1
|
Srinivas T, Siqueira E, Guil S. Techniques for investigating lncRNA transcript functions in neurodevelopment. Mol Psychiatry 2024; 29:874-890. [PMID: 38145986 PMCID: PMC11176085 DOI: 10.1038/s41380-023-02377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
Collapse
Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain.
- Germans Trias i Pujol Health Science Research Institute, 08916, Badalona, Barcelona, Catalonia, Spain.
| |
Collapse
|
2
|
Bryant L, Sangree A, Clark K, Bhoj E. Histone 3.3-related chromatinopathy: missense variants throughout H3-3A and H3-3B cause a range of functional consequences across species. Hum Genet 2024; 143:497-510. [PMID: 36867246 DOI: 10.1007/s00439-023-02536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
There has been considerable recent interest in the role that germline variants in histone genes play in Mendelian syndromes. Specifically, missense variants in H3-3A and H3-3B, which both encode Histone 3.3, were discovered to cause a novel neurodevelopmental disorder, Bryant-Li-Bhoj syndrome. Most of the causative variants are private and scattered throughout the protein, but all seem to have either a gain-of-function or dominant negative effect on protein function. This is highly unusual and not well understood. However, there is extensive literature about the effects of Histone 3.3 mutations in model organisms. Here, we collate the previous data to provide insight into the elusive pathogenesis of missense variants in Histone 3.3.
Collapse
Affiliation(s)
- Laura Bryant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Annabel Sangree
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Clark
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
| |
Collapse
|
3
|
Rhodes CT, Asokumar D, Sohn M, Naskar S, Elisha L, Stevenson P, Lee DR, Zhang Y, Rocha PP, Dale RK, Lee S, Petros TJ. Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles. Front Cell Neurosci 2024; 18:1334244. [PMID: 38419656 PMCID: PMC10899338 DOI: 10.3389/fncel.2024.1334244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Enhancer of zeste homolog 2 (Ezh2) is responsible for trimethylation of histone 3 at lysine 27 (H3K27me3), resulting in repression of gene expression. Here, we explore the role of Ezh2 in forebrain GABAergic interneuron development. Methods We removed Ezh2 in the MGE by generating Nkx2-1Cre;Ezh2 conditional knockout mice. We then characterized changes in MGE-derived interneuron fate and electrophysiological properties in juvenile mice, as well as alterations in gene expression, chromatin accessibility and histone modifications in the MGE. Results Loss of Ezh2 increases somatostatin-expressing (SST+) and decreases parvalbumin-expressing (PV+) interneurons in the forebrain. We observe fewer MGE-derived interneurons in the first postnatal week, indicating reduced interneuron production. Intrinsic electrophysiological properties in SST+ and PV+ interneurons are normal, but PV+ interneurons display increased axonal complexity in Ezh2 mutant mice. Single nuclei multiome analysis revealed differential gene expression patterns in the embryonic MGE that are predictive of these cell fate changes. Lastly, CUT&Tag analysis revealed that some genomic loci are particularly resistant or susceptible to shifts in H3K27me3 levels in the absence of Ezh2, indicating differential selectivity to epigenetic perturbation. Discussion Thus, loss of Ezh2 in the MGE alters interneuron fate, morphology, and gene expression and regulation. These findings have important implications for both normal development and potentially in disease etiologies.
Collapse
Affiliation(s)
- Christopher T Rhodes
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Dhanya Asokumar
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Mira Sohn
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Shovan Naskar
- Unit on Functional Neural Circuits, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, United States
| | - Lielle Elisha
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Parker Stevenson
- Unit on Functional Neural Circuits, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, United States
| | - Dongjin R Lee
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
- National Cancer Institute (NCI), NIH, Bethesda, MD, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| | - Soohyun Lee
- Unit on Functional Neural Circuits, National Institute of Mental Health (NIMH), NIH, Bethesda, MD, United States
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, United States
| |
Collapse
|
4
|
Kumari A, Vertii A. Perspective: "Current understanding of NADs dynamics and mechanisms of Disease". Gene 2024; 894:147960. [PMID: 37923094 DOI: 10.1016/j.gene.2023.147960] [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: 07/27/2023] [Revised: 10/09/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Chromatin architecture is essential for gene regulation, and multiple levels of the 3D chromatin organization exhibit dynamic changes during organismal development and cell differentiation. Heterochromatin, termed compartment B in Hi-C datasets, is a phase-separating gene-silencing form of chromatin, preferentially located at the two nuclear sites, nuclear (lamina-associate chromatin domains, LADs) and nucleoli (nucleoli-associated chromatin domains, NADs) peripheries. LADs and NADs contain both interchangeable and location-specific chromatin domains. Recent studies suggest striking dynamics in LADs and NADs during the differentiation of embryonic stem cells into neural progenitors and neurons. Here we discuss recent advances in understanding NADs changes during neuronal differentiation and future questions on how NADs integrity can contribute to healthy neurodevelopment and neurodevelopment diseases.
Collapse
Affiliation(s)
- Amrita Kumari
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 1605, US
| | - Anastassiia Vertii
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 1605, US.
| |
Collapse
|
5
|
Sharma S, Bhonde R. Applicability of mesenchymal stem cell-derived exosomes as a cell-free miRNA therapy and epigenetic modifiers for diabetes. Epigenomics 2023; 15:1323-1336. [PMID: 38018455 DOI: 10.2217/epi-2023-0302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Given that exosome nanovesicles constitute various growth factors, miRNAs and lncRNAs, they have implications for epigenetic modifications. Few studies have shown that exosomes from mesenchymal stem cells (MSCs) exhibit therapeutic effects on diabetic complications by substituting miRNAs and regulating histone modifications. Therefore, reversing epigenetic aberrations in diabetes may provide new insight into its treatment. This review discusses the impact of DNA and histone methylations on the development of diabetes and its complications. Further, we talk about miRNAs dysregulated in diabetic conditions and the possibility of utilizing mesenchymal stem cell (MSC) exosomes for the development of miRNA cell-free therapy and epigenetic modifiers in reversing diabetic-induced epigenetic alterations.
Collapse
Affiliation(s)
- Shikha Sharma
- Institute For Stem Cell Science & Regenerative Medicine, Bangalore, 560065, India
| | - Ramesh Bhonde
- Dr D.Y. Patil Vidyapeeth, Pimpri, Pune, 411018, India
| |
Collapse
|
6
|
Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
Collapse
Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| |
Collapse
|
7
|
Yang P, Qin Y, Zeng L, He Y, Xie Y, Cheng X, Huang W, Cao L. Crotonylation and disease: Current progress and future perspectives. Biomed Pharmacother 2023; 165:115108. [PMID: 37392654 DOI: 10.1016/j.biopha.2023.115108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/18/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Histone lysine crotonylation was first identified as a new type of post-translational modification in 2011. In recent years, prominent progress has been made in the study of histone and nonhistone crotonylation in reproduction, development, and disease. Although the regulatory enzyme systems and targets of crotonylation partially overlap with those of acetylation, the peculiar CC bond structure of crotonylation suggests that crotonylation may have specific biological functions. In this review, we summarize the latest research progress regarding crotonylation, especially its regulatory factors and relationship with diseases, which suggest further research directions for crotonylation and provide new ideas for developing disease intervention and treatment regimens.
Collapse
Affiliation(s)
- Ping Yang
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Yuanyuan Qin
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Lisha Zeng
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China
| | - Yanqiu He
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Yumei Xie
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Xi Cheng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China.
| | - Ling Cao
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China.
| |
Collapse
|
8
|
Improda T, Morgera V, Vitale M, Chiariotti L, Passaro F, Feola A, Porcellini A, Cuomo M, Pezone A. Specific Methyl-CpG Configurations Define Cell Identity through Gene Expression Regulation. Int J Mol Sci 2023; 24:9951. [PMID: 37373098 DOI: 10.3390/ijms24129951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Cell identity is determined by the chromatin structure and profiles of gene expression, which are dependent on chromatin accessibility and DNA methylation of the regions critical for gene expression, such as enhancers and promoters. These epigenetic modifications are required for mammalian development and are essential for the establishment and maintenance of the cellular identity. DNA methylation was once thought to be a permanent repressive epigenetic mark, but systematic analyses in various genomic contexts have revealed a more dynamic regulation than previously thought. In fact, both active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. To link methylation signatures of specific genes to their expression profiles, we determined the methyl-CpG configurations of the promoters of five genes switched on and off during murine postnatal brain differentiation by bisulfite-targeted sequencing. Here, we report the structure of significant, dynamic, and stable methyl-CpG profiles associated with silencing or activation of the expression of genes during neural stem cell and brain postnatal differentiation. Strikingly, these methylation cores mark different mouse brain areas and cell types derived from the same areas during differentiation.
Collapse
Affiliation(s)
- Teresa Improda
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Valentina Morgera
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Maria Vitale
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
| | - Fabiana Passaro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
| | - Antonia Feola
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Antonio Porcellini
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| | - Mariella Cuomo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
| | - Antonio Pezone
- Dipartimento di Biologia, Complesso Universitario di Monte Sant'Angelo, Università degli Studi di Napoli "Federico II", 80126 Napoli, Italy
| |
Collapse
|
9
|
Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
Collapse
Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| |
Collapse
|
10
|
Hassan Z, Coelho D, Bossenmeyer-Pourié C, Matmat K, Arnold C, Savladori A, Alberto JM, Umoret R, Guéant JL, Pourié G. Cognitive Impairment Is Associated with AMPAR Glutamatergic Dysfunction in a Mouse Model of Neuronal Methionine Synthase Deficiency. Cells 2023; 12:cells12091267. [PMID: 37174668 PMCID: PMC10177068 DOI: 10.3390/cells12091267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 05/15/2023] Open
Abstract
Impairment of one-carbon metabolism during pregnancy, either due to nutritional deficiencies in B9 or B12 vitamins or caused by specific genetic defects, is often associated with neurological defects, including cognitive dysfunction that persists even after vitamin supplementation. Animal nutritional models do not allow for conclusions regarding the specific brain mechanisms that may be modulated by systemic compensations. Using the Cre-lox system associated to the neuronal promoter Thy1.2, a knock-out model for the methionine synthase specifically in the brain was generated. Our results on the neurobehavioral development of offspring show that the absence of methionine synthase did not lead to growth retardation, despite an effective reduction of both its expression and the methylation status in brain tissues. Behaviors were differently affected according to their functional outcome. Only temporary retardations were recorded in the acquisition of vegetative functions during the suckling period, compared to a dramatic reduction in cognitive performance after weaning. Investigation of the glutamatergic synapses in cognitive areas showed a reduction of AMPA receptors phosphorylation and clustering, indicating an epigenomic effect of the neuronal deficiency of methionine synthase on the reduction of glutamatergic synapses excitability. Altogether, our data indicate that cognitive impairment associated with methionine synthase deficiency may not only result from neurodevelopmental abnormalities, but may also be the consequence of alterations in functional plasticity of the brain.
