1
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Dong HW, Weiss K, Baugh K, Meadows MJ, Niswender CM, Neul JL. Potentiation of the muscarinic acetylcholine receptor 1 modulates neurophysiological features in a mouse model of Rett syndrome. Neurotherapeutics 2024; 21:e00384. [PMID: 38880672 DOI: 10.1016/j.neurot.2024.e00384] [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: 04/17/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/18/2024] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder primarily caused by mutations in the X chromosome-linked gene Methyl-CpG Binding Protein 2 (MECP2). Restoring MeCP2 expression after disease onset in a mouse model of RTT reverses phenotypes, providing hope for development of treatments for RTT. Translatable biomarkers of improvement and treatment responses have the potential to accelerate both preclinical and clinical evaluation of targeted therapies in RTT. Studies in people with and mouse models of RTT have identified neurophysiological features, such as auditory event-related potentials, that correlate with disease severity, suggesting that they could be useful as biomarkers of disease improvement or early treatment response. We recently demonstrated that treatment of RTT mice with a positive allosteric modulator (PAM) of muscarinic acetylcholine subtype 1 receptor (M1) improved phenotypes, suggesting that modulation of M1 activity is a potential therapy in RTT. To evaluate whether neurophysiological features could be useful biomarkers to assess the effects of M1 PAM treatment, we acutely administered the M1 PAM VU0486846 (VU846) at doses of 1, 3, 10 and 30 mg/kg in wildtype and RTT mice. This resulted in an inverted U-shaped dose response with maximal improvement of AEP features at 3 mg/kg but with no marked effect on basal EEG power or epileptiform discharges in RTT mice and no significant changes in wildtype mice. These findings suggest that M1 potentiation can improve neural circuit synchrony to auditory stimuli in RTT mice and that neurophysiological features have potential as pharmacodynamic or treatment-responsive biomarkers for preclinical and clinical evaluation of putative therapies in RTT.
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Affiliation(s)
- Hong-Wei Dong
- Department of Pediatrics, Division of Neurology, Vanderbilt University Medical Center, USA; Vanderbilt University Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelly Weiss
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, USA; Warren Center for Neuroscience Drug Discovery, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Kathryn Baugh
- Department of Pediatrics, Division of Neurology, Vanderbilt University Medical Center, USA
| | - Mac J Meadows
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, USA; Warren Center for Neuroscience Drug Discovery, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Colleen M Niswender
- Vanderbilt University Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, USA; Warren Center for Neuroscience Drug Discovery, School of Medicine, Vanderbilt University, Nashville, TN, USA; Vanderbilt Institute for Chemical Biology, Nashville, TN, USA; Vanderbilt Brain Institute, Nashville, TN, USA.
| | - Jeffrey L Neul
- Department of Pediatrics, Division of Neurology, Vanderbilt University Medical Center, USA; Vanderbilt University Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Nashville, TN, USA.
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2
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Wits M, Becher C, de Man F, Sanchez-Duffhues G, Goumans MJ. Sex-biased TGFβ signalling in pulmonary arterial hypertension. Cardiovasc Res 2023; 119:2262-2277. [PMID: 37595264 PMCID: PMC10597641 DOI: 10.1093/cvr/cvad129] [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: 02/22/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 08/20/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a rare cardiovascular disorder leading to pulmonary hypertension and, often fatal, right heart failure. Sex differences in PAH are evident, which primarily presents with a female predominance and increased male severity. Disturbed signalling of the transforming growth factor-β (TGFβ) family and gene mutations in the bone morphogenetic protein receptor 2 (BMPR2) are risk factors for PAH development, but how sex-specific cues affect the TGFβ family signalling in PAH remains poorly understood. In this review, we aim to explore the sex bias in PAH by examining sex differences in the TGFβ signalling family through mechanistical and translational evidence. Sex hormones including oestrogens, progestogens, and androgens, can determine the expression of receptors (including BMPR2), ligands, and soluble antagonists within the TGFβ family in a tissue-specific manner. Furthermore, sex-related genetic processes, i.e. Y-chromosome expression and X-chromosome inactivation, can influence the TGFβ signalling family at multiple levels. Given the clinical and mechanistical similarities, we expect that the conclusions arising from this review may apply also to hereditary haemorrhagic telangiectasia (HHT), a rare vascular disorder affecting the TGFβ signalling family pathway. In summary, we anticipate that investigating the TGFβ signalling family in a sex-specific manner will contribute to further understand the underlying processes leading to PAH and likely HHT.
