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Sikder S, Baek S, McNeil T, Dalal Y. Unraveling the mechanism of centromere inactivation in human aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.30.573721. [PMID: 38313258 PMCID: PMC10836067 DOI: 10.1101/2023.12.30.573721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres during aging in human cells. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells, in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to mitotic rejuvenation of these cells. These results offer insights into a novel mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.
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Chowdhury SG, Karmakar P. Revealing the role of epigenetic and post-translational modulations of autophagy proteins in the regulation of autophagy and cancer: a therapeutic approach. Mol Biol Rep 2023; 51:3. [PMID: 38063905 DOI: 10.1007/s11033-023-08961-w] [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: 08/17/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023]
Abstract
Autophagy is a process that is characterized by the destruction of redundant components and the removal of dysfunctional ones to maintain cellular homeostasis. Autophagy dysregulation has been linked to various illnesses, such as neurodegenerative disorders and cancer. The precise transcription of the genes involved in autophagy is regulated by a network of epigenetic factors. This includes histone modifications and histone-modifying enzymes. Epigenetics is a broad category of heritable, reversible changes in gene expression that do not include changes to DNA sequences, such as chromatin remodeling, histone modifications, and DNA methylation. In addition to affecting the genes that are involved in autophagy, the epigenetic machinery can also alter the signals that control this process. In cancer, autophagy plays a dual role by preventing the development of tumors on one hand and this process may suppress tumor progression. This may be the control of an oncogene that prevents autophagy while, conversely, tumor suppression may promote it. The development of new therapeutic strategies for autophagy-related disorders could be initiated by gaining a deeper understanding of its intricate regulatory framework. There is evidence showing that certain machineries and regulators of autophagy are affected by post-translational and epigenetic modifications, which can lead to alterations in the levels of autophagy and these changes can then trigger disease or affect the therapeutic efficacy of drugs. The goal of this review is to identify the regulatory pathways associated with post-translational and epigenetic modifications of different proteins in autophagy which may be the therapeutic targets shortly.
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Affiliation(s)
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
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3
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Lee SJ, Emery D, Vukmanic E, Wang Y, Lu X, Wang W, Fortuny E, James R, Kaplan HJ, Liu Y, Du J, Dean DC. Metabolic transcriptomics dictate responses of cone photoreceptors to retinitis pigmentosa. Cell Rep 2023; 42:113054. [PMID: 37656622 PMCID: PMC10591869 DOI: 10.1016/j.celrep.2023.113054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/21/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023] Open
Abstract
Most mutations in retinitis pigmentosa (RP) arise in rod photoreceptors, but cone photoreceptors, responsible for high-resolution daylight and color vision, are subsequently affected, causing the most debilitating features of the disease. We used mass spectroscopy to follow 13C metabolites delivered to the outer retina and single-cell RNA sequencing to assess photoreceptor transcriptomes. The S cone metabolic transcriptome suggests engagement of the TCA cycle and ongoing response to ROS characteristic of oxidative phosphorylation, which we link to their histone modification transcriptome. Tumor necrosis factor (TNF) and its downstream effector RIP3, which drive ROS generation via mitochondrial dysfunction, are induced and activated as S cones undergo early apoptosis in RP. The long/medium-wavelength (L/M) cone transcriptome shows enhanced glycolytic capacity, which maintains their function as RP progresses. Then, as extracellular glucose eventually diminishes, L/M cones are sustained in long-term dormancy by lactate metabolism.
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Affiliation(s)
- Sang Joon Lee
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA; Department of Ophthalmology, Kosin University College of Medicine, #262 Gamcheon-ro, Seo-gu, Busan 49267, Korea
| | - Douglas Emery
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Eric Vukmanic
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Yekai Wang
- Departments of Ophthalmology and Visual Sciences and Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Xiaoqin Lu
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Wei Wang
- Department of Ophthalmology and Visual Sciences, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Enzo Fortuny
- Department of Neurosurgery, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Robert James
- Department of Neurosurgery, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Henry J Kaplan
- Department of Ophthalmology, St. Louis University School of Medicine, St. Louis MO 63110, USA
| | - Yongqing Liu
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Jianhai Du
- Departments of Ophthalmology and Visual Sciences and Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506, USA.
| | - Douglas C Dean
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA.
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4
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Lu CF, Zhou YN, Zhang J, Su S, Liu Y, Peng GH, Zang W, Cao J. The role of epigenetic methylation/demethylation in the regulation of retinal photoreceptors. Front Cell Dev Biol 2023; 11:1149132. [PMID: 37305686 PMCID: PMC10251769 DOI: 10.3389/fcell.2023.1149132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Photoreceptors are integral and crucial for the retina, as they convert light into electrical signals. Epigenetics plays a vital role in determining the precise expression of genetic information in space and time during the development and maturation of photoreceptors, cell differentiation, degeneration, death, and various pathological processes. Epigenetic regulation has three main manifestations: histone modification, DNA methylation, and RNA-based mechanisms, where methylation is involved in two regulatory mechanisms-histone methylation and DNA methylation. DNA methylation is the most studied form of epigenetic modification, while histone methylation is a relatively stable regulatory mechanism. Evidence suggests that normal methylation regulation is essential for the growth and development of photoreceptors and the maintenance of their functions, while abnormal methylation can lead to many pathological forms of photoreceptors. However, the role of methylation/demethylation in regulating retinal photoreceptors remains unclear. Therefore, this study aims to review the role of methylation/demethylation in regulating photoreceptors in various physiological and pathological situations and discuss the underlying mechanisms involved. Given the critical role of epigenetic regulation in gene expression and cellular differentiation, investigating the specific molecular mechanisms underlying these processes in photoreceptors may provide valuable insights into the pathogenesis of retinal diseases. Moreover, understanding these mechanisms could lead to the development of novel therapies that target the epigenetic machinery, thereby promoting the maintenance of retinal function throughout an individual's lifespan.