Collapse
Affiliation(s)
- Ziad Hassan
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - David Coelho
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, F-54000 Nancy, France
| | - Carine Bossenmeyer-Pourié
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - Karim Matmat
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - Carole Arnold
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - Aurélie Savladori
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - Jean-Marc Alberto
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - Rémy Umoret
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
- National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, F-54000 Nancy, France
| | - Grégory Pourié
- Inserm UMRS 1256 NGERE-Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, F-54000 Nancy, France
| |
Collapse
|
11
|
Sheppard SE, Bryant L, Wickramasekara RN, Vaccaro C, Robertson B, Hallgren J, Hulen J, Watson CJ, Faundes V, Duffourd Y, Lee P, Simon MC, de la Cruz X, Padilla N, Flores-Mendez M, Akizu N, Smiler J, Pellegrino Da Silva R, Li D, March M, Diaz-Rosado A, Peixoto de Barcelos I, Choa ZX, Lim CY, Dubourg C, Journel H, Demurger F, Mulhern M, Akman C, Lippa N, Andrews M, Baldridge D, Constantino J, van Haeringen A, Snoeck-Streef I, Chow P, Hing A, Graham JM, Au M, Faivre L, Shen W, Mao R, Palumbos J, Viskochil D, Gahl W, Tifft C, Macnamara E, Hauser N, Miller R, Maffeo J, Afenjar A, Doummar D, Keren B, Arn P, Macklin-Mantia S, Meerschaut I, Callewaert B, Reis A, Zweier C, Brewer C, Saggar A, Smeland MF, Kumar A, Elmslie F, Deshpande C, Nizon M, Cogne B, van Ierland Y, Wilke M, van Slegtenhorst M, Koudijs S, Chen JY, Dredge D, Pier D, Wortmann S, Kamsteeg EJ, Koch J, Haynes D, Pollack L, Titheradge H, Ranguin K, Denommé-Pichon AS, Weber S, Pérez de la Fuente R, Sánchez del Pozo J, Lezana Rosales JM, Joset P, Steindl K, Rauch A, Mei D, Mari F, Guerrini R, Lespinasse J, Tran Mau-Them F, Philippe C, Dauriat B, Raymond L, Moutton S, Cueto-González AM, Tan TY, Mignot C, Grotto S, Renaldo F, Drivas TG, Hennessy L, Raper A, Parenti I, Kaiser FJ, Kuechler A, Busk ØL, Islam L, Siedlik JA, Henderson LB, Juusola J, Person R, Schnur RE, Vitobello A, Banka S, Bhoj EJ, Stessman HA. Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice. SCIENCE ADVANCES 2023; 9:eade1463. [PMID: 36897941 PMCID: PMC10005179 DOI: 10.1126/sciadv.ade1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.
Collapse
Affiliation(s)
- Sarah E. Sheppard
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Unit on Vascular Malformations, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Laura Bryant
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rochelle N. Wickramasekara
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
- Molecular Diagnostic Laboratory, Boys Town National Research Hospital, Omaha, NE, USA
| | - Courtney Vaccaro
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brynn Robertson
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Jodi Hallgren
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Jason Hulen
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Cynthia J. Watson
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Yannis Duffourd
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M. Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xavier de la Cruz
- Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marco Flores-Mendez
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Smiler
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- 10x Genomics, Pleasanton, CA, USA
| | | | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael March
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abdias Diaz-Rosado
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Zhao Xiang Choa
- Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chin Yan Lim
- Epithelial Epigenetics and Development Laboratory, A*STAR Skin Research Labs, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Hubert Journel
- Service de Génétique Médicale, Hopital Chubert, Vannes, Bretagne, France
| | - Florence Demurger
- Department of Clinical Genetics, Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Maureen Mulhern
- Department of Pathology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cigdem Akman
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Marisa Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dustin Baldridge
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - John Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Irina Snoeck-Streef
- Department of Child Neurology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA
| | - Anne Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA, USA
| | - John M. Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Margaret Au
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Dijon, Bourgogne, France
| | - Wei Shen
- University of Utah, Salt Lake City, UT, USA
- Mayo Clinic, Rochester, MN, USA
| | - Rong Mao
- University of Utah, Salt Lake City, UT, USA
| | | | | | - William Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia Tifft
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Natalie Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Rebecca Miller
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Jessica Maffeo
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA, USA
| | - Alexandra Afenjar
- AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France
| | - Diane Doummar
- AP-HP, Sorbonne Université, Département de neuropediatrie, Hospital Armand Trousseau, Paris, France
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, Paris, France
| | - Pamela Arn
- Department of Pediatrics, Nemours Children’s Specialty Care, Jacksonville, FL, USA
| | | | - Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Carole Brewer
- Clinical Genetics Department, Royal Devon and Exeter Hospital (Heavitree), Exeter EX1 2ED, UK
| | - Anand Saggar
- Clinical Genetics Department, St George’s Hospital, St George’s Healthcare NHS Trust, London SW17 0QT, UK
| | - Marie F. Smeland
- Department of Medical Genetics, University Hospital of North Norway, Tromsø, Norway
- Department of Pediatric Rehabilitation, University Hospital of North Norway, Norway
| | - Ajith Kumar
- Northeast Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Frances Elmslie
- South West Thames Centre for Genomics, St George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Charu Deshpande
- Department of Medical Genetics, Guy’s Hospital, London SE1 9RT, UK
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
- Nantes Université, CNRS, INSERM, L’institut du thorax, F-44000 Nantes, France
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Suzanne Koudijs
- Department of Neurology, Erasmus University Medical Center–Sophia Children’s Hospital, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Jin Yun Chen
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | - David Dredge
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Danielle Pier
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | - Saskia Wortmann
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
- Amalia Children’s Hospital, RadboudUMC Nijmegen, Nijmegen, Netherlands
| | - Erik-Jan Kamsteeg
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes Koch
- University Children’s Hospital Salzburg, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA
| | - Lynda Pollack
- Division of Genetics, Arnold Palmer Hospital for Children–Orlando Health, Orlando, FL, USA
| | - Hannah Titheradge
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK
| | - Kara Ranguin
- Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Sacha Weber
- Department of Genetics, Reference Centre for Rare Diseases and Developmental Anomalies, Caen Hospital, Caen, France
| | | | - Jaime Sánchez del Pozo
- UDISGEN (Unidad de Dismorfología y Genética) 12 de Octubre University Hospital, Madrid, Spain
| | | | - Pascal Joset
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
| | - Anita Rauch
- University of Zurich, Institute of Medical Genetics, 8952 Schlieren-Zurich, Switzerland
- University of Zurich, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- University of Zurich, URPP Adaptive Brain Circuits in Development and Learning (AdaBD), Zurich, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, Zurich 8006, Switzerland
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Francesco Mari
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, Member of ERN Epicare, University of Florence, Florence, Italy
| | - James Lespinasse
- UF de Génétique Chromosomique, Centre Hospitalier de Chambéry, Hôtel-dieu, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Benjamin Dauriat
- Service de cytogénétique et génétique médicale, Centre Hospitalier Universitaire de Limoges, France
| | - Laure Raymond
- Service de génétique, Laboratoire Eurofins Biomnis, Lyon, France
| | | | - Anna M. Cueto-González
- Hospital Vall d'Hebron, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Cyril Mignot
- AP-HP, Sorbonne Université, Département de Génétique, Paris, France
| | - Sarah Grotto
- AP-HP, Sorbonne Université, Département de Génétique, Paris, France
| | - Florence Renaldo
- AP-HP, Sorbonne Université, Département de neuropediatrie, Centre de référence neurogénétique, Hôpital Armand Trousseau, Paris, France
| | - Theodore G. Drivas
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Hennessy
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Raper
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J. Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Øyvind L. Busk
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Lily Islam
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s NHS Trust, Birmingham B15 2TG, UK
| | - Jacob A. Siedlik
- Department of Exercise Science and Pre-Health Professions, Creighton University, Omaha, NE, USA
| | | | | | | | - Rhonda E. Schnur
- GeneDx, Gaithersburg, MD, USA
- Department of Pediatrics, Division of Genetics Cooper Medical School of Rowan University Cooper University Health Care 3, Cooper Plaza, Camden, NJ, USA
| | - Antonio Vitobello
- Unité Fonctionnelle d’Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UFR Des Sciences de Santé, INSERM–Université de Bourgogne UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD, Dijon, France
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Elizabeth J. Bhoj
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Holly A. F. Stessman
- Stessman Laboratory, Department of Pharmacology and Neuroscience, Creighton University Medical School, Omaha, NE, USA
| |
Collapse
|
12
|
Anitha A, Thanseem I, Iype M, Thomas SV. Mitochondrial dysfunction in cognitive neurodevelopmental disorders: Cause or effect? Mitochondrion 2023; 69:18-32. [PMID: 36621534 DOI: 10.1016/j.mito.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Mitochondria have a crucial role in brain development and neurogenesis, both in embryonic and adult brains. Since the brain is the highest energy consuming organ, it is highly vulnerable to mitochondrial dysfunction. This has been implicated in a range of brain disorders including, neurodevelopmental conditions, psychiatric illnesses, and neurodegenerative diseases. Genetic variations in mitochondrial DNA (mtDNA), and nuclear DNA encoding mitochondrial proteins, have been associated with several cognitive disorders. However, it is not yet clear whether mitochondrial dysfunction is a primary cause of these conditions or a secondary effect. Our review article deals with this topic, and brings out recent advances in mitochondria-oriented therapies. Mitochondrial dysfunction could be involved in the pathogenesis of a subset of disorders involving cognitive impairment. In these patients, mitochondrial dysfunction could be the cause of the condition, rather than the consequence. There are vast areas in this topic that remains to be explored and elucidated.
Collapse
Affiliation(s)
- Ayyappan Anitha
- Dept. of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Shoranur, Palakkad 679 523, Kerala, India.
| | - Ismail Thanseem
- Dept. of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Shoranur, Palakkad 679 523, Kerala, India
| | - Mary Iype
- Dept. of Pediatric Neurology, Government Medical College, Thiruvananthapuram 695 011, Kerala, India; Dept. of Neurology, ICCONS, Thiruvananthapuram 695 033, Kerala, India
| | - Sanjeev V Thomas
- Dept. of Neurology, ICCONS, Thiruvananthapuram 695 033, Kerala, India
| |
Collapse
|
13
|
Berry KJ, Chandran U, Mu F, Deochand DK, Lei T, Pagin M, Nicolis SK, Monaghan-Nichols AP, Rogatsky I, DeFranco DB. Genomic glucocorticoid action in embryonic mouse neural stem cells. Mol Cell Endocrinol 2023; 563:111864. [PMID: 36690169 PMCID: PMC10057471 DOI: 10.1016/j.mce.2023.111864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Prenatal exposure to synthetic glucocorticoids (sGCs) reprograms brain development and predisposes the developing fetus towards potential adverse neurodevelopmental outcomes. Using a mouse model of sGC administration, previous studies show that these changes are accompanied by sexually dimorphic alterations in the transcriptome of neural stem and progenitor cells (NSPCs) derived from the embryonic telencephalon. Because cell type-specific gene expression profiles tightly regulate cell fate decisions and are controlled by a flexible landscape of chromatin domains upon which transcription factors and enhancer elements act, we multiplexed data from four genome-wide assays: RNA-seq, ATAC-seq (assay for transposase accessible chromatin followed by genome wide sequencing), dual cross-linking ChIP-seq (chromatin immunoprecipitation followed by genome wide sequencing), and microarray gene expression to identify novel relationships between gene regulation, chromatin structure, and genomic glucocorticoid receptor (GR) action in NSPCs. These data reveal that GR binds preferentially to predetermined regions of accessible chromatin to influence gene programming and cell fate decisions. In addition, we identify SOX2 as a transcription factor that impacts the genomic response of select GR target genes to sGCs (i.e., dexamethasone) in NSPCs.