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Affiliation(s)
- Marius Wits
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Clarissa Becher
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Frances de Man
- Department of Pulmonary Medicine, Amsterdam University Medical Center (UMC) (Vrije Universiteit), 1081 HV Amsterdam, The Netherlands
| | - Gonzalo Sanchez-Duffhues
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
| | - Marie-José Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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3
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Garsetti DE, Sahay K, Wang Y, Rogers MB. Sex and the basal mRNA synthesis machinery. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1765. [PMID: 36195437 PMCID: PMC10070566 DOI: 10.1002/wrna.1765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022]
Abstract
Evolution and change generated an incredible diversity of organisms on this earth. Yet, some processes are so central to life that change is strongly selected against. Synthesis of the eukaryotic messenger RNA is one example. The assemblies that carry out transcription and processing (capping, polyadenylation, and splicing) are so conserved that most genes have recognizable orthologs in yeast and humans. Naturally, most would conclude transcription and processing are identical in both sexes. However, this is an assumption. Men and women vastly differ in their physiologies. The incidence of pathologies, symptom presentation, disease outcome, and therapeutic response in each sex vary enormously. Despite the harm ignorance causes women, biological research has been historically carried out without regard to sex. The male mouse was the default mammal. A cultured cell's sex was considered irrelevant. Attempts to fill this knowledge gap have revealed molecular dissimilarities. For example, the earliest embryonic male and female transcriptomes differ long before fetal sex hormones appear. We used public data to challenge the assumption of sameness by reviewing reports of sex-biased gene expression and gene targeting. We focused on 120 genes encoding nonregulatory proteins involved in mRNA synthesis. Remarkably, genes with recognizable orthologs in yeast and thus LEAST likely to differ, did differ between the sexes. The rapidly growing public databases can be used to compare the expression of any gene in male and female tissues. Appreciating the principles that drive sex differences will enrich our understanding of RNA biology in all humans-men and women. This article is categorized under: RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Diane E Garsetti
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Khushboo Sahay
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Yue Wang
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Melissa B Rogers
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
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4
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Nickbarg EB, Spencer KB, Mortison JD, Lee JT. Targeting RNA with small molecules: lessons learned from Xist RNA. RNA (NEW YORK, N.Y.) 2023; 29:463-472. [PMID: 36725318 PMCID: PMC10019374 DOI: 10.1261/rna.079523.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although more than 98% of the human genome is noncoding, nearly all drugs on the market target one of about 700 disease-related proteins. However, an increasing number of diseases are now being attributed to noncoding RNA and the ability to target them would vastly expand the chemical space for drug development. We recently devised a screening strategy based upon affinity-selection mass spectrometry and succeeded in identifying bioactive compounds for the noncoding RNA prototype, Xist. One such compound, termed X1, has drug-like properties and binds specifically to the RepA motif of Xist in vitro and in vivo. Small-angle X-ray scattering analysis reveals that X1 changes the conformation of RepA in solution, thereby explaining the displacement of cognate interacting protein factors (PRC2 and SPEN) and inhibition of X-chromosome inactivation. In this Perspective, we discuss lessons learned from these proof-of-concept experiments and suggest that RNA can be systematically targeted by drug-like compounds to disrupt RNA structure and function.
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Affiliation(s)
| | | | | | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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5
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Panayotis N, Ehinger Y, Felix MS, Roux JC. State-of-the-art therapies for Rett syndrome. Dev Med Child Neurol 2023; 65:162-170. [PMID: 36056801 PMCID: PMC10087176 DOI: 10.1111/dmcn.15383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Rett syndrome (RTT) is an X-linked neurogenetic disorder caused by mutations of the MECP2 (methyl-CpG-binding protein 2) gene. Over two decades of work established MeCP2 as a protein with pivotal roles in the regulation of the epigenome, neuronal physiology, synaptic maintenance, and behaviour. Given the genetic aetiology of RTT and the proof of concept of its reversal in a mouse model, considerable efforts have been made to design therapeutic approaches to re-express MeCP2. By being at the forefront of the development of innovative gene therapies, research on RTT is of paramount importance for the treatment of monogenic neurological diseases. Here we discuss the recent advances and challenges of promising genetic strategies for the treatment of RTT including gene replacement therapies, gene/RNA editing strategies, and reactivation of the silenced X chromosome. WHAT THIS PAPER ADDS: Recent advances shed light on the promises of gene replacement therapy with new vectors designed to control the levels of MeCP2 expression. New developments in DNA/RNA editing approaches or reactivation of the silenced X chromosome open the possibility to re-express the native MeCP2 locus at endogenous levels. Current strategies still face limitations in transduction efficiency and future work is needed to improve brain delivery.