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Affiliation(s)
- Chao-Fan Lu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Ya-Nan Zhou
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jingjing Zhang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Songxue Su
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Yupeng Liu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Guang-Hua Peng
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou, China
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Weidong Zang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cao
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
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5
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Yin W, Mao X, Xu M, Chen M, Xue M, Su N, Yuan S, Liu Q. Epigenetic regulation in the commitment of progenitor cells during retinal development and regeneration. Differentiation 2023:S0301-4681(23)00023-3. [PMID: 37069005 DOI: 10.1016/j.diff.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/19/2023]
Abstract
Retinal development is initiated by multipotent retinal progenitor cells, which undergo several rounds of cell divisions and subsequently terminal differentiation. Retinal regeneration is usually considered as the recapitulation of retinal development, which share common mechanisms underlying the cell cycle re-entry of adult retinal stem cells and the differentiation of retinal neurons. However, how proliferative retinal progenitor cells perform a precise transition to postmitotic retinal cell types during the process of development and regeneration remains elusive. It is proposed that both the intrinsic and extrinsic programming are involved in the transcriptional regulation of the spatio-temporal fate commitment. Epigenetic modifications and the regulatory mechanisms at both DNA and chromatin levels are also postulated to play an important role in the timing of differentiation of specific retinal cells. In the present review, we have summarized recent knowledge of epigenetic regulation that underlies the commitment of retinal progenitor cells in the settings of retinal development and regeneration.
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Affiliation(s)
- Wenjie Yin
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Xiying Mao
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Miao Xu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Mingkang Chen
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Mengting Xue
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Na Su
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China
| | - Songtao Yuan
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China.
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, People's Republic of China.
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Ferdous S, Shelton DA, Getz TE, Chrenek MA, L’Hernault N, Sellers JT, Summers VR, Iuvone PM, Boss JM, Boatright JH, Nickerson JM. Deletion of histone demethylase Lsd1 (Kdm1a) during retinal development leads to defects in retinal function and structure. Front Cell Neurosci 2023; 17:1104592. [PMID: 36846208 PMCID: PMC9950115 DOI: 10.3389/fncel.2023.1104592] [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: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
Purpose The purpose of this study was to investigate the role of Lysine specific demethylase 1 (Lsd1) in murine retinal development. LSD1 is a histone demethylase that can demethylate mono- and di-methyl groups on H3K4 and H3K9. Using Chx10-Cre and Rho-iCre75 driver lines, we generated novel transgenic mouse lines to delete Lsd1 in most retinal progenitor cells or specifically in rod photoreceptors. We hypothesize that Lsd1 deletion will cause global morphological and functional defects due to its importance in neuronal development. Methods We tested the retinal function of young adult mice by electroretinogram (ERG) and assessed retinal morphology by in vivo imaging by fundus photography and SD-OCT. Afterward, eyes were enucleated, fixed, and sectioned for subsequent hematoxylin and eosin (H&E) or immunofluorescence staining. Other eyes were plastic fixed and sectioned for electron microscopy. Results In adult Chx10-Cre Lsd1fl/fl mice, we observed a marked reduction in a-, b-, and c-wave amplitudes in scotopic conditions compared to age-matched control mice. Photopic and flicker ERG waveforms were even more sharply reduced. Modest reductions in total retinal thickness and outer nuclear layer (ONL) thickness were observed in SD-OCT and H&E images. Lastly, electron microscopy revealed significantly shorter inner and outer segments and immunofluorescence showed modest reductions in specific cell type populations. We did not observe any obvious functional or morphological defects in the adult Rho-iCre75 Lsd1fl/fl animals. Conclusion Lsd1 is necessary for neuronal development in the retina. Adult Chx10-Cre Lsd1fl/fl mice show impaired retinal function and morphology. These effects were fully manifested in young adults (P30), suggesting that Lsd1 affects early retinal development in mice.
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Affiliation(s)
- Salma Ferdous
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | | | - Tatiana E. Getz
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Micah A. Chrenek
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Nancy L’Hernault
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Jana T. Sellers
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Vivian R. Summers
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - P. Michael Iuvone
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Jeffrey H. Boatright
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
- Atlanta Veterans Administration Center for Visual and Neurocognitive Rehabilitation, Decatur, GA, United States
| | - John M. Nickerson
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
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Barnstable CJ. Epigenetics and Degenerative Retinal Diseases: Prospects for New Therapeutic Approaches. Asia Pac J Ophthalmol (Phila) 2022; 11:328-334. [PMID: 36041147 DOI: 10.1097/apo.0000000000000520] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
ABSTRACT There is growing evidence that retinal degenerative diseases are accompanied by epigenetic changes in both deoxyribonucleic acid methylation and histone modification. Even in the monogenic disease retinitis pigmentosa, there is a cascade of changes in gene expression that correlate with epigenetic changes, suggesting that many of the symptoms, and degenerative changes, may be a result of epigenetic changes downstream from the genetic mutation. This is supported by data from studies of diabetic retinopathy and macular degeneration, 2 diseases where it has been difficult to define a single causative change. Initial studies with modifiers of deoxyribonucleic acid methylation suggest that they can provide therapeutic benefit. A number of drugs are available to inhibit specific epigenetic histone modifier enzymes, and these offer the possibility of new therapeutic approaches to retinal disease. Systemic treatment with inhibitors of histone demethylases and histone deacetylases have arrested rod degeneration in rodent models of retinitis pigmentosa. Some evidence has suggested that similar treatments may provide benefits for patients with diabetic retinopathy. Because differentiation of retinal stem cells is regulated in part by epigenetic mechanisms, it may also be possible to direct stem cell differentiation pathways through the use of selective epigenetic modifiers. This is predicted to provide a valuable avenue to accelerate the introduction of regenerative approaches to retinal disease. Epigenetic modifiers are poised to become a powerful new approach to treat retinal degenerative diseases.