Collapse
Affiliation(s)
- Kimberly J Berry
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA; Center for Research Computing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fangping Mu
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA; Center for Research Computing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dinesh K Deochand
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, USA
| | - T Lei
- Department of Biomedical Sciences, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126, Milano, Italy
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126, Milano, Italy
| | - A Paula Monaghan-Nichols
- Department of Biomedical Sciences, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, USA; Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, USA
| | - Donald B DeFranco
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
14
|
Feil D, Abrishamcar S, Christensen GM, Vanker A, Koen N, Kilanowski A, Hoffman N, Wedderburn CJ, Donald KA, Kobor MS, Zar HJ, Stein DJ, Hüls A. DNA methylation as a potential mediator of the association between indoor air pollution and neurodevelopmental delay in a South African birth cohort. Clin Epigenetics 2023; 15:31. [PMID: 36855151 PMCID: PMC9972733 DOI: 10.1186/s13148-023-01444-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Exposure to indoor air pollution during pregnancy has been linked to neurodevelopmental delay in toddlers. Epigenetic modification, particularly DNA methylation (DNAm), may explain this link. In this study, we employed three high-dimensional mediation analysis methods (HIMA, DACT, and gHMA) followed by causal mediation analysis to identify differentially methylated CpG sites and genes that mediate the association between indoor air pollution and neurodevelopmental delay. Analyses were performed using data from 142 mother to child pairs from a South African birth cohort, the Drakenstein Child Health Study. DNAm from cord blood was measured using the Infinium MethylationEPIC and HumanMethylation450 arrays. Neurodevelopment was assessed at age 2 years using the Bayley Scores of Infant and Toddler Development, 3rd edition across four domains (cognitive development, general adaptive behavior, language, and motor function). Particulate matter with an aerodynamic diameter of 10 μm or less (PM10) was measured inside participants' homes during the second trimester of pregnancy. RESULTS A total of 29 CpG sites and 4 genes (GOPC, RP11-74K11.1, DYRK1A, RNMT) were identified as significant mediators of the association between PM10 and cognitive neurodevelopment. The estimated proportion mediated (95%-confidence interval) ranged from 0.29 [0.01, 0.86] for cg00694520 to 0.54 [0.11, 1.56] for cg05023582. CONCLUSIONS Our findings suggest that DNAm may mediate the association between prenatal PM10 exposure and cognitive neurodevelopment. DYRK1A and several genes that our CpG sites mapped to, including CNKSR1, IPO13, IFNGR1, LONP2, and CDH1, are associated with biological pathways implicated in cognitive neurodevelopment and three of our identified CpG sites (cg23560546 [DAPL1], cg22572779 [C6orf218], cg15000966 [NT5C]) have been previously associated with fetal brain development. These findings are novel and add to the limited literature investigating the relationship between indoor air pollution, DNAm, and neurodevelopment, particularly in low- and middle-income country settings and non-white populations.
Collapse
Affiliation(s)
- Dakotah Feil
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
| | - Sarina Abrishamcar
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
| | - Grace M Christensen
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
| | - Aneesa Vanker
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anna Kilanowski
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA
- German Research Center for Environmental Health, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology, Pettenkofer School of Public Health, LMU Munich, Munich, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Nadia Hoffman
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Catherine J Wedderburn
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Atlanta, GA, 30322, USA.
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| |
Collapse
|
15
|
Rhodes C, Lin CH. Role of the histone methyltransferases Ezh2 and Suv4-20h1/Suv4-20h2 in neurogenesis. Neural Regen Res 2023; 18:469-473. [DOI: 10.4103/1673-5374.350188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
16
|
Sokolov PL, Chebanenko NV, Mednaya DM. [Epigenetic influences and brain development]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:12-19. [PMID: 36946391 DOI: 10.17116/jnevro202312303112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
In recent years, the amount of scientific data on the involvement of epigenetic processes in the regulation of brain development in postnatal ontogenesis has been rapidly growing. The article provides an overview of scientific research on the mechanisms of epigenetic influences on brain development. Information was searched in the Scopus, Web of Science, MedLine, The Cochrane Library, PubMed, Pedro, Scholar, eLibrary, CyberLeninka and RSCI databases for the period 1940-2022 by keywords: brain development, epigenetics, neuroontogenesis, methylation, histone modifications, chromatin remodeling, non-coding RNAs. Today, the mechanisms of epigenetic influence on the genome include DNA and RNA methylation, covalent modification of histones, chromatin remodeling, and the influence of non-coding RNAs. Epigenetic modifications are often reversible and provide the necessary plasticity for the response of progenitor cells to environmental signals. The influence of each of these factors on the neurodevelopment is considered. The possibility of transsynaptic transmission of hereditary material by means of circular RNA is indicated. The main ways of microRNA influence on brain development are presented and their universality as an «overgenic» regulator of organism adaptation to external conditions is indicated. Data on the relationship of long non-coding RNAs with the regulation of the functional activity of oligodendroglia are presented. Also, the data presented indicate the paths to the pathogenetically determined prevention of congenital brain pathology.
Collapse
Affiliation(s)
- P L Sokolov
- Voyno-Yasenetsky Scientific and Practical Center for Specialized Assistance for Children, Moscow, Russia
| | - N V Chebanenko
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - D M Mednaya
- Pirogov Russian National Research Medical University, Moscow, Russia
| |
Collapse
|
17
|
Pan J, Li X, Liu H, Wang C, Xu S, Xu B, Deng Y, Yang T, Liu W. Exploring the molecular mechanisms underlie the endoplasmic reticulum stress-mediated methylmercury-induced neuronal developmental damage. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 245:114099. [PMID: 36152427 DOI: 10.1016/j.ecoenv.2022.114099] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Methylmercury (MeHg) is a ubiquitous environmental pollutant, which can cross the placenta and blood brain barrier, thus affecting fetal growth and development. Although previous studies have demonstrated that MeHg induces endoplasmic reticulum (ER) stress in rat cerebral cortex and primary neurons, the role of ER stress in MeHg-induced neurodevelopmental toxicity remains unclear. Here, we used ICR pregnant mice and hippocampal neurons cells (HT22 cells) to investigate the molecular mechanism by which MeHg exposure during pregnancy affects neurodevelopment. We found that prenatal MeHg exposure caused developmental delay in offspring, accompanied with ER stress, cell apoptosis, cell cycle arrest and abnormal DNA methylation. Then, we used ER stress specific inhibitor 4-PBA and CHOP siRNA to investigate the role of ER stress on HT22 cells damage caused by MeHg. The results showed that 4-PBA pretreatment restored MeHg-induced axonal shortening and alleviated apoptosis, cell cycle arrest and DNA methylation. At the same time, the activation of CHOP/c-Jun/GADD45A signaling pathway was inhibited, and the interaction between CHOP and c-Jun was weakened. In addition, CHOP siRNA reduced the expression of c-Jun and GADD45A, and relieved DNA methylation levels to some extent. In summary, our study suggested that ER stress induced by MeHg mediated cell apoptosis and cell cycle arrest, and may affect DNA methylation through activation of CHOP/c-Jun/GADD45A signaling pathway, thus leading to neuronal damage.
Collapse
Affiliation(s)
- Jingjing Pan
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Xiaoyang Li
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Haihui Liu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Chen Wang
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Si Xu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Tianyao Yang
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, China.
| |
Collapse
|
18
|
Qazi REM, Khan I, Haneef K, Malick TS, Naeem N, Ahmad W, Salim A, Mohsin S. Combination of mesenchymal stem cells and three-dimensional collagen scaffold preserves ventricular remodeling in rat myocardial infarction model. World J Stem Cells 2022; 14:633-657. [PMID: 36157910 PMCID: PMC9453269 DOI: 10.4252/wjsc.v14.i8.633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cardiovascular diseases are the major cause of mortality worldwide. Regeneration of the damaged myocardium remains a challenge due to mechanical constraints and limited healing ability of the adult heart tissue. Cardiac tissue engineering using biomaterial scaffolds combined with stem cells and bioactive molecules could be a highly promising approach for cardiac repair. Use of biomaterials can provide suitable microenvironment to the cells and can solve cell engraftment problems associated with cell transplantation alone. Mesenchymal stem cells (MSCs) are potential candidates in cardiac tissue engineering because of their multilineage differentiation potential and ease of isolation. Use of DNA methyl transferase inhibitor, such as zebularine, in combination with three-dimensional (3D) scaffold can promote efficient MSC differentiation into cardiac lineage, as epigenetic modifications play a fundamental role in determining cell fate and lineage specific gene expression.
AIM To investigate the role of collagen scaffold and zebularine in the differentiation of rat bone marrow (BM)-MSCs and their subsequent in vivo effects.
METHODS MSCs were isolated from rat BM and characterized morphologically, immunophenotypically and by multilineage differentiation potential. MSCs were seeded in collagen scaffold and treated with 3 μmol/L zebularine in three different ways. Cytotoxicity analysis was done and cardiac differentiation was analyzed at the gene and protein levels. Treated and untreated MSC-seeded scaffolds were transplanted in the rat myocardial infarction (MI) model and cardiac function was assessed by echocardiography. Cell tracking was performed by DiI dye labeling, while regeneration and neovascularization were evaluated by histological and immunohistochemical analysis, respectively.
RESULTS MSCs were successfully isolated and seeded in collagen scaffold. Cytotoxicity analysis revealed that zebularine was not cytotoxic in any of the treatment groups. Cardiac differentiation analysis showed more pronounced results in the type 3 treatment group which was subsequently chosen for the transplantation in the in vivo MI model. Significant improvement in cardiac function was observed in the zebularine treated MSC-seeded scaffold group as compared to the MI control. Histological analysis also showed reduction in fibrotic scar, improvement in left ventricular wall thickness and preservation of ventricular remodeling in the zebularine treated MSC-seeded scaffold group. Immunohistochemical analysis revealed significant expression of cardiac proteins in DiI labeled transplanted cells and a significant increase in the number of blood vessels in the zebularine treated MSC-seeded collagen scaffold transplanted group.
CONCLUSION Combination of 3D collagen scaffold and zebularine treatment enhances cardiac differentiation potential of MSCs, improves cell engraftment at the infarcted region, reduces infarct size and improves cardiac function.
Collapse
Affiliation(s)
- Rida-e-Maria Qazi
- Stem Cell Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi 75270, Sindh, Pakistan
| | - Irfan Khan
- Stem Cell Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi 75270, Sindh, Pakistan
| | - Kanwal Haneef
- Dr.Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi 75270, Sindh, Pakistan
| | - Tuba Shakil Malick
- Stem Cell Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi 75270, Sindh, Pakistan
| | - Nadia Naeem
- Dow Research Institute of Biotechnology and Biomedical Sciences (DRIBBS), Dow University of Health and Sciences, Ojha Campus, Karachi 74200, Sindh, Pakistan
| | - Waqas Ahmad
- Stem Cell Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi 75270, Sindh, Pakistan
| | - Asmat Salim
- Stem Cell Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi 75270, Sindh, Pakistan
| | - Sadia Mohsin
- Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, United States
| |
Collapse
|
19
|
Rhodes CT, Thompson JJ, Mitra A, Asokumar D, Lee DR, Lee DJ, Zhang Y, Jason E, Dale RK, Rocha PP, Petros TJ. An epigenome atlas of neural progenitors within the embryonic mouse forebrain. Nat Commun 2022; 13:4196. [PMID: 35858915 PMCID: PMC9300614 DOI: 10.1038/s41467-022-31793-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
A comprehensive characterization of epigenomic organization in the embryonic mouse forebrain will enhance our understanding of neurodevelopment and provide insight into mechanisms of neurological disease. Here we collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters with associated transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a 'ground truth' epigenomic landscape at this critical stage of neurogenesis.