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Affiliation(s)
- Nicolas Panayotis
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.,Université Paris Cité, CNRS, Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Yann Ehinger
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
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6
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Qian J, Guan X, Xie B, Xu C, Niu J, Tang X, Li CH, Colecraft HM, Jaenisch R, Liu XS. Multiplex epigenome editing of MECP2 to rescue Rett syndrome neurons. Sci Transl Med 2023; 15:eadd4666. [PMID: 36652535 DOI: 10.1126/scitranslmed.add4666] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of methyl CpG-binding protein 2 (MECP2) on the X chromosome in young females. Reactivation of the silent wild-type MECP2 allele from the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female patients with RTT. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 from Xi in RTT human embryonic stem cells (hESCs) and derived neurons. Demethylation of the MECP2 promoter by dCas9-Tet1 with target single-guide RNA reactivated MECP2 from Xi in RTT hESCs without detectable off-target effects at the transcriptional level. Neurons derived from methylation-edited RTT hESCs maintained MECP2 reactivation and reversed the smaller soma size and electrophysiological abnormalities, two hallmarks of RTT. In RTT neurons, insulation of the methylation-edited MECP2 locus by dCpf1-CTCF (a catalytically dead Cpf1 fused with CCCTC-binding factor) with target CRISPR RNA enhanced MECP2 reactivation and rescued RTT-related neuronal defects, providing a proof-of-concept study for epigenome editing to treat RTT and potentially other dominant X-linked diseases.
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Affiliation(s)
- Junming Qian
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, Columbia University, New York, NY 10032, USA
| | - Xiaonan Guan
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, Columbia University, New York, NY 10032, USA
| | - Bing Xie
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Chuanyun Xu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jacqueline Niu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, Columbia University, New York, NY 10032, USA
| | - Xin Tang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Neurosurgery, Boston Children's Hospital, Boston, MA 02465, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, Columbia University, New York, NY 10032, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - X Shawn Liu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, Columbia University, New York, NY 10032, USA.,Columbia Stem Cell Initiative, Columbia University Medical Center, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, Columbia University, New York, NY 10032, USA
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7
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Megagiannis P, Suresh R, Rouleau GA, Zhou Y. Reversibility and therapeutic development for neurodevelopmental disorders, insights from genetic animal models. Adv Drug Deliv Rev 2022; 191:114562. [PMID: 36183904 DOI: 10.1016/j.addr.2022.114562] [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: 04/25/2022] [Revised: 08/30/2022] [Accepted: 09/24/2022] [Indexed: 01/24/2023]
Abstract
Neurodevelopmental Disorders (NDDs) encompass a broad spectrum of conditions resulting from atypical brain development. Over the past decades, we have had the fortune to witness enormous progress in diagnosis, etiology discovery, modeling, and mechanistic understanding of NDDs from both fundamental and clinical research. Here, we review recent neurobiological advances from experimental models of NDDs. We introduce several examples and highlight breakthroughs in reversal studies of phenotypes using genetically engineered models of NDDs. The in-depth understanding of brain pathophysiology underlying NDDs and evaluations of reversibility in animal models paves the foundation for discovering novel treatment options. We discuss how the expanding property of cutting-edge technologies, such as gene editing and AAV-mediated gene delivery, are leveraged in animal models for the therapeutic development of NDDs. We envision opportunities and challenges toward faithful modeling and fruitful clinical translation.
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Affiliation(s)
- Platon Megagiannis
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Rahul Suresh
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Guy A Rouleau
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Yang Zhou
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada.
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8
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Pallier PN, Ferrara M, Romagnolo F, Ferretti MT, Soreq H, Cerase A. Chromosomal and environmental contributions to sex differences in the vulnerability to neurological and neuropsychiatric disorders: Implications for therapeutic interventions. Prog Neurobiol 2022; 219:102353. [PMID: 36100191 DOI: 10.1016/j.pneurobio.2022.102353] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Neurological and neuropsychiatric disorders affect men and women differently. Multiple sclerosis, Alzheimer's disease, anxiety disorders, depression, meningiomas and late-onset schizophrenia affect women more frequently than men. By contrast, Parkinson's disease, autism spectrum condition, attention-deficit hyperactivity disorder, Tourette's syndrome, amyotrophic lateral sclerosis and early-onset schizophrenia are more prevalent in men. Women have been historically under-recruited or excluded from clinical trials, and most basic research uses male rodent cells or animals as disease models, rarely studying both sexes and factoring sex as a potential source of variation, resulting in a poor understanding of the underlying biological reasons for sex and gender differences in the development of such diseases. Putative pathophysiological contributors include hormones and epigenetics regulators but additional biological and non-biological influences may be at play. We review here the evidence for the underpinning role of the sex chromosome complement, X chromosome inactivation, and environmental and epigenetic regulators in sex differences in the vulnerability to brain disease. We conclude that there is a pressing need for a better understanding of the genetic, epigenetic and environmental mechanisms sustaining sex differences in such diseases, which is critical for developing a precision medicine approach based on sex-tailored prevention and treatment.
