong Agricultural University, Wuhan, Hu Bei 430070, China
| | - Yi Yan
- College of Veterinary Medicine/Bio-medical Center, Huazhong Agricultural University, Wuhan, Hu Bei 430070, China
| | - Jiayan Wu
- College of Veterinary Medicine/Bio-medical Center, Huazhong Agricultural University, Wuhan, Hu Bei 430070, China
| | - Lihua Meng
- College of Veterinary Medicine/Bio-medical Center, Huazhong Agricultural University, Wuhan, Hu Bei 430070, China
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Liqiang Wang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, 28th Fuxing Road, Beijing 100853, China
| | - Xiangmei Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, 28th Fuxing Road, Beijing 100853, China
| | - Lisheng Zhang
- College of Veterinary Medicine/Bio-medical Center, Huazhong Agricultural University, Wuhan, Hu Bei 430070, China
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7
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Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev 2021; 35:1142-1160. [PMID: 34244292 PMCID: PMC8336893 DOI: 10.1101/gad.345843.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Here, Urrutia et al. set out to study the mechanism that regulates the choice between pluripotency and differentiation in embryonic stem cells (ESCs). Using biochemical and genomic analyses, the authors identify SUMO2 modification of Satb2 by the E3 ligase Zfp451 as a driver of ESC differentiation. The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2K →R) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2K →R or Zfp451−/− ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog. The differentiation defect of Satb2K →R ESCs correlates with altered higher-order chromatin interactions relative to Satb2wt ESCs. Upon RA treatment of Satb2wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2K →R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
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Affiliation(s)
- Gustavo Antonio Urrutia
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kyungjin Boo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Soeren Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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8
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Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
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Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
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Abstract
The first crucial step in the developmental program occurs during pre-implantation, the time after the oocyte has been fertilized and before the embryo implants in the uterus. This period represents a vulnerable window as the epigenome undergoes dynamic changes in DNA methylation profiles. Alterations in the early embryonic reprogramming wave can impair DNA methylation patterns and induce permanent changes to the developmental program, leading to the onset of adverse health outcomes in offspring. Although there is an increasing body of evidence indicating that harmful exposures during pre-implantation embryo development can trigger lasting epigenetic alterations in offspring, the mechanisms are still not fully understood. Since physiological or pathological changes in DNA methylation can occur as a response to environmental cues, proper environmental milieu plays a critical role in the success of embryonic development. In this review, we depict the mechanisms behind the embryonic epigenetic reprogramming of DNA methylation and highlight how maternal environmental stressors (e.g., alcohol, heat stress, nutrient availability) during pre-implantation and assisted reproductive technology procedures affect development and DNA methylation marks.
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Affiliation(s)
- Mélanie Breton-Larrivée
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada
| | - Elizabeth Elder
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada
| | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Research Center of the CHU Sainte-Justine. Montreal, Canada.,Department of Obstetrics & Gynecology, Université de Montréal, Research Center of the CHU Sainte-Justine, Montréal, Canada
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10
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Zhao Q, Ji K, Wang T, Li G, Lu W, Ji J. Effect of the Histone Deacetylases Inhibitors on the Differentiation of Stem Cells in Bone Damage Repairing and Regeneration. Curr Stem Cell Res Ther 2019; 15:24-31. [PMID: 31486757 DOI: 10.2174/1574888x14666190905155516] [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: 06/01/2019] [Revised: 07/24/2019] [Accepted: 08/08/2019] [Indexed: 01/02/2023]
Abstract
Tissue damage repairing and regeneration is a research hot topic. Tissue engineering arises at the historic moment which is a defect repair compound composed of seed cells, tissue engineering scaffolds, and inducing factors. Stem cells have a limited growth period in vitro culture, and they have a pattern of replicating ageing, and these disadvantages are limiting the applications of stem cells in basic research and clinical treatment. The enhancement of stem cell differentiation ability is a difficult problem to overcome, and it is possible to enhance the differentiation ability of stem cells through histone modification so as to provide a more robust foundation for damage repairing and regeneration. Studies have shown that Histone Deacetylases (HDAC) inhibitors can improve mesenchymal stem cells in vitro induced in different directions, conversion efficiency, increasing the feasibility and safety of stem cell therapy and tissue engineering, to offer reference to promote the stem cell therapy in clinical application. Therefore, this paper mainly focusing on the usage and achievements of the deacetylase inhibitors in stem cell differentiation studies and their use and prospects in repair of bone tissue defects.
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Affiliation(s)
- Qing Zhao
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.,Nanjing Key Laboratory, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Kun Ji
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Tiancong Wang
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Guifeng Li
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wei Lu
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jun Ji
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China.,Nanjing Key Laboratory, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
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11
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GASC1 Promotes Stemness of Esophageal Squamous Cell Carcinoma via NOTCH1 Promoter Demethylation. JOURNAL OF ONCOLOGY 2019; 2019:1621054. [PMID: 31031809 PMCID: PMC6457298 DOI: 10.1155/2019/1621054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/25/2019] [Indexed: 12/31/2022]
Abstract
The highest incidence of esophageal squamous cell carcinoma (ESCC) occurs in China. Cancer stem cells play key roles for tumor progression. Gene amplified in squamous cell carcinoma 1 (GASC1) is essential to maintain self-renewal and differentiation potential of embryonic stem cells. This study aimed to reveal the effect and mechanism of GASC1 on ESCC stemness. The biological function of GASC1 in ESCC was evaluated both in vitro and in vivo. ChIP assay was performed to determine the molecular mechanism of GASC1 in epigenetic regulation of NOTCH1. We found that GASC1 expression was increased in poor differentiated ESCC cells and tissues. ESCC patients with a high level of GASC1 presented a significantly worse survival rate. GASC1 expression in purified ALDH+ ESCC cells was significantly higher than that in ALDH− cells. The stemness of ESCC was dramatically decreased after GASC1 blockade. Furthermore, blockade of GASC1 decreased NOTCH1 expression via increase of NOTCH1 promoter H3K9me2 and H3K9me3. Moreover, the impaired stemness after blockade of GASC1 could be reversed after transfection of NOTCH1 overexpression lentiviral vector. GASC1 promoted stemness in ESCC cells via NOTCH1 promoter demethylation. Therefore, GASC1/NOTCH1 signaling might be a potential therapeutic target for the treatment of ESCC patients.
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The Impact of Epigenetic Signatures on Amniotic Fluid Stem Cell Fate. Stem Cells Int 2018; 2018:4274518. [PMID: 30627172 PMCID: PMC6304862 DOI: 10.1155/2018/4274518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications play a significant role in determining the fate of stem cells and in directing the differentiation into multiple lineages. Current evidence indicates that mechanisms involved in chromatin regulation are essential for maintaining stable cell identities. There is a tight correlation among DNA methylation, histone modifications, and small noncoding RNAs during the epigenetic control of stem cells' differentiation; however, to date, the precise mechanism is still not clear. In this context, amniotic fluid stem cells (AFSCs) represent an interesting model due to their unique features and the possible advantages of their use in regenerative medicine. Recent studies have elucidated epigenetic profiles involved in AFSCs' lineage commitment and differentiation. In order to use these cells effectively for therapeutic purposes, it is necessary to understand the basis of multiple-lineage potential and elaborate in detail how cell fate decisions are made and memorized. The present review summarizes the most recent findings on epigenetic mechanisms of AFSCs with a focus on DNA methylation, histone modifications, and microRNAs (miRNAs) and addresses how their unique signatures contribute to lineage-specific differentiation.
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