Collapse
Affiliation(s)
- Christopher T Rhodes
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Joyce J Thompson
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Dhanya Asokumar
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.,Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Dongjin R Lee
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Daniel J Lee
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.,Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Eva Jason
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.,National Cancer Institute (NCI), NIH, Bethesda, MD, 20982, USA
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| |
Collapse
|
20
|
Hara T, Tominaga Y, Ueda K, Mihara K, Yanagihara K, Takei Y. Elevated METTL9 is associated with peritoneal dissemination in human scirrhous gastric cancers. Biochem Biophys Rep 2022; 30:101255. [PMID: 35402738 PMCID: PMC8983939 DOI: 10.1016/j.bbrep.2022.101255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Toshifumi Hara
- Department of Medicinal Biochemistry, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, 464-8650, Japan
| | - Yuuki Tominaga
- Department of Medicinal Biochemistry, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, 464-8650, Japan
| | - Koji Ueda
- Project for Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Keichiro Mihara
- Department of International Center for Cell and Gene Therapy, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, 470-1192, Japan
| | - Kazuyoshi Yanagihara
- Division of Translational Research, Exploratory Oncology and Clinical Trial Center, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, 277-8577, Japan
| | - Yoshifumi Takei
- Department of Medicinal Biochemistry, School of Pharmacy, Aichi Gakuin University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, 464-8650, Japan
- Corresponding author.
| |
Collapse
|
21
|
Macht VA, Vetreno RP, Crews FT. Cholinergic and Neuroimmune Signaling Interact to Impact Adult Hippocampal Neurogenesis and Alcohol Pathology Across Development. Front Pharmacol 2022; 13:849997. [PMID: 35308225 PMCID: PMC8926387 DOI: 10.3389/fphar.2022.849997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 01/21/2023] Open
Abstract
Alcohol (ethanol) use and misuse is a costly societal issue that can affect an individual across the lifespan. Alcohol use and misuse typically initiates during adolescence and generally continues into adulthood. Not only is alcohol the most widely abused drug by adolescents, but it is also one of the most widely abused drugs in the world. In fact, high rates of maternal drinking make developmental ethanol exposure the most preventable cause of neurological deficits in the Western world. Preclinical studies have determined that one of the most consistent effects of ethanol is its disruption of hippocampal neurogenesis. However, the severity, persistence, and reversibility of ethanol’s effects on hippocampal neurogenesis are dependent on developmental stage of exposure and age at assessment. Complicating the neurodevelopmental effects of ethanol is the concurrent development and maturation of neuromodulatory systems which regulate neurogenesis, particularly the cholinergic system. Cholinergic signaling in the hippocampus directly regulates hippocampal neurogenesis through muscarinic and nicotinic receptor actions and indirectly regulates neurogenesis by providing anti-inflammatory regulatory control over the hippocampal environmental milieu. Therefore, this review aims to evaluate how shifting maturational patterns of the cholinergic system and its regulation of neuroimmune signaling impact ethanol’s effects on adult neurogenesis. For example, perinatal ethanol exposure decreases basal forebrain cholinergic neuron populations, resulting in long-term developmental disruptions to the hippocampus that persist into adulthood. Exaggerated neuroimmune responses and disruptions in adult hippocampal neurogenesis are evident after environmental, developmental, and pharmacological challenges, suggesting that perinatal ethanol exposure induces neurogenic deficits in adulthood that can be unmasked under conditions that strain neural and immune function. Similarly, adolescent ethanol exposure persistently decreases basal forebrain cholinergic neuron populations, increases hippocampal neuroimmune gene expression, and decreases hippocampal neurogenesis in adulthood. The effects of neither perinatal nor adolescent ethanol are mitigated by abstinence whereas adult ethanol exposure-induced reductions in hippocampal neurogenesis are restored following abstinence, suggesting that ethanol-induced alterations in neurogenesis and reversibility are dependent upon the developmental period. Thus, the focus of this review is an examination of how ethanol exposure across critical developmental periods disrupts maturation of cholinergic and neuroinflammatory systems to differentially affect hippocampal neurogenesis in adulthood.
Collapse
Affiliation(s)
- Victoria A Macht
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ryan P Vetreno
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Fulton T Crews
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
22
|
Wang W, Cho H, Lee JW, Lee SK. The histone demethylase Kdm6b regulates subtype diversification of mouse spinal motor neurons during development. Nat Commun 2022; 13:958. [PMID: 35177643 PMCID: PMC8854633 DOI: 10.1038/s41467-022-28636-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 01/28/2022] [Indexed: 11/09/2022] Open
Abstract
How a single neuronal population diversifies into subtypes with distinct synaptic targets is a fundamental topic in neuroscience whose underlying mechanisms are unclear. Here, we show that the histone H3-lysine 27 demethylase Kdm6b regulates the diversification of motor neurons to distinct subtypes innervating different muscle targets during spinal cord development. In mouse embryonic motor neurons, Kdm6b promotes the medial motor column (MMC) and hypaxial motor column (HMC) fates while inhibiting the lateral motor column (LMC) and preganglionic motor column (PGC) identities. Our single-cell RNA-sequencing analyses reveal the heterogeneity of PGC, LMC, and MMC motor neurons. Further, our single-cell RNA-sequencing data, combined with mouse model studies, demonstrates that Kdm6b acquires cell fate specificity together with the transcription factor complex Isl1-Lhx3. Our study provides mechanistic insight into the gene regulatory network regulating neuronal cell-type diversification and defines a regulatory role of Kdm6b in the generation of motor neuron subtypes in the mouse spinal cord.
Collapse
Affiliation(s)
- Wenxian Wang
- Department of Biological Sciences, College of Arts and Sciences, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, 14260, USA
| | - Hyeyoung Cho
- Computational Biology Program, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Jae W Lee
- Department of Biological Sciences, College of Arts and Sciences, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, 14260, USA
| | - Soo-Kyung Lee
- Department of Biological Sciences, College of Arts and Sciences, University at Buffalo, The State University of New York (SUNY), Buffalo, NY, 14260, USA.
| |
Collapse
|
23
|
Poeta E, Petralla S, Babini G, Renzi B, Celauro L, Magnifico MC, Barile SN, Masotti M, De Chirico F, Massenzio F, Viggiano L, Palmieri L, Virgili M, Lasorsa FM, Monti B. Histone Acetylation Defects in Brain Precursor Cells: A Potential Pathogenic Mechanism Causing Proliferation and Differentiation Dysfunctions in Mitochondrial Aspartate-Glutamate Carrier Isoform 1 Deficiency. Front Cell Neurosci 2022; 15:773709. [PMID: 35095421 PMCID: PMC8790092 DOI: 10.3389/fncel.2021.773709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial aspartate-glutamate carrier isoform 1 (AGC1) deficiency is an ultra-rare genetic disease characterized by global hypomyelination and brain atrophy, caused by mutations in the SLC25A12 gene leading to a reduction in AGC1 activity. In both neuronal precursor cells and oligodendrocytes precursor cells (NPCs and OPCs), the AGC1 determines reduced proliferation with an accelerated differentiation of OPCs, both associated with gene expression dysregulation. Epigenetic regulation of gene expression through histone acetylation plays a crucial role in the proliferation/differentiation of both NPCs and OPCs and is modulated by mitochondrial metabolism. In AGC1 deficiency models, both OPCs and NPCs show an altered expression of transcription factors involved in the proliferation/differentiation of brain precursor cells (BPCs) as well as a reduction in histone acetylation with a parallel alteration in the expression and activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, histone acetylation dysfunctions have been dissected in in vitro models of AGC1 deficiency OPCs (Oli-Neu cells) and NPCs (neurospheres), in physiological conditions and following pharmacological treatments. The inhibition of HATs by curcumin arrests the proliferation of OPCs leading to their differentiation, while the inhibition of HDACs by suberanilohydroxamic acid (SAHA) has only a limited effect on proliferation, but it significantly stimulates the differentiation of OPCs. In NPCs, both treatments determine an alteration in the commitment toward glial cells. These data contribute to clarifying the molecular and epigenetic mechanisms regulating the proliferation/differentiation of OPCs and NPCs. This will help to identify potential targets for new therapeutic approaches that are able to increase the OPCs pool and to sustain their differentiation toward oligodendrocytes and to myelination/remyelination processes in AGC1 deficiency, as well as in other white matter neuropathologies.
Collapse
Affiliation(s)
- Eleonora Poeta
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sabrina Petralla
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Babini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Brunaldo Renzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luigi Celauro
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maria Chiara Magnifico
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy
| | - Simona Nicole Barile
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Martina Masotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Francesca Massenzio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luigi Viggiano
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Marco Virgili
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Francesco Massimo Lasorsa
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy,*Correspondence: Francesco Massimo Lasorsa,
| | - Barbara Monti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy,Barbara Monti,
| |
Collapse
|
24
|
Jang S, Hwang J, Jeong HS. The Role of Histone Acetylation in Mesenchymal Stem Cell Differentiation. Chonnam Med J 2022; 58:6-12. [PMID: 35169553 PMCID: PMC8813658 DOI: 10.4068/cmj.2022.58.1.6] [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: 11/29/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/06/2022] Open
Abstract
The mechanism and action concerning epigenetic modifications, especially that of histone modifications, are not fully understood. However, it is clear that histone modifications play an essential role in several biological processes that are involved in cell proliferation and differentiation. In this article, we focused on how histone acetylation may result in differentiation into mesenchymal stem cells as well as histone acetylation function. Moreover, histone acetylation followed by the action of histone deacetylase inhibitors, which can result in the differentiation of stem cells into other types of cells such as adipocytes, chondrocytes, osteocytes, neurons, and other lineages, were also reviewed.
Collapse
Affiliation(s)
- Sujeong Jang
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| | - Jinsu Hwang
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| | - Han-Seong Jeong
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| |
Collapse
|
25
|
Issah MA, Wu D, Zhang F, Zheng W, Liu Y, Fu H, Zhou H, Chen R, Shen J. Epigenetic modifications in acute myeloid leukemia: The emerging role of circular RNAs (Review). Int J Oncol 2021; 59:107. [PMID: 34792180 PMCID: PMC8651224 DOI: 10.3892/ijo.2021.5287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/13/2021] [Indexed: 11/06/2022] Open
Abstract
Canonical epigenetic modifications, which include histone modification, chromatin remodeling and DNA methylation, play key roles in numerous cellular processes. Epigenetics underlies how cells that posses DNA with similar sequences develop into different cell types with different functions in an organism. Earlier epigenetic research has primarily been focused at the chromatin level. However, the number of studies on epigenetic modifications of RNA, such as N1‑methyladenosine, 2'‑O‑ribosemethylation, inosine, 5‑methylcytidine, N6‑methyladenosine (m6A) and pseudouridine, has seen an increase. Circular RNAs (circRNAs), a type of RNA species that lacks a 5' cap or 3' poly(A) tail, are abundantly expressed in acute myeloid leukemia (AML) and may regulate disease progression. circRNAs possess various functions, including microRNA sponging, gene transcription regulation and RNA‑binding protein interaction. Furthermore, circRNAs are m6A methylated in other types of cancer, such as colorectal and hypopharyngeal squamous cell cancers. Therefore, the critical roles of circRNA epigenetic modifications, particularly m6A, and their possible involvement in AML are discussed in the present review. Epigenetic modification of circRNAs may become a diagnostic and therapeutic target for AML in the future.