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Affiliation(s)
- Patrick N Pallier
- Blizard Institute, Centre for Neuroscience, Surgery and Trauma, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
| | - Maria Ferrara
- Institute of Psychiatry, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy; Department of Psychiatry, Yale University, School of Medicine, New Haven, CT, United States; Women's Brain Project (WBP), Switzerland
| | - Francesca Romagnolo
- Institute of Psychiatry, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | | | - Hermona Soreq
- The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, 9190401, Israel
| | - Andrea Cerase
- EMBL-Rome, Via Ramarini 32, 00015 Monterotondo, RM, Italy; Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; Department of Biology, University of Pisa, SS12 Abetone e Brennero 4, 56127 Pisa, Italy.
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9
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Grimm NB, Lee JT. Selective Xi reactivation and alternative methods to restore MECP2 function in Rett syndrome. Trends Genet 2022; 38:920-943. [PMID: 35248405 PMCID: PMC9915138 DOI: 10.1016/j.tig.2022.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
The human X-chromosome harbors only 4% of our genome but carries over 20% of genes associated with intellectual disability. Given that they inherit only one X-chromosome, males are more frequently affected by X-linked neurodevelopmental genetic disorders than females. However, despite inheriting two X-chromosomes, females can also be affected because X-chromosome inactivation enables only one of two X-chromosomes to be expressed per cell. For Rett syndrome and similar X-linked disorders affecting females, disease-specific treatments have remained elusive. However, a cure may be found within their own cells because every sick cell carries a healthy copy of the affected gene on the inactive X (Xi). Therefore, selective Xi reactivation may be a viable approach that would address the root cause of various X-linked disorders. Here, we discuss Rett syndrome and compare current approaches in the pharmaceutical pipeline to restore MECP2 function. We then focus on Xi reactivation and review available methods, lessons learned, and future directions.
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Affiliation(s)
- Niklas-Benedikt Grimm
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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10
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Cloutier M, Kumar S, Buttigieg E, Keller L, Lee B, Williams A, Mojica-Perez S, Erliandri I, Rocha AMD, Cadigan K, Smith GD, Kalantry S. Preventing erosion of X-chromosome inactivation in human embryonic stem cells. Nat Commun 2022; 13:2516. [PMID: 35523820 PMCID: PMC9076865 DOI: 10.1038/s41467-022-30259-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
X-chromosome inactivation is a paradigm of epigenetic transcriptional regulation. Female human embryonic stem cells (hESCs) often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that culture media composition dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined xenofree medium stably maintained XIST RNA expression and coating, whereas hESCs cultured in the widely used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of lithium chloride or inhibitors of GSK-3 proteins that are targeted by lithium to the defined hESC culture medium impeded XIST RNA expression. GSK-3 inhibition in differentiating female mouse embryonic stem cells and epiblast stem cells also resulted in a loss of XIST RNA expression. Together, these data may reconcile observed variations in X-inactivation in hESCs and inform the faithful culture of pluripotent stem cells.
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Affiliation(s)
- Marissa Cloutier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Surinder Kumar
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emily Buttigieg
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Laura Keller
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brandon Lee
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Aaron Williams
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sandra Mojica-Perez
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Indri Erliandri
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andre Monteiro Da Rocha
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine & Cardiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Cadigan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Gary D Smith
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Obstetrics & Gynecology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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11
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Li J, Ming Z, Yang L, Wang T, Liu G, Ma Q. Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities. Genes Dis 2022; 9:1478-1492. [PMID: 36157489 PMCID: PMC9485286 DOI: 10.1016/j.gendis.2022.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
Sexual dimorphism has been reported in various human diseases including autoimmune diseases, neurological diseases, pulmonary arterial hypertension, and some types of cancers, although the underlying mechanisms remain poorly understood. The long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) is involved in X chromosome inactivation (XCI) in female placental mammals, a process that ensures the balanced expression dosage of X-linked genes between sexes. XIST is abnormally expressed in many sex-biased diseases. In addition, escape from XIST-mediated XCI and skewed XCI also contribute to sex-biased diseases. Therefore, its expression or modification can be regarded as a biomarker for the diagnosis and prognosis of many sex-biased diseases. Genetic manipulation of XIST expression can inhibit the progression of some of these diseases in animal models, and therefore XIST has been proposed as a potential therapeutic target. In this manuscript, we summarize the current knowledge about the mechanisms for XIST-mediated XCI and the roles of XIST in sex-biased diseases, and discuss potential therapeutic strategies targeting XIST.