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Affiliation(s)
- Colin J Barnstable
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, PA, US
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8
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Shen DD, Pang JR, Bi YP, Zhao LF, Li YR, Zhao LJ, Gao Y, Wang B, Wang N, Wei L, Guo H, Liu HM, Zheng YC. LSD1 deletion decreases exosomal PD-L1 and restores T-cell response in gastric cancer. Mol Cancer 2022; 21:75. [PMID: 35296335 PMCID: PMC8925194 DOI: 10.1186/s12943-022-01557-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/01/2022] [Indexed: 12/20/2022] Open
Abstract
Background Histone lysine-specific demethylase 1 (LSD1) expression has been shown to be significantly elevated in gastric cancer (GC) and may be associated with the proliferation and metastasis of GC. It has been reported that LSD1 repressed tumor immunity through programmed cell death 1 ligand 1 (PD-L1) in melanoma and breast cancer. The role of LSD1 in the immune microenvironment of GC is unknown. Methods Expression LSD1 and PD-L1 in GC patients was analyzed by immunohistochemical (IHC) and Western blotting. Exosomes were isolated from the culture medium of GC cells using an ultracentrifugation method and characterized by transmission electronic microscopy (TEM), nanoparticle tracking analysis (NTA), sucrose gradient centrifugation, and Western blotting. The role of exosomal PD-L1 in T-cell dysfunction was assessed by flow cytometry, T-cell killing and enzyme-linked immunosorbent assay (ELISA). Results Through in vivo exploration, mouse forestomach carcinoma (MFC) cells with LSD1 knockout (KO) showed significantly slow growth in 615 mice than T-cell-deficient BALB/c nude mice. Meanwhile, in GC specimens, expression of LSD1 was negatively correlated with that of CD8 and positively correlated with that of PD-L1. Further study showed that LSD1 inhibited the response of T cells in the microenvironment of GC by inducing the accumulation of PD-L1 in exosomes, while the membrane PD-L1 stayed constant in GC cells. Using exosomes as vehicles, LSD1 also obstructed T-cell response of other cancer cells while LSD1 deletion rescued T-cell function. It was found that while relying on the existence of LSD1 in donor cells, exosomes can regulate MFC cells proliferation with distinct roles depending on exosomal PD-L1-mediated T-cell immunity in vivo. Conclusion LSD1 deletion decreases exosomal PD-L1 and restores T-cell response in GC; this finding indicates a new mechanism with which LSD1 may regulate cancer immunity in GC and provides a new target for immunotherapy against GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01557-1.
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Affiliation(s)
- Dan-Dan Shen
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Jing-Ru Pang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Ya-Ping Bi
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Long-Fei Zhao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Yin-Rui Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Li-Juan Zhao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Academy of Medical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, China
| | - Ya Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Bo Wang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China
| | - Ning Wang
- The School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, Hebei, China
| | - Huiqin Guo
- Thoracic Department, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China. .,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Academy of Medical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, China.
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Henan, 450052, Zhengzhou, China. .,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Academy of Medical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, China.
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Gahan JM, Kouzel IU, Jansen KO, Burkhardt P, Rentzsch F. Histone demethylase Lsd1 is required for the differentiation of neural cells in Nematostella vectensis. Nat Commun 2022; 13:465. [PMID: 35075108 PMCID: PMC8786827 DOI: 10.1038/s41467-022-28107-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/26/2021] [Indexed: 12/21/2022] Open
Abstract
Chromatin regulation is a key process in development but its contribution to the evolution of animals is largely unexplored. Chromatin is regulated by a diverse set of proteins, which themselves are tightly regulated in a cell/tissue-specific manner. Using the cnidarian Nematostella vectensis as a basal metazoan model, we explore the function of one such chromatin regulator, Lysine specific demethylase 1 (Lsd1). We generated an endogenously tagged allele and show that NvLsd1 expression is developmentally regulated and higher in differentiated neural cells than their progenitors. We further show, using a CRISPR/Cas9 generated mutant that loss of NvLsd1 leads to developmental abnormalities. This includes the almost complete loss of differentiated cnidocytes, cnidarian-specific neural cells, as a result of a cell-autonomous requirement for NvLsd1. Together this suggests that the integration of chromatin modifying proteins into developmental regulation predates the split of the cnidarian and bilaterian lineages and constitutes an ancient feature of animal development. The evolutionary point where chromatin modifier function integrated into regulation of specific cell types is unclear. In the cnidarian Nematostella vectensis, the authors here show that lysine specific demethylase Lsd1 is developmentally regulated and required for normal development including cnidocyte differentiation.
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Affiliation(s)
- James M Gahan
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5006, Bergen, Norway.
| | - Ian U Kouzel
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5006, Bergen, Norway
| | - Kamilla Ormevik Jansen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5006, Bergen, Norway
| | - Pawel Burkhardt
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5006, Bergen, Norway
| | - Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5006, Bergen, Norway. .,Department for Biological Sciences, University of Bergen, Thormøhlensgt 53, 5006, Bergen, Norway.
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10
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Han J, Ye S, Chen J, Wang K, Jin J, Zeng Z, Xue S. Lysine-Specific Histone Demethylase 1 Promotes Oncogenesis of the Esophageal Squamous Cell Carcinoma by Upregulating DUSP4. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1624-1634. [PMID: 34937541 DOI: 10.1134/s0006297921120117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a predominant subtype of esophageal cancer (EC) and has a poor prognosis due to its aggressive nature. Accordingly, it is necessary to find novel prognostic biomarkers and therapeutic targets for ESCC. Lysine-specific histone demethylase 1 (LSD1) plays a core role in the regulation of ESCC oncogenesis. However, the detailed mechanism of LSD1-regulated ESCC growth has not been elucidated. This study aims to explore molecular mechanism underlying the LSD1-regulated ESCC's oncogenesis. After LSD1 silencing, we detected differentially expressed genes (DEGs) in human ESCC cell line, TE-1, by transcriptome sequencing. Subsequently, we investigated expression pattern of the selected molecules in the ESCC tissues and cell lines by qRT-PCR and Western blotting. Furthermore, we explored the roles of selected molecules in ESCC using gene silencing and overexpression assays. Transcriptome sequencing showed that the expression of dual specificity phosphatase 4 (DUSP4) in TE-1 was significantly attenuated after the LSD1 silencing. In addition, the DUSP4 mRNA expression level was significantly higher in the ESCC tissues, especially in those derived from patients with invasion or metastasis. Moreover, the DUSP4 expression was positively associated with the LSD1 expression in the ESCC tissues. DUSP4 overexpression promoted proliferation, invasion, and migration of the ESCC cells, while DUSP4 silencing had an opposite effect. DUSP4 overexpression also enhanced tumorigenicity of the ESCC cells in vivo, while DUSP4 silencing inhibited tumor growth. Importantly, inhibition of cell proliferation, invasion, and migration by the LSD1 inhibitor (ZY0511) was reversed by DUSP4 overexpression. Conclusively, we found that LSD1 promotes ESCC's oncogenesis by upregulating DUSP4, the potential therapeutic and diagnostic target in ESCC.