Collapse
Affiliation(s)
- Mohammed Awal Issah
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Dansen Wu
- Medical Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Feng Zhang
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Weili Zheng
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yanquan Liu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Haiying Fu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Huarong Zhou
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Rong Chen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jianzhen Shen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| |
Collapse
|
26
|
Kornsuthisopon C, Photichailert S, Nowwarote N, Tompkins KA, Osathanon T. Wnt signaling in dental pulp homeostasis and dentin regeneration. Arch Oral Biol 2021; 134:105322. [PMID: 34844087 DOI: 10.1016/j.archoralbio.2021.105322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Wnt signaling is crucial in the physiological and pathological processes of dental pulp tissues. The present study described the effects of Wnt signaling in dental pulp homeostasis and regeneration. DESIGN Publications in Pubmed and Scopus database were searched, and a narrative review was performed. The roles of Wnt signaling in dental pulp tissue were reviewed and discussed. RESULT In vitro and in vivo evidence have confirmed the involvement of Wnt signaling in tooth development, dental pulp homeostasis, and physiological processes in dental pulp responses. Manipulating Wnt signaling components generates beneficial effects on pulp healing, dentin repair, and epigenetic regulation related to stemness maintenance, implying that Wnt signaling is a potential therapeutic target for future clinical dental applications. Additionally, an overview of the epigenetic control of dental pulp stem cells by Wnt signaling is provided. CONCLUSION This review provides basic knowledge on Wnt signaling and outlines its functions in dental pulp tissues, focusing on their potential as therapeutic treatments by targeting the Wnt signaling pathway.
Collapse
Affiliation(s)
- Chatvadee Kornsuthisopon
- Dental Stem Cell Biology Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suphalak Photichailert
- Dental Stem Cell Biology Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nunthawan Nowwarote
- Centre de Recherche des Cordeliers, Universite de Paris, Sorbonne Universite, INSERM UMRS 1138, Molecular Oral Pathophysiology and Universite de Paris, Dental Faculty Garanciere, Oral Biology Department, Paris F-75006, France
| | - Kevin A Tompkins
- Office of Research Affairs, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanaphum Osathanon
- Dental Stem Cell Biology Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand.
| |
Collapse
|
27
|
Nandakumar S, Shahani P, Datta I, Pal R. Interventional Strategies for Parkinson Disease: Can Neural Precursor Cells Forge a Path Ahead? ACS Chem Neurosci 2021; 12:3785-3794. [PMID: 34628850 DOI: 10.1021/acschemneuro.1c00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neural precursor cells (NPCs), derived from pluripotent stem cells (PSCs), with their unique ability to generate multiple neuronal and glial cell types are extremely useful for understanding biological mechanisms in normal and diseased states. However, generation of specific neuronal subtypes (mature) from NPCs in large numbers adequate for cell therapy is challenging due to lack of a thorough understanding of the cues that govern their differentiation. Interestingly, neural stem cells (NSCs) themselves are in consideration for therapy given their potency to form different neural cell types, release of trophic factors, and immunomodulatory effects that confer neuroprotection. With the recent COVID-19 outbreak and its accompanying neurological indications, the immunomodulatory role of NSCs may gain additional significance in the prevention of disease progression in vulnerable populations. In this regard, small-molecule mediated NPC generation from PSCs via NSC formation has become an important strategy that ensures consistency and robustness of the process. The development of the mammalian brain occurs along the rostro-caudal axis, and the establishment of anterior identity is an early event. Wnt signaling, along with fibroblast growth factor and retinoic acid, acts as a caudalization signal. Further, the increasing amount of epigenetic data available from human fetal brain development has enhanced both our understanding of and ability to experimentally manipulate these developmental regulatory programs in vitro. However, the impact on homing and engraftment after transplantation and subsequently on therapeutic efficacy of NPCs based on their derivation strategy is not yet clear. Another formidable challenge in cell replacement therapy for neurodegenerative disorders is the mode of delivery. In this Perspective, we discuss these core ideas with insights from our preliminary studies exploring the role of PSC-derived NPCs in rat models of MPTP-induced Parkinson's disease following intranasal injections.
Collapse
Affiliation(s)
- Swapna Nandakumar
- Eyestem Research, Centre for Cellular and Molecular Platforms (C-CAMP), Bengaluru 560065, Karnataka, India
| | - Pradnya Shahani
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru 560029, Karnataka, India
| | - Indrani Datta
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru 560029, Karnataka, India
| | - Rajarshi Pal
- Eyestem Research, Centre for Cellular and Molecular Platforms (C-CAMP), Bengaluru 560065, Karnataka, India
| |
Collapse
|
28
|
Meng Y, Zhang T, Zheng R, Ding S, Yang J, Liu R, Jiang Y, Jiang W. Depletion of Demethylase KDM6 Enhances Early Neuroectoderm Commitment of Human PSCs. Front Cell Dev Biol 2021; 9:702462. [PMID: 34568320 PMCID: PMC8455897 DOI: 10.3389/fcell.2021.702462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022] Open
Abstract
Epigenetic modifications play a crucial role in neurogenesis, learning, and memory, but the study of their role in early neuroectoderm commitment from pluripotent inner cell mass is relatively lacking. Here we utilized the system of directed neuroectoderm differentiation from human embryonic stem cells and identified that KDM6B, an enzyme responsible to erase H3K27me3, was the most upregulated enzyme of histone methylation during neuroectoderm differentiation by transcriptome analysis. We then constructed KDM6B-null embryonic stem cells and found strikingly that the pluripotent stem cells with KDM6B knockout exhibited much higher neuroectoderm induction efficiency. Furthermore, we constructed a series of embryonic stem cell lines knocking out the other H3K27 demethylase KDM6A, and depleting both KDM6A and KDM6B, respectively. These cell lines together confirmed that KDM6 impeded early neuroectoderm commitment. By RNA-seq, we found that the expression levels of a panel of WNT genes were significantly affected upon depletion of KDM6. Importantly, the result that WNT agonist and antagonist could abolish the differential neuroectoderm induction due to manipulating KDM6 further demonstrated that WNT was the major downstream of KDM6 during early neural induction. Moreover, we found that the chemical GSK-J1, an inhibitor of KDM6, could enhance neuroectoderm induction from both embryonic stem cells and induced pluripotent stem cells. Taken together, our findings not only illustrated the important role of the histone methylation modifier KDM6 in early neurogenesis, providing insights into the precise epigenetic regulation in cell fate determination, but also showed that the inhibitor of KDM6 could facilitate neuroectoderm differentiation from human pluripotent stem cells.
Collapse
Affiliation(s)
- Yajing Meng
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ran Zheng
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Song Ding
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jie Yang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ran Liu
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yingan Jiang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
| |
Collapse
|
29
|
Tay EXY, Chia K, Ong DST. Epigenetic plasticity and redox regulation of neural stem cell state and fate. Free Radic Biol Med 2021; 170:116-130. [PMID: 33684459 DOI: 10.1016/j.freeradbiomed.2021.02.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/20/2021] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
The neural stem cells (NSCs) are essential for normal brain development and homeostasis. The cell state (i.e. quiescent versus activated) and fate (i.e. the cell lineage of choice upon differentiation) of NSCs are tightly controlled by various redox and epigenetic regulatory mechanisms. There is an increasing appreciation that redox and epigenetic regulations are intimately linked, but how this redox-epigenetics crosstalk affects NSC activity remains poorly understood. Another unresolved topic is whether the NSCs actually contribute to brain ageing and neurodegenerative diseases. In this review, we aim to 1) distill concepts that underlie redox and epigenetic regulation of NSC state and fate; 2) provide examples of the redox-epigenetics crosstalk in NSC biology; and 3) highlight potential redox- and epigenetic-based therapeutic opportunities to rescue NSC dysfunctions in ageing and neurodegenerative diseases.
Collapse
Affiliation(s)
- Emmy Xue Yun Tay
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore
| | - Kimberly Chia
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore; National Neuroscience Institute, Singapore, 308433, Singapore.
| |
Collapse
|
30
|
Panisi C, Guerini FR, Abruzzo PM, Balzola F, Biava PM, Bolotta A, Brunero M, Burgio E, Chiara A, Clerici M, Croce L, Ferreri C, Giovannini N, Ghezzo A, Grossi E, Keller R, Manzotti A, Marini M, Migliore L, Moderato L, Moscone D, Mussap M, Parmeggiani A, Pasin V, Perotti M, Piras C, Saresella M, Stoccoro A, Toso T, Vacca RA, Vagni D, Vendemmia S, Villa L, Politi P, Fanos V. Autism Spectrum Disorder from the Womb to Adulthood: Suggestions for a Paradigm Shift. J Pers Med 2021; 11:70. [PMID: 33504019 PMCID: PMC7912683 DOI: 10.3390/jpm11020070] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/10/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
The wide spectrum of unique needs and strengths of Autism Spectrum Disorders (ASD) is a challenge for the worldwide healthcare system. With the plethora of information from research, a common thread is required to conceptualize an exhaustive pathogenetic paradigm. The epidemiological and clinical findings in ASD cannot be explained by the traditional linear genetic model, hence the need to move towards a more fluid conception, integrating genetics, environment, and epigenetics as a whole. The embryo-fetal period and the first two years of life (the so-called 'First 1000 Days') are the crucial time window for neurodevelopment. In particular, the interplay and the vicious loop between immune activation, gut dysbiosis, and mitochondrial impairment/oxidative stress significantly affects neurodevelopment during pregnancy and undermines the health of ASD people throughout life. Consequently, the most effective intervention in ASD is expected by primary prevention aimed at pregnancy and at early control of the main effector molecular pathways. We will reason here on a comprehensive and exhaustive pathogenetic paradigm in ASD, viewed not just as a theoretical issue, but as a tool to provide suggestions for effective preventive strategies and personalized, dynamic (from womb to adulthood), systemic, and interdisciplinary healthcare approach.