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12
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BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation. Nat Commun 2022; 13:1658. [PMID: 35351876 PMCID: PMC8964718 DOI: 10.1038/s41467-022-29333-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
The process of epigenetic silencing, while fundamentally important, is not yet completely understood. Here we report a replenishable female mouse embryonic stem cell (mESC) system, Xmas, that allows rapid assessment of X chromosome inactivation (XCI), the epigenetic silencing mechanism of one of the two X chromosomes that enables dosage compensation in female mammals. Through a targeted genetic screen in differentiating Xmas mESCs, we reveal that the BAF complex is required to create nucleosome-depleted regions at promoters on the inactive X chromosome during the earliest stages of establishment of XCI. Without this action gene silencing fails. Xmas mESCs provide a tractable model for screen-based approaches that enable the discovery of unknown facets of the female-specific process of XCI and epigenetic silencing more broadly. Female embryonic stem cells (ESCs) are the ideal model to study X chromosome inactivation (XCI) establishment; however, these cells are challenging to keep in culture. Here the authors create fluorescent ‘Xmas’ reporter mice as a renewable source of ESCs and show nucleosome remodelers Smarcc1 and Smarca4 create a nucleosome-free promoter region prior to the establishment of silencing.
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Mira-Bontenbal H, Tan B, Gontan C, Goossens S, Boers RG, Boers JB, Dupont C, van Royen ME, IJcken WFJ, French P, Bedalov A, Gribnau J. Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells. Stem Cell Reports 2022; 17:693-706. [PMID: 35148843 PMCID: PMC9039756 DOI: 10.1016/j.stemcr.2022.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 01/17/2023] Open
Abstract
Rett syndrome may be treated by reactivating the silent copy of Mecp2 from the inactive X chromosome in female cells. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequate sensitivity. Here, we present a mouse model based on a dual bioluminescent and fluorescent reporter to assess the level of reactivation of Mecp2 and the inactive X chromosome by treating neural stem cells with 5-azacytidine and Xist knockdown. We show that reactivation of Mecp2 and other X-linked genes correlates with CpG density, with distance from escapees, and, very strongly, with the presence of short interspersed nuclear elements. In addition, X-linked genes reactivated in neural stem cells overlap substantially with early reactivating genes by induced pluripotent stem cell reprogramming of fibroblasts or neuronal progenitors, indicating that X chromosome reactivation follows similar paths regardless of the technique or cell type used.
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Affiliation(s)
- H Mira-Bontenbal
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands.
| | - B Tan
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - C Gontan
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - S Goossens
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - R G Boers
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - J B Boers
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - C Dupont
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands
| | - M E van Royen
- Department of Pathology, Erasmus MC, Rotterdam, the Netherlands
| | - W F J IJcken
- Center for Biomics, Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - P French
- Department of Neurology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - A Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - J Gribnau
- Oncode Institue, Department of Developmental Biology, Erasmus MC, Rotterdam, the Netherlands.
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14
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Gjaltema RAF, Schwämmle T, Kautz P, Robson M, Schöpflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Mol Cell 2022; 82:190-208.e17. [PMID: 34932975 DOI: 10.1016/j.molcel.2021.11.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Pauline Kautz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael Robson
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, Edinburgh, UK
| | - Robert Schöpflin
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lennart Brandenburg
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Carolina Vechiatto
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vera Schmiedel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center München, 85764 Neuherberg, Germany
| | - Stefan Mundlos
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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15
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X-chromosome reactivation: a concise review. Biochem Soc Trans 2021; 49:2797-2805. [PMID: 34821360 DOI: 10.1042/bst20210777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Mammalian females (XX) silence transcription on one of the two X chromosomes to compensate the expression dosage with males (XY). This process - named X-chromosome inactivation - entails a variety of epigenetic modifications that act synergistically to maintain silencing and make it heritable through cell divisions. Genes along the inactive X chromosome are, indeed, refractory to reactivation. Nonetheless, X-chromosome reactivation can occur alongside with epigenome reprogramming or by perturbing multiple silencing pathways. Here we review the events associated with X-chromosome reactivation during in vivo and in vitro reprogramming and highlight recent efforts in inducing Xi reactivation by molecular perturbations. This provides us with a first understanding of the mechanisms underlying X-chromosome reactivation, which could be tackled for therapeutic purposes.