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Affiliation(s)
- Junyong Han
- Department of Immunization, Fujian Academy of Medical Sciences, Fuzhou, Fujian, 350003, China. .,Fujian Institute of Medical Sciences, Fujian Provincial Key Laboratory of Medical Analysis, Fuzhou, Fujian, 350003, China
| | - Shixin Ye
- Department of Cardiothoracic Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, Fujian, 350025, China.
| | - Jinyan Chen
- Department of Immunization, Fujian Academy of Medical Sciences, Fuzhou, Fujian, 350003, China. .,Fujian Institute of Medical Sciences, Fujian Provincial Key Laboratory of Medical Analysis, Fuzhou, Fujian, 350003, China
| | - Kun Wang
- Department of Immunization, Fujian Academy of Medical Sciences, Fuzhou, Fujian, 350003, China. .,Fujian Institute of Medical Sciences, Fujian Provincial Key Laboratory of Medical Analysis, Fuzhou, Fujian, 350003, China
| | - Jingjun Jin
- Department of Immunization, Fujian Academy of Medical Sciences, Fuzhou, Fujian, 350003, China. .,Fujian Institute of Medical Sciences, Fujian Provincial Key Laboratory of Medical Analysis, Fuzhou, Fujian, 350003, China
| | - Zhiyong Zeng
- Department of Cardiothoracic Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, Fujian, 350025, China.
| | - Shijie Xue
- Department of Immunization, Fujian Academy of Medical Sciences, Fuzhou, Fujian, 350003, China. .,Fujian Institute of Medical Sciences, Fujian Provincial Key Laboratory of Medical Analysis, Fuzhou, Fujian, 350003, China
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11
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Inhibition of Epigenetic Modifiers LSD1 and HDAC1 Blocks Rod Photoreceptor Death in Mouse Models of Retinitis Pigmentosa. J Neurosci 2021; 41:6775-6792. [PMID: 34193554 DOI: 10.1523/jneurosci.3102-20.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Epigenetic modifiers are increasingly being investigated as potential therapeutics to modify and overcome disease phenotypes. Diseases of the nervous system present a particular problem as neurons are postmitotic and demonstrate relatively stable gene expression patterns and chromatin organization. We have explored the ability of epigenetic modifiers to prevent degeneration of rod photoreceptors in a mouse model of retinitis pigmentosa (RP), using rd10 mice of both sexes. The histone modification eraser enzymes lysine demethylase 1 (LSD1) and histone deacetylase 1 (HDAC1) are known to have dramatic effects on the development of rod photoreceptors. In the RP mouse model, inhibitors of these enzymes blocked rod degeneration, preserved vision, and affected the expression of multiple genes including maintenance of rod-specific transcripts and downregulation of those involved in inflammation, gliosis, and cell death. The neuroprotective activity of LSD1 inhibitors includes two pathways. First, through targeting histone modifications, they increase accessibility of chromatin and upregulate neuroprotective genes, such as from the Wnt pathway. We propose that this process is going in rod photoreceptors. Second, through nonhistone targets, they inhibit transcription of inflammatory genes and inflammation. This process is going in microglia, and lack of inflammation keeps rod photoreceptors alive.SIGNIFICANCE STATEMENT Retinal degenerations are a leading cause of vision loss. RP is genetically very heterogeneous, and the multiple pathways leading to cell death are one reason for the slow progress in identifying suitable treatments for patients. Here we demonstrate that inhibition of LSD1and HDAC1 in a mouse model of RP leads to preservation of rod photoreceptors and visual function, retaining of expression of rod-specific genes, and with decreased inflammation, cell death, and Müller cell gliosis. We propose that these epigenetic inhibitors cause more open and accessible chromatin, allowing expression of neuroprotective genes. A second mechanism that allows rod photoreceptor survival is suppression of inflammation by epigenetic inhibitors in microglia. Manipulation of epigenetic modifiers is a new strategy to fight neurodegeneration in RP.
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12
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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13
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Vinckier NK, Patel NA, Geusz RJ, Wang A, Wang J, Matta I, Harrington AR, Wortham M, Wetton N, Wang J, Jhala US, Rosenfeld MG, Benner CW, Shih HP, Sander M. LSD1-mediated enhancer silencing attenuates retinoic acid signalling during pancreatic endocrine cell development. Nat Commun 2020; 11:2082. [PMID: 32350257 PMCID: PMC7190832 DOI: 10.1038/s41467-020-16017-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/07/2020] [Indexed: 01/22/2023] Open
Abstract
Developmental progression depends on temporally defined changes in gene expression mediated by transient exposure of lineage intermediates to signals in the progenitor niche. To determine whether cell-intrinsic epigenetic mechanisms contribute to signal-induced transcriptional responses, here we manipulate the signalling environment and activity of the histone demethylase LSD1 during differentiation of hESC-gut tube intermediates into pancreatic endocrine cells. We identify a transient requirement for LSD1 in endocrine cell differentiation spanning a short time-window early in pancreas development, a phenotype we reproduced in mice. Examination of enhancer and transcriptome landscapes revealed that LSD1 silences transiently active retinoic acid (RA)-induced enhancers and their target genes. Furthermore, prolonged RA exposure phenocopies LSD1 inhibition, suggesting that LSD1 regulates endocrine cell differentiation by limiting the duration of RA signalling. Our findings identify LSD1-mediated enhancer silencing as a cell-intrinsic epigenetic feedback mechanism by which the duration of the transcriptional response to a developmental signal is limited.