Collapse
Affiliation(s)
- Cristina Panisi
- Fondazione Istituto Sacra Famiglia ONLUS, Cesano Boscone, 20090 Milan, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Franca Rosa Guerini
- IRCCS Fondazione Don Carlo Gnocchi, ONLUS, 20148 Milan, Italy; (M.C.); (M.S.)
| | | | - Federico Balzola
- Division of Gastroenterology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, University of Turin, 10126 Turin, Italy;
| | - Pier Mario Biava
- Scientific Institute of Research and Care Multimedica, 20138 Milan, Italy;
| | - Alessandra Bolotta
- DIMES, School of Medicine, University of Bologna, 40126 Bologna, Italy; (P.M.A.); (A.B.); (A.G.)
| | - Marco Brunero
- Department of Pediatric Surgery, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Ernesto Burgio
- ECERI—European Cancer and Environment Research Institute, Square de Meeus 38-40, 1000 Bruxelles, Belgium;
| | - Alberto Chiara
- Dipartimento Materno Infantile ASST, 27100 Pavia, Italy;
| | - Mario Clerici
- IRCCS Fondazione Don Carlo Gnocchi, ONLUS, 20148 Milan, Italy; (M.C.); (M.S.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Luigi Croce
- Centro Domino per l’Autismo, Universita’ Cattolica Brescia, 20139 Milan, Italy;
| | - Carla Ferreri
- National Research Council of Italy, Institute of Organic Synthesis and Photoreactivity (ISOF), 40129 Bologna, Italy;
| | - Niccolò Giovannini
- Department of Obstetrics and Gynecology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Alessandro Ghezzo
- DIMES, School of Medicine, University of Bologna, 40126 Bologna, Italy; (P.M.A.); (A.B.); (A.G.)
| | - Enzo Grossi
- Autism Research Unit, Villa Santa Maria Foundation, 22038 Tavernerio, Italy;
| | - Roberto Keller
- Adult Autism Centre DSM ASL Città di Torino, 10138 Turin, Italy;
| | - Andrea Manzotti
- RAISE Lab, Foundation COME Collaboration, 65121 Pescara, Italy;
| | - Marina Marini
- DIMES, School of Medicine, University of Bologna, 40126 Bologna, Italy; (P.M.A.); (A.B.); (A.G.)
| | - Lucia Migliore
- Medical Genetics Laboratories, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy; (L.M.); (A.S.)
| | - Lucio Moderato
- Fondazione Istituto Sacra Famiglia ONLUS, Cesano Boscone, 20090 Milan, Italy;
| | - Davide Moscone
- Associazione Spazio Asperger ONLUS, Centro Clinico CuoreMenteLab, 00141 Rome, Italy;
| | - Michele Mussap
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Puericulture Institute and Neonatal Section, Azienda Ospedaliera Universitaria, 09100 Cagliari, Italy; (M.M.); (V.F.)
| | - Antonia Parmeggiani
- Child Neurology and Psychiatry Unit, IRCCS ISNB, S. Orsola-Malpighi Hospital, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Valentina Pasin
- Milan Institute for health Care and Advanced Learning, 20124 Milano, Italy;
| | | | - Cristina Piras
- Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy;
| | - Marina Saresella
- IRCCS Fondazione Don Carlo Gnocchi, ONLUS, 20148 Milan, Italy; (M.C.); (M.S.)
| | - Andrea Stoccoro
- Medical Genetics Laboratories, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy; (L.M.); (A.S.)
| | - Tiziana Toso
- Unione Italiana Lotta alla Distrofia Muscolare UILDM, 35100 Padova, Italy;
| | - Rosa Anna Vacca
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council of Italy, 70126 Bari, Italy;
| | - David Vagni
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy, 98164 Messina, Italy;
| | | | - Laura Villa
- Scientific Institute, IRCCS Eugenio Medea, Via Don Luigi Monza 20, 23842 Bosisio Parini, Italy;
| | - Pierluigi Politi
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, Puericulture Institute and Neonatal Section, Azienda Ospedaliera Universitaria, 09100 Cagliari, Italy; (M.M.); (V.F.)
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria, 09042 Cagliari, Italy
| |
Collapse
|
31
|
Fallah MS, Szarics D, Robson CM, Eubanks JH. Impaired Regulation of Histone Methylation and Acetylation Underlies Specific Neurodevelopmental Disorders. Front Genet 2021; 11:613098. [PMID: 33488679 PMCID: PMC7820808 DOI: 10.3389/fgene.2020.613098] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic processes are critical for governing the complex spatiotemporal patterns of gene expression in neurodevelopment. One such mechanism is the dynamic network of post-translational histone modifications that facilitate recruitment of transcription factors or even directly alter chromatin structure to modulate gene expression. This is a tightly regulated system, and mutations affecting the function of a single histone-modifying enzyme can shift the normal epigenetic balance and cause detrimental developmental consequences. In this review, we will examine select neurodevelopmental conditions that arise from mutations in genes encoding enzymes that regulate histone methylation and acetylation. The methylation-related conditions discussed include Wiedemann-Steiner, Kabuki, and Sotos syndromes, and the acetylation-related conditions include Rubinstein-Taybi, KAT6A, genitopatellar/Say-Barber-Biesecker-Young-Simpson, and brachydactyly mental retardation syndromes. In particular, we will discuss the clinical/phenotypic and genetic basis of these conditions and the model systems that have been developed to better elucidate cellular and systemic pathological mechanisms.
Collapse
Affiliation(s)
- Merrick S Fallah
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Dora Szarics
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Clara M Robson
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - James H Eubanks
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Surgery (Neurosurgery), University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
32
|
Saw G, Tang FR. Epigenetic Regulation of the Hippocampus, with Special Reference to Radiation Exposure. Int J Mol Sci 2020; 21:ijms21249514. [PMID: 33327654 PMCID: PMC7765140 DOI: 10.3390/ijms21249514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/12/2020] [Indexed: 01/28/2023] Open
Abstract
The hippocampus is crucial in learning, memory and emotion processing, and is involved in the development of different neurological and neuropsychological disorders. Several epigenetic factors, including DNA methylation, histone modifications and non-coding RNAs, have been shown to regulate the development and function of the hippocampus, and the alteration of epigenetic regulation may play important roles in the development of neurocognitive and neurodegenerative diseases. This review summarizes the epigenetic modifications of various cell types and processes within the hippocampus and their resulting effects on cognition, memory and overall hippocampal function. In addition, the effects of exposure to radiation that may induce a myriad of epigenetic changes in the hippocampus are reviewed. By assessing and evaluating the current literature, we hope to prompt a more thorough understanding of the molecular mechanisms that underlie radiation-induced epigenetic changes, an area which can be further explored.
Collapse
|
33
|
Oh S, Boo K, Kim J, Baek SA, Jeon Y, You J, Lee H, Choi HJ, Park D, Lee JM, Baek SH. The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes. Nucleic Acids Res 2020; 48:9037-9052. [PMID: 32735658 PMCID: PMC7498345 DOI: 10.1093/nar/gkaa626] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.
Collapse
Affiliation(s)
- Sungryong Oh
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyungjin Boo
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jaebeom Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seon Ah Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Jeon
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Junghyun You
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, Research Institute, National Cancer Center, Goyang 10408, South Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, South Korea
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| |
Collapse
|
34
|
Ferrari F, Arrigoni L, Franz H, Izzo A, Butenko L, Trompouki E, Vogel T, Manke T. DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility. Nat Commun 2020; 11:5200. [PMID: 33060580 PMCID: PMC7562744 DOI: 10.1038/s41467-020-19001-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023] Open
Abstract
During neuronal differentiation, the transcriptional profile and the epigenetic context of neural committed cells is subject to significant rearrangements, but a systematic quantification of global histone modification changes is still missing. Here, we show that H3K79me2 increases and H3K27ac decreases globally during in-vitro neuronal differentiation of murine embryonic stem cells. DOT1L mediates all three degrees of methylation of H3K79 and its enzymatic activity is critical to modulate cellular differentiation and reprogramming. In this context, we find that inhibition of DOT1L in neural progenitor cells biases the transcriptional state towards neuronal differentiation, resulting in transcriptional upregulation of genes marked with H3K27me3 on the promoter region. We further show that DOT1L inhibition affects accessibility of SOX2-bound enhancers and impairs SOX2 binding in neural progenitors. Our work provides evidence that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.
Collapse
Affiliation(s)
- Francesco Ferrari
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Henriette Franz
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annalisa Izzo
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludmila Butenko
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Tanja Vogel
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Center for Basics in NeuroModulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| |
Collapse
|
35
|
Nicaise AM, Willis CM, Crocker SJ, Pluchino S. Stem Cells of the Aging Brain. Front Aging Neurosci 2020; 12:247. [PMID: 32848716 PMCID: PMC7426063 DOI: 10.3389/fnagi.2020.00247] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The adult central nervous system (CNS) contains resident stem cells within specific niches that maintain a self-renewal and proliferative capacity to generate new neurons, astrocytes, and oligodendrocytes throughout adulthood. Physiological aging is associated with a progressive loss of function and a decline in the self-renewal and regenerative capacities of CNS stem cells. Also, the biggest risk factor for neurodegenerative diseases is age, and current in vivo and in vitro models of neurodegenerative diseases rarely consider this. Therefore, combining both aging research and appropriate interrogation of animal disease models towards the understanding of the disease and age-related stem cell failure is imperative to the discovery of new therapies. This review article will highlight the main intrinsic and extrinsic regulators of neural stem cell (NSC) aging and discuss how these factors impact normal homeostatic functions within the adult brain. We will consider established in vivo animal and in vitro human disease model systems, and then discuss the current and future trajectories of novel senotherapeutics that target aging NSCs to ameliorate brain disease.
Collapse
Affiliation(s)
- Alexandra M Nicaise
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Cory M Willis
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Stephen J Crocker
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Stefano Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
36
|
MacLeod G, Bozek DA, Rajakulendran N, Monteiro V, Ahmadi M, Steinhart Z, Kushida MM, Yu H, Coutinho FJ, Cavalli FMG, Restall I, Hao X, Hart T, Luchman HA, Weiss S, Dirks PB, Angers S. Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells. Cell Rep 2020; 27:971-986.e9. [PMID: 30995489 DOI: 10.1016/j.celrep.2019.03.047] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 12/19/2018] [Accepted: 03/13/2019] [Indexed: 01/14/2023] Open
Abstract
Glioblastoma therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells (GSCs) to interrogate function of the coding genome, we identify actionable pathways responsible for growth, which reveal the gene-essential circuitry of GBM stemness and proliferation. In particular, we characterize members of the SOX transcription factor family, SOCS3, USP8, and DOT1L, and protein ufmylation as important for GSC growth. Additionally, we reveal mechanisms of temozolomide resistance that could lead to combination strategies. By reaching beyond static genome analysis of bulk tumors, with a genome-wide functional approach, we reveal genetic dependencies within a broad range of biological processes to provide increased understanding of GBM growth and treatment resistance.
Collapse
Affiliation(s)
- Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Danielle A Bozek
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Vernon Monteiro
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Moloud Ahmadi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Zachary Steinhart
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Michelle M Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Yu
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian Restall
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Xiaoguang Hao
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - H Artee Luchman
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, Department of Laboratory Medicine and Pathobiology, Division of Neurosurgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
37
|
Park JH, Lee TK, Kim DW, Park CW, Park YE, Kim B, Lee JC, Lee HA, Won MH, Ahn JH. RbAp48 expression and neuronal damage in the gerbil hippocampus following 5 min of transient ischemia. Lab Anim Res 2020; 35:12. [PMID: 32257900 PMCID: PMC7081550 DOI: 10.1186/s42826-019-0011-3] [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: 05/26/2019] [Accepted: 07/14/2019] [Indexed: 11/10/2022] Open
Abstract
Histone-binding protein RbAp48 has been known to be involved in histone acetylation, and epigenetic alterations of histone modifications are closely associated with the pathogenesis of ischemic reperfusion injury. In the current study, we investigated chronological change of RbAp48 expression in the hippocampus following 5 min of transient ischemia in gerbils. RbAp48 expression was examined 1, 2, 5, and 10 days after transient ischemia using immunohistochemistry. In sham operated gerbils, RbAp48 immunoreactivity was strong in pyramidal and non-pyramidal cells in the hippocampus. After transient ischemia, RbAp48 immunoreactivity was changed in the cornu ammonis 1 subfield (CA1), not in CA2/3. RbAp48 immunoreactivity in CA1 pyramidal neurons was gradually decreased and not detected at 5 and 10 days after ischemia. RbAp48 immunoreactivity in non-pyramidal cells was maintained until 2 days post-ischemia and significantly increased from 5 days post-ischemia. Double immunohistofluorescence staining revealed that RbAp48 immunoreactive non-pyramidal cells were astrocytes. At 5 days post-ischemia, death of pyramidal neurons occurred only in the CA1. These results showed that RbAp48 immunoreactivity was distinctively altered in pyramidal neurons and astrocytes in the hippocampal CA1 following 5 mins of transient ischemia. Ischemia-induced change in RbAp48 expression may be closely associated with neuronal death and astrocyte activation following 5 min of transient ischemia.