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16
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Fang H, Deng X, Disteche CM. X-factors in human disease: Impact of gene content and dosage regulation. Hum Mol Genet 2021; 30:R285-R295. [PMID: 34387327 DOI: 10.1093/hmg/ddab221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
The gene content of the X and Y chromosomes has dramatically diverged during evolution. The ensuing dosage imbalance within the genome of males and females has led to unique chromosome-wide regulatory mechanisms with significant and sex-specific impacts on X-linked gene expression. X inactivation or silencing of most genes on one X chromosome chosen at random in females profoundly affects the manifestation of X-linked diseases, as males inherit a single maternal allele, while females express maternal and paternal alleles in a mosaic manner. An additional complication is the existence of genes that escape X inactivation and thus are ubiquitously expressed from both alleles in females. The mosaic nature of X-linked gene expression and the potential for escape can vary between individuals, tissues, cell types, and stages of life. Our understanding of the specialized nature of X-linked genes and of the multilayer epigenetic regulation that influence their expression throughout the organism has been helped by molecular studies conducted by tissue-specific and single-cell-specific approaches. In turn, the definition of molecular events that control X silencing has helped develop new approaches for the treatment of some X-linked disorders. This review focuses on the peculiarities of the X chromosome genetic content and epigenetic regulation in shaping the manifestation of congenital and acquired X-linked disorders in a sex-specific manner.
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Affiliation(s)
- He Fang
- Department of Laboratory Medicine and Pathology
| | | | - Christine M Disteche
- Department of Laboratory Medicine and Pathology.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
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17
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Villani C, Carli M, Castaldo AM, Sacchetti G, Invernizzi RW. Fluoxetine increases brain MeCP2 immuno-positive cells in a female Mecp2 heterozygous mouse model of Rett syndrome through endogenous serotonin. Sci Rep 2021; 11:14690. [PMID: 34282222 PMCID: PMC8290043 DOI: 10.1038/s41598-021-94156-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Motor skill deficit is a common and invalidating symptom of Rett syndrome (RTT), a rare disease almost exclusively affecting girls during the first/second year of life. Loss-of-function mutations of the methyl-CpG-binding protein2 (MECP2; Mecp2 in rodents) gene is the cause in most patients. We recently found that fluoxetine, a selective serotonin (5-HT) reuptake inhibitor and antidepressant drug, fully rescued motor coordination deficits in Mecp2 heterozygous (Mecp2 HET) mice acting through brain 5-HT. Here, we asked whether fluoxetine could increase MeCP2 expression in the brain of Mecp2 HET mice, under the same schedule of treatment improving motor coordination. Fluoxetine increased the number of MeCP2 immuno-positive (MeCP2+) cells in the prefrontal cortex, M1 and M2 motor cortices, and in dorsal, ventral and lateral striatum. Fluoxetine had no effect in the CA3 region of the hippocampus or in any of the brain regions of WT mice. Inhibition of 5-HT synthesis abolished the fluoxetine-induced rise of MeCP2+ cells. These findings suggest that boosting 5-HT transmission is sufficient to enhance the expression of MeCP2 in several brain regions of Mecp2 HET mice. Fluoxetine-induced rise of MeCP2 could potentially rescue motor coordination and other deficits of RTT.
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Affiliation(s)
- Claudia Villani
- Laboratory Neurochemistry and Behavior, Neuroscience Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Mirjana Carli
- Laboratory Neurochemistry and Behavior, Neuroscience Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Anna Maria Castaldo
- Laboratory Neurochemistry and Behavior, Neuroscience Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Giuseppina Sacchetti
- Laboratory Neurochemistry and Behavior, Neuroscience Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Roberto William Invernizzi
- Laboratory Neurochemistry and Behavior, Neuroscience Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy.