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Affiliation(s)
- Nicholas K Vinckier
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nisha A Patel
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan J Geusz
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Allen Wang
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jinzhao Wang
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ileana Matta
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Austin R Harrington
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Matthew Wortham
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nichole Wetton
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jianxun Wang
- Howard Hughes Medical Institute and Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ulupi S Jhala
- Department of Pediatrics and Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute and Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Christopher W Benner
- Department of Cellular & Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hung-Ping Shih
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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14
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Ferdous S, Grossniklaus HE, Boatright JH, Nickerson JM. Characterization of LSD1 Expression Within the Murine Eye. Invest Ophthalmol Vis Sci 2020; 60:4619-4631. [PMID: 31675426 PMCID: PMC6827424 DOI: 10.1167/iovs.19-26728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Purpose The purpose of this study was to extend the current understanding of endogenous lysine-specific demethylase 1 (LSD1) expression spatially and temporally in the retina. Toward that end, we determined the localization and levels of LSD1 and its substrates H3K4me1 and H3K4me2 (H3K4me1/2) within the murine eye. Methods Immunofluorescent microscopy for LSD1, H3K4me1, and H3K4me2 was conducted on murine formalin-fixed paraffin-embedded eye sections across development in addition to Western immunoblotting to assess localization and protein levels. Results Retinal LSD1 protein levels were highest at postnatal day 7 (P7), whereas its substrates H3K4me1 and H3K4me2 had equally high levels at P2 and P14. Concentrations of all three proteins gradually decreased over developmental time until reaching a basement level of ∼60% of maximum at P36. LSD1 and H3K4me1/2 were expressed uniformly in all retinal progenitor cells. By P36, there was variability in LSD1 expression in the ganglion cell layer, uniform expression in the inner nuclear layer, and dichotomous expression between photoreceptors in the outer nuclear layer. This contrasted with H3K4me1/2 expression, which remained uniform. Additionally, LSD1 was widely expressed in the lens, cornea, and retinal pigment epithelium. Conclusions Consistent with its known role in neuronal differentiation, LSD1 is highly and uniformly expressed throughout all retinal progenitor cells. Variability in LSD1 expression, particularly in photoreceptors, may be indicative of their unique transcriptomes and epigenetic patterns of rods and cones. Murine rod nuclei exhibit LSD1 expression in a ring or shell, rather than throughout the nucleus, consistent with their unique inverted chromatin organization. LSD1 has substantial expression throughout adulthood, especially in cone nuclei. By providing insight into endogenous LSD1 expression, our current findings could directly inform future studies to determine the exact role of Lsd1 in the development and maintenance of specific structures and cell types within the eye.
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Affiliation(s)
- Salma Ferdous
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Hans E Grossniklaus
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Jeffrey H Boatright
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States.,Atlanta Veterans Administration Center for Visual and Neurocognitive Rehabilitation, Decatur, Georgia, United States
| | - John M Nickerson
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
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15
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LSD1/KDM1A, a Gate-Keeper of Cancer Stemness and a Promising Therapeutic Target. Cancers (Basel) 2019; 11:cancers11121821. [PMID: 31756917 PMCID: PMC6966601 DOI: 10.3390/cancers11121821] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
A new exciting area in cancer research is the study of cancer stem cells (CSCs) and the translational implications for putative epigenetic therapies targeted against them. Accumulating evidence of the effects of epigenetic modulating agents has revealed their dramatic consequences on cellular reprogramming and, particularly, reversing cancer stemness characteristics, such as self-renewal and chemoresistance. Lysine specific demethylase 1 (LSD1/KDM1A) plays a well-established role in the normal hematopoietic and neuronal stem cells. Overexpression of LSD1 has been documented in a variety of cancers, where the enzyme is, usually, associated with the more aggressive types of the disease. Interestingly, recent studies have implicated LSD1 in the regulation of the pool of CSCs in different leukemias and solid tumors. However, the precise mechanisms that LSD1 uses to mediate its effects on cancer stemness are largely unknown. Herein, we review the literature on LSD1's role in normal and cancer stem cells, highlighting the analogies of its mode of action in the two biological settings. Given its potential as a pharmacological target, we, also, discuss current advances in the design of novel therapeutic regimes in cancer that incorporate LSD1 inhibitors, as well as their future perspectives.
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16
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Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat Protoc 2019; 14:3275-3302. [PMID: 31723301 DOI: 10.1038/s41596-019-0218-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/25/2019] [Indexed: 01/20/2023]
Abstract
Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) has served as the central method for the study of histone modifications for the past decade. In ChIP-seq analyses, antibodies selectively capture nucleosomes bearing a modification of interest and the associated DNA is then mapped to the genome to determine the distribution of the mark. This approach has several important drawbacks: (i) ChIP interpretation necessitates the assumption of perfect antibody specificity, despite growing evidence that this is often not the case. (ii) Common methods for evaluating antibody specificity in other formats have little or no bearing on specificity within a ChIP experiment. (iii) Uncalibrated ChIP is reported as relative enrichment, which is biologically meaningless outside the experimental reference frame defined by a discrete immunoprecipitation (IP), thus preventing facile comparison across experimental conditions or modifications. (iv) Differential library amplification and loading onto next-generation sequencers, as well as computational normalization, can further compromise quantitative relationships that may exist between samples. Consequently, the researcher is presented with a series of potential pitfalls and is blind to nearly all of them. Here we provide a detailed protocol for internally calibrated ChIP (ICeChIP), a method we recently developed to resolve these problems by spike-in of defined nucleosomal standards within a ChIP procedure. This protocol is optimized for specificity and quantitative power, allowing for measurement of antibody specificity and absolute measurement of histone modification density (HMD) at genomic loci on a biologically meaningful scale enabling unambiguous comparisons. We provide guidance on optimal conditions for next-generation sequencing (NGS) and instructions for data analysis. This protocol takes between 17 and 18 h, excluding time for sequencing or bioinformatic analysis. The ICeChIP procedure enables accurate measurement of histone post-translational modifications (PTMs) genome-wide in mammalian cells as well as Drosophila melanogaster and Caenorhabditis elegans, indicating suitability for use in eukaryotic cells more broadly.
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17
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Swahari V, West AE. Histone demethylases in neuronal differentiation, plasticity, and disease. Curr Opin Neurobiol 2019; 59:9-15. [PMID: 30878844 DOI: 10.1016/j.conb.2019.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/14/2019] [Indexed: 12/29/2022]
Abstract
For more than 40 years after its discovery, histone methylation was thought to be largely irreversible. However, the first histone demethylase (HDM) was identified in 2004, challenging this notion. Since that time, more than 20 HDMs have been identified and characterized, and many have been shown to have critical roles in organismal development, cell fate, and disease. Here, we highlight some of the recent advances in our understanding of the function of HDMs in the context of neuronal development, plasticity, and disease. We focus, in particular, on molecular genetic studies of LSD1, Kdm6b, and Kdm5c that have elucidated both enzymatic and non-enzymatic gene regulatory functions of these HDMs in neurons.