Collapse
Affiliation(s)
- Joon Ha Park
- 1Department of Biomedical Science, Research Institute of Bioscience and Biotechnology, Hallym University, Chuncheon, Gangwon 24252 Republic of Korea
| | - Tae-Kyeong Lee
- 2Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Dae Won Kim
- Department of Biochemistry and Molecular Biology, and Research Institute of Oral Sciences, College of Dentistry, Gangnung-Wonju National University, Gangneung, Gangwon 25457 Republic of Korea
| | - Cheol Woo Park
- 2Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Young Eun Park
- 2Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Bora Kim
- 2Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Jae-Chul Lee
- 2Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Hyang-Ah Lee
- 4Department of Obstetrics and Gynecology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Moo-Ho Won
- 2Department of Neurobiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Ji Hyeon Ahn
- 1Department of Biomedical Science, Research Institute of Bioscience and Biotechnology, Hallym University, Chuncheon, Gangwon 24252 Republic of Korea
| |
Collapse
|
38
|
Zong D, Liu X, Li J, Ouyang R, Chen P. The role of cigarette smoke-induced epigenetic alterations in inflammation. Epigenetics Chromatin 2019; 12:65. [PMID: 31711545 PMCID: PMC6844059 DOI: 10.1186/s13072-019-0311-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Exposure to cigarette smoke (CS) is a major threat to human health worldwide. It is well established that smoking increases the risk of respiratory diseases, cardiovascular diseases and different forms of cancer, including lung, liver, and colon. CS-triggered inflammation is considered to play a central role in various pathologies by a mechanism that stimulates the release of pro-inflammatory cytokines. During this process, epigenetic alterations are known to play important roles in the specificity and duration of gene transcription. Main text Epigenetic alterations include three major modifications: DNA modifications via methylation; various posttranslational modifications of histones, namely, methylation, acetylation, phosphorylation, and ubiquitination; and non-coding RNA sequences. These modifications work in concert to regulate gene transcription in a heritable fashion. The enzymes that regulate these epigenetic modifications can be activated by smoking, which further mediates the expression of multiple inflammatory genes. In this review, we summarize the current knowledge on the epigenetic alterations triggered by CS and assess how such alterations may affect smoking-mediated inflammatory responses. Conclusion The recognition of the molecular mechanisms of the epigenetic changes in abnormal inflammation is expected to contribute to the understanding of the pathophysiology of CS-related diseases such that novel epigenetic therapies may be identified in the near future.
Collapse
Affiliation(s)
- Dandan Zong
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Xiangming Liu
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Jinhua Li
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Ruoyun Ouyang
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Ping Chen
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China.
| |
Collapse
|
39
|
Zamani ARN, Saberianpour S, Geranmayeh MH, Bani F, Haghighi L, Rahbarghazi R. Modulatory effect of photobiomodulation on stem cell epigenetic memory: a highlight on differentiation capacity. Lasers Med Sci 2019; 35:299-306. [PMID: 31494789 DOI: 10.1007/s10103-019-02873-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023]
Abstract
Differentiation potential of stem cells into various lineages makes these cells as promising sources to treat multiple diseases. In this regard, the use of different strategies and protocols to increase differentiation capacity is highly demanded. Low-level laser therapy, a relatively noninvasive technique, has the capacity to accelerate the healing of numerous injuries and a portion of restorative capacity could be correlated with the stem cell activation and differentiation. Several mechanisms have been diagnosed to participate in orientation of stem cells to functional mature cells. Among them, the status of DNA methylation orchestrates the maintenance of tissue-specific gene expression during the differentiation procedure. DNA methylation is a momentous event in embryogenesis and functional maturation. This review article highlighted the potency of laser irradiation (low-level intensities) in the differentiation of stem cells by modulation of methylation. The analysis of these modalities could help us to understand the underlying mechanisms participating in the therapeutic effects of photobiomodulation.
Collapse
Affiliation(s)
| | - Shirin Saberianpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Farhad Bani
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Haghighi
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
40
|
Császár-Nagy N, Kapócs G, Bókkon I. Classic psychedelics: the special role of the visual system. Rev Neurosci 2019; 30:651-669. [PMID: 30939118 DOI: 10.1515/revneuro-2018-0092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/05/2018] [Indexed: 12/23/2022]
Abstract
Here, we briefly overview the various aspects of classic serotonergic hallucinogens reported by a number of studies. One of the key hypotheses of our paper is that the visual effects of psychedelics might play a key role in resetting fears. Namely, we especially focus on visual processes because they are among the most prominent features of hallucinogen-induced hallucinations. We hypothesize that our brain has an ancient visual-based (preverbal) intrinsic cognitive process that, during the transient inhibition of top-down convergent and abstract thinking (mediated by the prefrontal cortex) by psychedelics, can neutralize emotional fears of unconscious and conscious life experiences from the past. In these processes, the decreased functional integrity of the self-referencing processes of the default mode network, the modified multisensory integration (linked to bodily self-consciousness and self-awareness), and the modified amygdala activity may also play key roles. Moreover, the emotional reset (elimination of stress-related emotions) by psychedelics may induce psychological changes and overwrite the stress-related neuroepigenetic information of past unconscious and conscious emotional fears.
Collapse
Affiliation(s)
- Noemi Császár-Nagy
- National University of Public Services, Budapest, Hungary.,Psychosomatic Outpatient Clinics, Budapest, Hungary
| | - Gábor Kapócs
- Saint John Hospital, Budapest, Hungary.,Institute of Behavioral Sciences, Semmelweis University, Budapest, Hungary
| | - István Bókkon
- Psychosomatic Outpatient Clinics, Budapest, Hungary.,Vision Research Institute, Neuroscience and Consciousness Research Department, Lowell, MA, USA
| |
Collapse
|
41
|
Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Wu M. Epigenetics in Neurodevelopment: Emerging Role of Circular RNA. Front Cell Neurosci 2019; 13:327. [PMID: 31379511 PMCID: PMC6658887 DOI: 10.3389/fncel.2019.00327] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/03/2019] [Indexed: 01/16/2023] Open
Abstract
Canonical epigenetic modifications, including DNA methylation, histone modification and chromatin remodeling, play a role in numerous life processes, particularly neurodevelopment. Epigenetics explains the development of cells in an organism with the same DNA sequence into different cell types with various functions. However, previous studies on epigenetics have only focused on the chromatin level. Recently, epigenetic modifications of RNA, which mainly include 6-methyladenosine (m6A), pseudouridine, 5-methylcytidine (m5C), inosine (I), 2′-O-ribosemethylation, and 1-methyladenosine (m1A), have gained increasing attention. Circular RNAs (circRNAs), which are a type of non-coding RNA without a 5′ cap or 3′ poly (A) tail, are abundantly found in the brain and might respond to and regulate synaptic function. Also, circRNAs have various functions, such as microRNA sponge, regulation of gene transcription and interaction with RNA binding protein. In addition, circRNAs are methylated by N6-methyladenosine (m6A). In this review, we discuss the crucial roles of epigenetic modifications of circRNAs, such as m6A, in the genesis and development of neurons and in synaptic function and plasticity. Thus, this type of changes in circRNAs might be a therapeutic target in central nervous system (CNS) disorders and could aid the diagnosis and treatment of these disorders.
Collapse
Affiliation(s)
- Shujuan Meng
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Hecheng Zhou
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Ziyang Feng
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Zihao Xu
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Ying Tang
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| |
Collapse
|
42
|
Goodarzi P, Alavi-Moghadam S, Payab M, Larijani B, Rahim F, Gilany K, Bana N, Tayanloo-Beik A, Foroughi Heravani N, Hadavandkhani M, Arjmand B. Metabolomics Analysis of Mesenchymal Stem Cells. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2019; 8:30-40. [PMID: 32351907 PMCID: PMC7175611 DOI: 10.22088/ijmcm.bums.8.2.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022]
Abstract
Various mesenchymal stem cells as easily accessible and multipotent cells can share different essential signaling pathways related to their stemness ability. Understanding the mechanism of stemness ability can be useful for controlling the stem cells for regenerative medicine targets. In this context, OMICs studies can analyze the mechanism of different stem cell properties or stemness ability via a broad range of current high-throughput techniques. This field is fundamentally directed toward the analysis of whole genome (genomics), mRNAs (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in biological samples. According to several studies, metabolomics is more effective than other OMICs ّfor various system biology concerns. Metabolomics can elucidate the biological mechanisms of various mesenchymal stem cell function by measuring their metabolites such as their secretome components. Analyzing the metabolic alteration of mesenchymal stem cells can be useful to promote their regenerative medicine application.
Collapse
Affiliation(s)
- Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran .,Department of Biomedical Sciences, University of Antwerp, Belgium
| | - Nikoo Bana
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular- Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Najmeh Foroughi Heravani
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Hadavandkhani
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran .,Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular- Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
43
|
Kouter K, Zupanc T, Videtič Paska A. Genome-wide DNA methylation in suicide victims revealing impact on gene expression. J Affect Disord 2019; 253:419-425. [PMID: 31103807 DOI: 10.1016/j.jad.2019.04.077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Suicidal behavior is a multifactorial, polygenic state that affects millions worldwide. It is a result of interplay between hereditary and environmental factors, tied together by epigenetics. Despite vast knowledge on suicidality complete mechanism and factors leading to suicide are unknown. However there is an indication between changes in DNA methylation patterns and suicidal behavior. METHODS To identify differential methylation we formed a homogenous group of male suicide victims who died by hanging and control group. Altogether our study included 18 subjects in which two brain regions, Brodmann area 9 (9 suicide victims and 9 controls)) and hippocampus (6 suicide victims and 6 controls) were investigated using next-generation sequencing (NGS). RESULTS Our results have shown several differences in methylation level between suicide victims and controls in both brain regions (>25% difference in methylation and q-value < 0.01), with gene ontology pointing towards cell structural integrity and nervous system regulation. Additional gene expression analysis identified changes in two genes, ZNF714 (p-value = 0.002) and NRIP3 (p-value = 0.046). LIMITATIONS Major limitation is small sample size. Our analysis was conducted on brain tissue including different cell types so the results are a representation of a methylation pattern for the whole brain tissue sample. CONCLUSIONS We performed a preliminary methylation study with single base pair resolution using NGS on one of the world populations with a very high suicide risk. Obtained results offer novel insights into altered methylation patterns in suicide victims, which could provide a starting point for further studies on clinical samples with highly expressed suicide risk.