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18
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Wang W, Min L, Qiu X, Wu X, Liu C, Ma J, Zhang D, Zhu L. Biological Function of Long Non-coding RNA (LncRNA) Xist. Front Cell Dev Biol 2021; 9:645647. [PMID: 34178980 PMCID: PMC8222981 DOI: 10.3389/fcell.2021.645647] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Accumulating evidence suggests that lncRNA X-inactive specific transcript (lncRNA Xist) serves as an important regulator of cell growth and development. Despites its original roles in X-chromosome dosage compensation, lncRNA Xist also participates in the development of tumor and other human diseases by functioning as a competing endogenous RNA (ceRNA). In this review, we comprehensively summarized recent progress in understanding the cellular functions of lncRNA Xist in mammalian cells and discussed current knowledge regarding the ceRNA network of lncRNA Xist in various diseases. Long non-coding RNAs (lncRNAs) are transcripts that are more than 200 nt in length and without an apparent protein-coding capacity (Furlan and Rougeulle, 2016; Maduro et al., 2016). These RNAs are believed to be transcribed by the approximately 98-99% non-coding regions of the human genome (Derrien et al., 2012; Fu, 2014; Montalbano et al., 2017; Slack and Chinnaiyan, 2019), as well as a large variety of genomic regions, such as exonic, tronic, and intergenic regions. Hence, lncRNAs are also divided into eight categories: Intergenic lncRNAs, Intronic lncRNAs, Enhancer lncRNAs, Promoter lncRNAs, Natural antisense/sense lncRNAs, Small nucleolar RNA-ended lncRNAs (sno-lncRNAs), Bidirectional lncRNAs, and non-poly(A) lncRNAs (Ma et al., 2013; Devaux et al., 2015; St Laurent et al., 2015; Chen, 2016; Quinn and Chang, 2016; Richard and Eichhorn, 2018; Connerty et al., 2020). A range of evidence has suggested that lncRNAs function as key regulators in crucial cellular functions, including proliferation, differentiation, apoptosis, migration, and invasion, by regulating the expression level of target genes via epigenomic, transcriptional, or post-transcriptional approaches (Cao et al., 2018). Moreover, lncRNAs detected in body fluids were also believed to serve as potential biomarkers for the diagnosis, prognosis, and monitoring of disease progression, and act as novel and potential drug targets for therapeutic exploitation in human disease (Jiang W. et al., 2018; Zhou et al., 2019a). Long non-coding RNA X-inactive specific transcript (lncRNA Xist) are a set of 15,000-20,000 nt sequences localized in the X chromosome inactivation center (XIC) of chromosome Xq13.2 (Brown et al., 1992; Debrand et al., 1998; Kay, 1998; Lee et al., 2013; da Rocha and Heard, 2017; Yang Z. et al., 2018; Brockdorff, 2019). Previous studies have indicated that lncRNA Xist regulate X chromosome inactivation (XCI), resulting in the inheritable silencing of one of the X-chromosomes during female cell development. Also, it serves a vital regulatory function in the whole spectrum of human disease (notably cancer) and can be used as a novel diagnostic and prognostic biomarker and as a potential therapeutic target for human disease in the clinic (Liu et al., 2018b; Deng et al., 2019; Dinescu et al., 2019; Mutzel and Schulz, 2020; Patrat et al., 2020; Wang et al., 2020a). In particular, lncRNA Xist have been demonstrated to be involved in the development of multiple types of tumors including brain tumor, Leukemia, lung cancer, breast cancer, and liver cancer, with the prominent examples outlined in Table 1. It was also believed that lncRNA Xist (Chaligne and Heard, 2014; Yang Z. et al., 2018) contributed to other diseases, such as pulmonary fibrosis, inflammation, neuropathic pain, cardiomyocyte hypertrophy, and osteoarthritis chondrocytes, and more specific details can be found in Table 2. This review summarizes the current knowledge on the regulatory mechanisms of lncRNA Xist on both chromosome dosage compensation and pathogenesis (especially cancer) processes, with a focus on the regulatory network of lncRNA Xist in human disease.