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Affiliation(s)
- Vijay Swahari
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anne E West
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
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18
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Pluripotent Stem Cells as Models of Retina Development. Mol Neurobiol 2019; 56:6056-6070. [DOI: 10.1007/s12035-019-1504-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/21/2019] [Indexed: 01/01/2023]
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19
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Lian Y, Yang J, Lian Y, Xiao C, Hu X, Xu H. DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2. Cancer Commun (Lond) 2018; 38:64. [PMID: 30367681 PMCID: PMC6235391 DOI: 10.1186/s40880-018-0333-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/08/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent studies highlight pseudogene derived long non-coding RNAs (lncRNAs) as key regulators of cancer biology. However, few of them have been well characterized in pancreatic cancer. Here, we aimed to identify the association between pseudogene derived lncRNA DUXAP8 and growth of pancreatic cancer cells. METHODS We screened for pseudogene derived lncRNAs associated with human pancreatic cancer by comparative analysis of three independent datasets from GEO. Quantitative real-time reverse transcription polymerase chain reaction was used to assess the relative expression of DUXAP8 in pancreatic cancer tissues and cells. Loss-of-function approaches were used to investigate the potential functional roles of DUXAP8 in pancreatic cancer cell proliferation and apoptosis in vitro and in vivo. RNA immunoprecipitation, chromosome immunoprecipitation assay and rescue experiments were performed to analyze the association of DUXAP8 with target proteins and genes in pancreatic cancer cells. RESULTS Pancreatic cancer tissues had significantly higher DUXAP8 levels than paired adjacent normal tissues. High DUXAP8 expression was associated with a larger tumor size, advanced pathological stage and shorter overall survival of pancreatic cancer patients. Moreover, silencing DUXAP8 expression by siRNA or shRNA inhibited pancreatic cancer cell proliferation and promoted apoptosis in vitro and in vivo. Mechanistic analyses indicated that DUXAP8 regulates PC cell proliferation partly through downregulation of tumor suppressor CDKN1A and KLF2 expression. CONCLUSION Our results suggest that tumor expression of pseudogene derived lncRNA DUXAP8 plays an important role in pancreatic cancer progression. DUXAP8 may serve as a candidate biomarker and represent a novel therapeutic target of pancreatic cancer.
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Affiliation(s)
- Yifan Lian
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Jiebin Yang
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Yikai Lian
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Chuangxing Xiao
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China.,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China
| | - Xuezhen Hu
- Jiangsu Province Hospital of TCM, Affiliated Hospital of Nanjing University of TCM, Nanjing, 210029, Jiangsu, P. R. China.
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, 361005, Fujian, P. R. China. .,Institute for Microbial Ecology, Xiamen University, Xiamen, 361005, Fujian, P. R. China.
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20
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Miesfeld JB, Moon MS, Riesenberg AN, Contreras AN, Kovall RA, Brown NL. Rbpj direct regulation of Atoh7 transcription in the embryonic mouse retina. Sci Rep 2018; 8:10195. [PMID: 29977079 PMCID: PMC6033939 DOI: 10.1038/s41598-018-28420-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/22/2018] [Indexed: 12/24/2022] Open
Abstract
In vertebrate retinal progenitor cells, the proneural factor Atoh7 exhibits a dynamic tissue and cellular expression pattern. Although the resulting Atoh7 retinal lineage contains all seven major cell types, only retinal ganglion cells require Atoh7 for proper differentiation. Such specificity necessitates complex regulation of Atoh7 transcription during retina development. The Notch signaling pathway is an evolutionarily conserved suppressor of proneural bHLH factor expression. Previous in vivo mouse genetic studies established the cell autonomous suppression of Atoh7 transcription by Notch1, Rbpj and Hes1. Here we identify four CSL binding sites within the Atoh7 proximal regulatory region and demonstrate Rbpj protein interaction at these sequences by in vitro electromobility shift, calorimetry and luciferase assays and, in vivo via colocalization and chromatin immunoprecipitation. We found that Rbpj simultaneously represses Atoh7 transcription using both Notch-dependent and –independent pathways.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, One Shields Avenue, Davis, CA, 95616, USA
| | - Myung-Soon Moon
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, One Shields Avenue, Davis, CA, 95616, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Amy N Riesenberg
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Ashley N Contreras
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati School of Medicine, Cincinnati, OH, 45267, USA.,Department of Biology, University of Cincinnati Blue Ash College, Cincinnati, OH, 45236, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati School of Medicine, Cincinnati, OH, 45267, USA
| | - Nadean L Brown
- Department of Cell Biology & Human Anatomy, University of California Davis School of Medicine, One Shields Avenue, Davis, CA, 95616, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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21
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Corso-Díaz X, Jaeger C, Chaitankar V, Swaroop A. Epigenetic control of gene regulation during development and disease: A view from the retina. Prog Retin Eye Res 2018; 65:1-27. [PMID: 29544768 PMCID: PMC6054546 DOI: 10.1016/j.preteyeres.2018.03.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 12/20/2022]
Abstract
Complex biological processes, such as organogenesis and homeostasis, are stringently regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates and/or to respond to the microenvironment. Gene regulatory networks that guide cell differentiation and function are modulated and stabilized by modifications to DNA, RNA and proteins. In this review, we focus on two key epigenetic changes - DNA methylation and histone modifications - and discuss their contribution to retinal development, aging and disease, especially in the context of age-related macular degeneration (AMD) and diabetic retinopathy. We highlight less-studied roles of DNA methylation and provide the RNA expression profiles of epigenetic enzymes in human and mouse retina in comparison to other tissues. We also review computational tools and emergent technologies to profile, analyze and integrate epigenetic information. We suggest implementation of editing tools and single-cell technologies to trace and perturb the epigenome for delineating its role in transcriptional regulation. Finally, we present our thoughts on exciting avenues for exploring epigenome in retinal metabolism, disease modeling, and regeneration.