Collapse
Affiliation(s)
- Katarina Kouter
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova ulica 2, SI-1000 Ljubljana, Slovenia
| | - Alja Videtič Paska
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|
44
|
Jarmasz JS, Stirton H, Basalah D, Davie JR, Clarren SK, Astley SJ, Del Bigio MR. Global DNA Methylation and Histone Posttranslational Modifications in Human and Nonhuman Primate Brain in Association with Prenatal Alcohol Exposure. Alcohol Clin Exp Res 2019; 43:1145-1162. [PMID: 31074890 PMCID: PMC6593679 DOI: 10.1111/acer.14052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/26/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022]
Abstract
Background Based upon experimental animal studies, the neurodevelopmental abnormalities associated with prenatal alcohol exposure (PNAE)/fetal alcohol spectrum disorder (FASD) have been attributed, at least in part, to epigenetic modifications. However, there are no direct analyses of human brain tissue. Methods Immunohistochemical detection of global epigenetic markers was performed on temporal lobe samples of autopsied fetuses and infants with documented PNAE. They were compared to age‐, sex‐, and postmortem delay‐matched control cases (18 pairs; 20 to 70.5 weeks postconception). Temporal lobe tissue from a macaque monkey model of PNAE was also studied (5.7 to 6 months of age). We used antibodies targeting 4 DNA cytosine, 4 histone methylation, and 6 histone acetylation modifications and assigned scores based upon the semiquantitatively graded intensity and proportion of positively labeled nuclei in the ventricular and subventricular zones, ependyma, temporal cortex, temporal white matter, dentate gyrus (DG), and CA1 pyramidal layer. Results Temporal changes were identified for almost all marks according to the state of maturation in the human brain. In the DG (and 3 other brain regions), a statistically significant increase in H3K9ac was associated with PNAE. Statistically significant decreases were seen among 5mC, H3K4me3, H3K9ac, H3K27ac, H4K12ac, and H4K16ac in select regions. In the macaques, H3K36me3 decreased in the DG, and the ependyma showed decreases in 5fC and H3K36me3. Conclusions In human brain, global intranuclear epigenetic modifications are brain region and maturation state‐specific. These exploratory results support the general hypothesis that PNAE is associated with a global decrease in DNA methylation, a global decrease in histone methylation, and a global increase in histone acetylation. Although the human and monkey subjects are not directly comparable in terms of brain maturation, considering the rapid temporal changes in global epigenetic modifications during brain development, interspecies comparisons may be extremely difficult.
Collapse
Affiliation(s)
- Jessica S Jarmasz
- Department of Pathology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hannah Stirton
- Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Duaa Basalah
- Department of Pathology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sterling K Clarren
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Pediatrics, University of British Columbia Faculty of Medicine, Vancouver, British Columbia
| | - Susan J Astley
- Departments of Epidemiology/Pediatrics, University of Washington, Seattle, Washington
| | - Marc R Del Bigio
- Department of Pathology, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
45
|
Wever I, Wagemans CMRJ, Smidt MP. EZH2 Is Essential for Fate Determination in the Mammalian Isthmic Area. Front Mol Neurosci 2019; 12:76. [PMID: 31024250 PMCID: PMC6465967 DOI: 10.3389/fnmol.2019.00076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/11/2019] [Indexed: 11/25/2022] Open
Abstract
The polycomb group proteins (PcGs) are a group of epigenetic factors associated with gene silencing. They are found in several families of multiprotein complexes, including polycomb repressive complex 2 (PRC2). EZH2, EED and SUZ12 form the core components of the PRC2 complex, which is responsible for the mono, di- and trimethylation of lysine 27 of histone 3 (H3K27Me3), the chromatin mark associated with gene silencing. Loss-of-function studies of Ezh2, the catalytic subunit of PRC2, have shown that PRC2 plays a role in regulating developmental transitions of neuronal progenitor cells (NPCs); from self-renewal to differentiation and the neurogenic-to-gliogenic fate switch. To further address the function of EZH2 and H3K27me3 during neuronal development, we generated a conditional mutant in which Ezh2 was removed in the mammalian isthmic (mid-hindbrain) region from E10.5 onward. Loss of Ezh2 changed the molecular coding of the anterior ventral hindbrain leading to a fate switch and the appearance of ectopic dopaminergic (DA) neurons. The correct specification of the isthmic region is dependent on the signaling factors produced by the Isthmic organizer (IsO), located at the border of the mid- and hindbrain. We propose that the change of cellular fate is a result of the presence of Otx2 in the hindbrain of Ezh2 conditional knock-outs (cKOs) and a dysfunctional IsO, as represented by the loss of Fgf8 and Wnt1. Our work implies that next to controlling developmental transitions, EZH2 mediated gene silencing is important for specification of the isthmic region by influencing IsO functioning and repressing Otx2 in the hindbrain.
Collapse
Affiliation(s)
- Iris Wever
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Cindy M R J Wagemans
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Marten P Smidt
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
46
|
Fellous A, Earley RL, Silvestre F. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Gene 2019; 687:173-187. [DOI: 10.1016/j.gene.2018.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
|
47
|
Fawal MA, Davy A. Impact of Metabolic Pathways and Epigenetics on Neural Stem Cells. Epigenet Insights 2018; 11:2516865718820946. [PMID: 30627699 PMCID: PMC6311566 DOI: 10.1177/2516865718820946] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 11/22/2018] [Indexed: 12/18/2022] Open
Abstract
Balancing self-renewal with differentiation is crucial for neural stem cells (NSC) functions to ensure tissue development and homeostasis. Over the last years, multiple studies have highlighted the coupling of either metabolic or epigenetic reprogramming to NSC fate decisions. Metabolites are essential as they provide the energy and building blocks for proper cell function. Moreover, metabolites can also function as substrates and/or cofactors for epigenetic modifiers. It is becoming more evident that metabolic alterations and epigenetics rewiring are highly intertwined; however, their relation regarding determining NSC fate is not well understood. In this review, we summarize the major metabolic pathways and epigenetic modifications that play a role in NSC. We then focus on the notion that nutrients availability can function as a switch to modify the epigenetic machinery and drive NSC sequential differentiation during embryonic neurogenesis.
Collapse
Affiliation(s)
- Mohamad-Ali Fawal
- Centre de Biologie Intégrative (CBI) and Centre de Biologie du Développement (CBD), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Alice Davy
- Centre de Biologie Intégrative (CBI) and Centre de Biologie du Développement (CBD), Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
48
|
Fan SJ, Sun AB, Liu L. Epigenetic modulation during hippocampal development. Biomed Rep 2018; 9:463-473. [PMID: 30546873 DOI: 10.3892/br.2018.1160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/11/2018] [Indexed: 12/24/2022] Open
Abstract
The hippocampus is located in the limbic system and is vital in learning ability, memory formation and emotion regulation, and is associated with depression, epilepsy and mental retardation in an abnormal developmental situation. Several factors have been found to modulate the development of the hippocampus, and epigenetic modification have a crucial effect in this progress. The present review summarizes the epigenetic modifications, including DNA methylation, histone acetylation, and non-coding RNAs, regulating all stages of hippocampal development, focusing on the growth of Ammons horn and the dentate gyrus in humans and rodents. These modifications may significantly affect hippocampal development and health in addition to cognitive processes.
Collapse
Affiliation(s)
- Si-Jing Fan
- Department of Pharmacology, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China.,Laboratory of Neuronal and Brain Diseases Modulation, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - An-Bang Sun
- Laboratory of Neuronal and Brain Diseases Modulation, Yangtze University, Jingzhou, Hubei 434023, P.R. China.,Department of Anatomy, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Lian Liu
- Department of Pharmacology, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China.,Laboratory of Neuronal and Brain Diseases Modulation, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| |
Collapse
|
49
|
Rezaei F, Tiraihi T, Abdanipour A, Hassoun HK, Taheri T. Immunocytochemical analysis of valproic acid induced histone H3 and H4 acetylation during differentiation of rat adipose derived stem cells into neuron-like cells. Biotech Histochem 2018; 93:589-600. [PMID: 30273059 DOI: 10.1080/10520295.2018.1511063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Valproic acid (VPA) is an inhibitor of histone deacetylases (HDACs) that can regulate differentiation and proliferation of stem cells by epigenetic mechanisms. We investigated VPA induced histone H3 and H4 acetylation in adipose derived stem cells (ADSCs) transdifferentiated into neuron-like cells (NLCs). Rat ADSCs were transdifferentiated into neural stem cells (NSCs) that had been generated from neurospheres. The NSCs were differentiated into NLCs by induction with different concentrations of VPA at 24, 48 and 72 h. The NLCs were evaluated using anti-H3 and -H4 antibodies, and ADSCs, NSCs and NLCs were evaluated using immunofluorescence. The ADSCs were immunoreactive to CD90 and CD49d, but not to CD45 and CD31. Both the neurospheres and NSCs were immunostained with nestin and neurofilament 68. The neurospheres expressed Musashi1, Sox2 and Neu N genes as determined by RT-PCR. Our dose-response study indicated that the optimal concentration of VPA was 1 mM at 72 h. Histone acetylation levels of H3 and H4 immunostaining intensities in NLCs were significantly greater than for ADSCs and NSCs. VPA alters H4 and H3 acetylation immunoreactivities of ADSCs transdifferentiated into NLCs.
Collapse
Affiliation(s)
- F Rezaei
- a Department of Anatomical Sciences, Faculty of Medical Sciences , Tarbiat Modares University , Tehran , Iran
| | - T Tiraihi
- a Department of Anatomical Sciences, Faculty of Medical Sciences , Tarbiat Modares University , Tehran , Iran
| | - A Abdanipour
- b Department of Anatomy, School of Medicine , Zanjan University of Medical Sciences (ZUMS) , Zanjan , Iran
| | - H K Hassoun
- c Middle Euphrates Neuroscience Center, College of medicine , Kufa University , Kufa , Iraq
| | - T Taheri
- d Shefa Neuroscience Research Center , Khatam Alanbia Hospital , Tehran , Iran
| |
Collapse
|
50
|
Bruzzone MJ, Grünberg S, Kubik S, Zentner GE, Shore D. Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes. Genes Dev 2018; 32:1252-1265. [PMID: 30108132 PMCID: PMC6120713 DOI: 10.1101/gad.312173.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
Abstract
Here, Bruzzone et al. explore the relative contributions of the transcriptional coactivators Mediator and two histone acetyltransferase (HAT) complexes, NuA4 and SAGA, to RNA polymerase II association at specific genes and gene classes by rapid nuclear depletion of key complex subunits. They show that the NuA4 HAT Esa1 differentially affects certain groups of genes, whereas the SAGA HAT Gcn5 has a weaker but more uniform effect, and their findings suggest that at least three distinct combinations of coactivator deployment are used to generate moderate or high transcription levels. The transcriptional coactivators Mediator and two histone acetyltransferase (HAT) complexes, NuA4 and SAGA, play global roles in transcriptional activation. Here we explore the relative contributions of these factors to RNA polymerase II association at specific genes and gene classes by rapid nuclear depletion of key complex subunits. We show that the NuA4 HAT Esa1 differentially affects certain groups of genes, whereas the SAGA HAT Gcn5 has a weaker but more uniform effect. Relative dependence on Esa1 and Tra1, a shared component of NuA4 and SAGA, distinguishes two large groups of coregulated growth-promoting genes. In contrast, we show that the activity of Mediator is particularly important at a separate, small set of highly transcribed TATA-box-containing genes. Our analysis indicates that at least three distinct combinations of coactivator deployment are used to generate moderate or high transcription levels and suggests that each may be associated with distinct forms of regulation.
Collapse
Affiliation(s)
- Maria Jessica Bruzzone
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, 1211 Geneva 4, Switzerland
| | - Sebastian Grünberg
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Slawomir Kubik
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, 1211 Geneva 4, Switzerland
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics in Geneva, 1211 Geneva 4, Switzerland
| |
Collapse
|