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Affiliation(s)
- Ximena Corso-Díaz
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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22
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Nguyen H, Kerimoglu C, Pirouz M, Pham L, Kiszka KA, Sokpor G, Sakib MS, Rosenbusch J, Teichmann U, Seong RH, Stoykova A, Fischer A, Staiger JF, Tuoc T. Epigenetic Regulation by BAF Complexes Limits Neural Stem Cell Proliferation by Suppressing Wnt Signaling in Late Embryonic Development. Stem Cell Reports 2018; 10:1734-1750. [PMID: 29779894 PMCID: PMC5993560 DOI: 10.1016/j.stemcr.2018.04.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/21/2022] Open
Abstract
During early cortical development, neural stem cells (NSCs) divide symmetrically to expand the progenitor pool, whereas, in later stages, NSCs divide asymmetrically to self-renew and produce other cell types. The timely switch from such proliferative to differentiative division critically determines progenitor and neuron numbers. However, the mechanisms that limit proliferative division in late cortical development are not fully understood. Here, we show that the BAF (mSWI/SNF) complexes restrict proliferative competence and promote neuronal differentiation in late corticogenesis. Inactivation of BAF complexes leads to H3K27me3-linked silencing of neuronal differentiation-related genes, with concurrent H3K4me2-mediated activation of proliferation-associated genes via de-repression of Wnt signaling. Notably, the deletion of BAF complexes increased proliferation of neuroepithelial cell-like NSCs, impaired neuronal differentiation, and exerted a Wnt-dependent effect on neocortical and hippocampal development. Thus, these results demonstrate that BAF complexes act as both activators and repressors to control global epigenetic and gene expression programs in late corticogenesis. Loss of BAF complexes increases H3K27me3 and H3K4me2 marks in late corticogenesis BAF complexes epigenetically regulate neural proliferation and differentiation BAF complexes suppress neuroepithelial cell fate and Wnt signaling BAF complexes control cortical development in a Wnt signaling-dependent manner
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Affiliation(s)
- Huong Nguyen
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany
| | - Cemil Kerimoglu
- Department of Psychiatry and Psychotherapy, University Medical Center, Georg- August-University Goettingen, 37077 Goettingen, Germany; Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases, 37075 Goettingen, Germany
| | - Mehdi Pirouz
- Max-Planck-Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Linh Pham
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany
| | - Kamila A Kiszka
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany; DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB), 37075 Goettingen, Germany
| | - Godwin Sokpor
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany
| | - M Sadman Sakib
- Department of Psychiatry and Psychotherapy, University Medical Center, Georg- August-University Goettingen, 37077 Goettingen, Germany; Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases, 37075 Goettingen, Germany
| | - Joachim Rosenbusch
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany
| | - Ulrike Teichmann
- Max-Planck-Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Rho H Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Research Center for Functional Cellulomics, Seoul National University, Seoul 151- 742, Korea
| | - Anastassia Stoykova
- Max-Planck-Institute for Biophysical Chemistry, 37077 Goettingen, Germany; DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB), 37075 Goettingen, Germany
| | - Andre Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center, Georg- August-University Goettingen, 37077 Goettingen, Germany; Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases, 37075 Goettingen, Germany
| | - Jochen F Staiger
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany; DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB), 37075 Goettingen, Germany
| | - Tran Tuoc
- Institute of Neuroanatomy, University Medical Center, Georg-August- University, 37075 Goettingen, Germany; DFG Center for Nanoscale Microscopy & Molecular Physiology of the Brain (CNMPB), 37075 Goettingen, Germany.
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23
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Ahmed M, Streit A. Lsd1 interacts with cMyb to demethylate repressive histone marks and maintain inner ear progenitor identity. Development 2018; 145:dev.160325. [PMID: 29437831 DOI: 10.1242/dev.160325] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/20/2018] [Indexed: 01/30/2023]
Abstract
During development, multipotent progenitor cells must maintain their identity while retaining the competence to respond to new signalling cues that drive cell fate decisions. This depends on both DNA-bound transcription factors and surrounding histone modifications. Here, we identify the histone demethylase Lsd1 as a crucial component of the molecular machinery that preserves progenitor identity in the developing ear prior to lineage commitment. Although Lsd1 is mainly associated with repressive complexes, we show that, in ear precursors, it is required to maintain active transcription of otic genes. We reveal a novel interaction between Lsd1 and the transcription factor cMyb, which in turn recruits Lsd1 to the promoters of key ear transcription factors. Here, Lsd1 prevents the accumulation of repressive H3K9me2, while allowing H3K9 acetylation. Loss of Lsd1 function causes rapid silencing of active promoters and loss of ear progenitor genes, and shuts down the entire ear developmental programme. Our data suggest that Lsd1-cMyb acts as a co-activator complex that maintains a regulatory module at the top of the inner ear gene network.
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Affiliation(s)
- Mohi Ahmed
- Centre for Craniofacial and Regenerative Biology, Floor 27 Tower Wing, Guy's Hospital, Dental Institute, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, Floor 27 Tower Wing, Guy's Hospital, Dental Institute, King's College London, London SE1 9RT, UK
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24
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Patent highlights August-September 2017. Pharm Pat Anal 2017; 7:7-14. [PMID: 29219751 DOI: 10.4155/ppa-2017-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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25
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Xiong Y, Wang E, Huang Y, Guo X, Yu Y, Du Q, Ding X, Sun Y. Inhibition of Lysine-Specific Demethylase-1 (LSD1/KDM1A) Promotes the Adipogenic Differentiation of hESCs Through H3K4 Methylation. Stem Cell Rev Rep 2017; 12:298-304. [PMID: 27059868 PMCID: PMC4879152 DOI: 10.1007/s12015-016-9650-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Given their totipotency, human embryonic stem cells (hESCs) can differentiate into all types of cells, including adipocytes, and provide an excellent research model for studying diseases associated with the metabolism of adipocytes, such as obesity and diabetes mellitus. Epigenetic regulation, including DNA methylation and histone modification, plays an essential role in the development and differentiation of hESCs. Lysine-specific demethylase 1 (LSD1), a well-characterized histone-modifying enzyme, demethylates dimethylated histone H3 lysine 4 (H3K4) through a flavin adenine dinucleotide (FAD)-dependent oxidative reaction. LSD1 affects the growth and differentiation of human and mouse ES cells, and the deletion of this gene in mice leads to embryonic lethality. Here, we investigated the functional role of LSD1 during the adipogenic differentiation of hESCs involving the demethylation of H3K4. We also found that treating hESCs with the LSD1 inhibitor CBB1007 promotes the adipogenic differentiation of hESCs.
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Affiliation(s)
- Yujing Xiong
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Enyin Wang
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yan Huang
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xiaoyi Guo
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yiping Yu
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Qingyun Du
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xiaoyan Ding
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai, 200031, People's Republic of China
| | - Yingpu Sun
- Reproductive Medical Centre, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, People's Republic of China.
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26
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Lu AQ, Popova EY, Barnstable CJ. Activin Signals through SMAD2/3 to Increase Photoreceptor Precursor Yield during Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:838-852. [PMID: 28781074 PMCID: PMC5599185 DOI: 10.1016/j.stemcr.2017.06.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 01/23/2023] Open
Abstract
In vitro differentiation of mouse embryonic stem cells (ESCs) into retinal fates can be used to study the roles of exogenous factors acting through multiple signaling pathways during retina development. Application of activin A during a specific time frame that corresponds to early embryonic retinogenesis caused increased generation of CRX+ photoreceptor precursors and decreased PAX6+ retinal progenitor cells (RPCs). Following activin A treatment, SMAD2/3 was activated in RPCs and bound to promoter regions of key RPC and photoreceptor genes. The effect of activin on CRX expression was repressed by pharmacological inhibition of SMAD2/3 phosphorylation. Activin signaling through SMAD2/3 in RPCs regulates expression of transcription factors involved in cell type determination and promotes photoreceptor lineage specification. Our findings can contribute to the production of photoreceptors for cell replacement therapy.
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Affiliation(s)
- Amy Q Lu
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Evgenya Y Popova
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Colin J Barnstable
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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27
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Coleman JH, Lin B, Schwob JE. Dissecting LSD1-Dependent Neuronal Maturation in the Olfactory Epithelium. J Comp Neurol 2017; 525:3391-3413. [PMID: 28597915 DOI: 10.1002/cne.24259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/19/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022]
Abstract
Neurons in the olfactory epithelium (OE) each express a single dominant olfactory receptor (OR) allele from among roughly 1,000 different OR genes. While monogenic and monoallelic OR expression has been appreciated for over two decades, regulators of this process are still being described; most recently, epigenetic modifiers have been of high interest as silent OR genes are decorated with transcriptionally repressive trimethylated histone 3 lysine 9 (H3K9me3) whereas active OR genes are decorated with transcriptionally activating trimethylated histone 3 lysine 4 (H3K4me3). The lysine specific demethylase 1 (LSD1) demethylates at both of these lysine residues and has been shown to disrupt neuronal maturation and OR expression in the developing embryonic OE. Despite the growing literature on LSD1 expression in the OE, a complete characterization of the timing of LSD1 expression relative to neuronal maturation and of the function of LSD1 in the adult OE have yet to be reported. To fill this gap, the present study determined that LSD1 (1) is expressed in early dividing cells before OR expression and neuronal maturation and decreases at the time of OR stabilization; (2) colocalizes with the repressor CoREST (also known as RCOR1) and histone deacetylase 2 in these early dividing cells; and (3) is required for neuronal maturation during a distinct time window between activating reserve stem cells (horizontal basal cells) and Neurogenin1 (+) immediate neuronal precursors. Thus, this study clarifies the role of LSD1 in olfactory neuronal maturation.
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Affiliation(s)
- Julie H Coleman
- Department of Developmental, Molecular & Chemical Biology, School of Medicine, Tufts University, Boston, Massachusetts.,Program in Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
| | - Brian Lin
- Department of Developmental, Molecular & Chemical Biology, School of Medicine, Tufts University, Boston, Massachusetts.,Program in Cell, Molecular & Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
| | - James E Schwob
- Department of Developmental, Molecular & Chemical Biology, School of Medicine, Tufts University, Boston, Massachusetts
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28
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Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes. PLoS One 2017. [PMID: 28640837 PMCID: PMC5480877 DOI: 10.1371/journal.pone.0179230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transcriptome complexity is substantially increased by the use of multiple transcription start sites for a given gene. By utilizing a rod photoreceptor-specific chromatin signature, and the RefSeq database of established transcription start sites, we have identified essentially all known rod photoreceptor genes as well as a group of novel genes that have a high probability of being expressed in rod photoreceptors. Approximately half of these novel rod genes are transcribed into multiple mRNA and/or protein isoforms through alternative transcriptional start sites (ATSS), only one of which has a rod-specific epigenetic signature and gives rise to a rod transcript. This suggests that, during retina development, some genes use ATSS to regulate cell type and temporal specificity, effectively generating a rod transcript from otherwise ubiquitously expressed genes. Biological confirmation of the relationship between epigenetic signatures and gene expression, as well as comparison of our genome-wide chromatin signature maps with available data sets for retina, namely a ChIP-on-Chip study of Polymerase-II (Pol-II) binding sites, ChIP-Seq studies for NRL- and CRX- binding sites and DHS (University of Washington data, available on UCSC mouse Genome Browser as a part of ENCODE project) fully support our hypothesis and together accurately identify and predict an array of new rod transcripts. The same approach was used to identify a number of TSS that are not currently in RefSeq. Biological conformation of the use of some of these TSS suggests that this method will be valuable for exploring the range of transcriptional complexity in many tissues. Comparison of mouse and human genome-wide data indicates that most of these alternate TSS appear to be present in both species, indicating that our approach can be useful for identification of regulatory regions that might play a role in human retinal disease.
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29
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Ferreira RC, Popova EY, James J, Briones MRS, Zhang SS, Barnstable CJ. Histone Deacetylase 1 Is Essential for Rod Photoreceptor Differentiation by Regulating Acetylation at Histone H3 Lysine 9 and Histone H4 Lysine 12 in the Mouse Retina. J Biol Chem 2016; 292:2422-2440. [PMID: 28028172 DOI: 10.1074/jbc.m116.756643] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/22/2016] [Indexed: 01/19/2023] Open
Abstract
Histone acetylation has a regulatory role in gene expression and is necessary for proper tissue development. To investigate the specific roles of histone deacetylases (HDACs) in rod differentiation in neonatal mouse retinas, we used a pharmacological approach that showed that inhibition of class I but not class IIa HDACs caused the same phenotypic changes seen with broad spectrum HDAC inhibitors, most notably a block in the differentiation of rod photoreceptors. Inhibition of HDAC1 resulted in increase of acetylation of lysine 9 of histone 3 (H3K9) and lysine 12 of histone 4 (H4K12) but not lysine 27 of histone 3 (H3K27) and led to maintained expression of progenitor-specific genes such as Vsx2 and Hes1 with concomitant block of expression of rod-specific genes. ChiP experiments confirmed these changes in the promoters of a group of progenitor genes. Based on our results, we suggest that HDAC1-specific inhibition prevents progenitor cells of the retina from exiting the cell cycle and differentiating. HDAC1 may be an essential epigenetic regulator of the transition from progenitor cells to terminally differentiated photoreceptors.
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Affiliation(s)
- Renata C Ferreira
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Laboratory of Evolutionary Genomics and Biocomplexity, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Evgenya Y Popova
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
| | - Jessica James
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033
| | - Marcelo R S Briones
- Laboratory of Evolutionary Genomics and Biocomplexity, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Samuel S Zhang
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
| | - Colin J Barnstable
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033, .,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
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