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Affiliation(s)
| | | | | | | | | | | | - Dongyi Zhang
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
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19
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Generation of cryopreserved macrophages from normal and genetically engineered human pluripotent stem cells for disease modelling. PLoS One 2021; 16:e0250107. [PMID: 33886609 PMCID: PMC8061979 DOI: 10.1371/journal.pone.0250107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/30/2021] [Indexed: 11/19/2022] Open
Abstract
Macrophages are innate immune cells that play critical roles in tissue homeostasis, inflammation, and immune oncology. Macrophages differentiated from human induced pluripotent stem cells (iPSCs) overcome many limitations of using peripheral blood derived macrophages. The ability to scale up and cryopreserve a large amount of end stage macrophages from single clonal iPSCs from normal and disease specific donors offers a unique opportunity for genomic analysis and drug screening. The present study describes the step wise generation and characterization of macrophages from iPSCs using a defined serum free method amenable to scale up to generate a large batch of pure end stage cryopreservable macrophages expressing CD68, CD33, CD11c, CD11b, CD1a, HLA-DR, CD86, CD64, CD80, CD206, CD169, CD47, HLA-ABC, and CX3CR. The end stage macrophages pre and post cryopreservation retain purity, morphology, responsiveness to stimuli and display robust phagocytic function coming right out of cryopreservation. The same differentiation process was used to generate end stage macrophages from isogenic iPSCs engineered to mimic mutations associated with Parkinson's disease (SNCA A53T), neuronal ceroid lipofuscinosis (GRN2/GRN R493X), and Rett syndrome (MECP2-Knockout). End stage macrophages from isogenic engineered clones displayed differential macrophage-specific purity markers, phagocytic function, and response to specific stimuli. Thus, generating a panel of functional, physiologically relevant iPSC-derived macrophages can potentially facilitate the understanding of neural inflammatory responses associated with neurodegeneration.
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20
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Good KV, Vincent JB, Ausió J. MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. Front Genet 2021; 12:620859. [PMID: 33552148 PMCID: PMC7859524 DOI: 10.3389/fgene.2021.620859] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable degrees of protein stability exhibited by MeCP2 and its mutated versions. Also, past and emerging relationships that MeCP2 has with mRNA splicing, miRNA processing, and other non-coding RNAs (ncRNA) will be explored, and we suggest that these molecules could be missing links in understanding the epigenetic consequences incurred from genetic ablation of this important chromatin modifier. Importantly, although MeCP2 is highly expressed in the brain, where it has been most extensively studied, the role of this protein and its alterations in other tissues cannot be ignored and will also be discussed. Finally, the additional complexity to RTT pathology introduced by structural and functional implications of the two MeCP2 isoforms (MeCP2-E1 and MeCP2-E2) will be described. Epigenetic therapeutics are gaining clinical popularity, yet treatment for Rett syndrome is more complicated than would be anticipated for a purely epigenetic disorder, which should be taken into account in future clinical contexts.
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Affiliation(s)
- Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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21
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Panda A, Zylicz JJ, Pasque V. New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency. Cells 2020; 9:E2706. [PMID: 33348832 PMCID: PMC7766869 DOI: 10.3390/cells9122706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.
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Affiliation(s)
- Amitesh Panda
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| | - Jan J. Zylicz
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Vincent Pasque
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
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22
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Lee HM, Kuijer MB, Ruiz Blanes N, Clark EP, Aita M, Galiano Arjona L, Kokot A, Sciaky N, Simon JM, Bhatnagar S, Philpot BD, Cerase A. A small-molecule screen reveals novel modulators of MeCP2 and X-chromosome inactivation maintenance. J Neurodev Disord 2020; 12:29. [PMID: 33172406 PMCID: PMC7657357 DOI: 10.1186/s11689-020-09332-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/22/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the X-linked methyl-CpG binding protein 2 (MeCP2) gene. While MeCP2 mutations are lethal in most males, females survive birth but show severe neurological defects. Because X-chromosome inactivation (XCI) is a random process, approximately 50% of the cells silence the wild-type (WT) copy of the MeCP2 gene. Thus, reactivating the silent WT copy of MeCP2 could provide therapeutic intervention for RTT. METHODS Toward this goal, we screened ~ 28,000 small-molecule compounds from several libraries using a MeCP2-luciferase reporter cell line and cortical neurons from a MeCP2-EGFP mouse model. We used gain/increase of luminescence or fluorescence as a readout of MeCP2 reactivation and tested the efficacy of these drugs under different drug regimens, conditions, and cellular contexts. RESULTS We identified inhibitors of the JAK/STAT pathway as XCI-reactivating agents, both by in vitro and ex vivo assays. In particular, we show that AG-490, a Janus Kinase 2 (JAK2) kinase inhibitor, and Jaki, a pan JAK/STAT inhibitor, are capable of reactivating MeCP2 from the inactive X chromosome, in different cellular contexts. CONCLUSIONS Our results suggest that inhibition of the JAK/STAT pathway is a new potential pathway to reinstate MeCP2 gene expression as an efficient RTT treatment.
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Affiliation(s)
- Hyeong-Min Lee
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Current Address: High-Throughput Bioscience Center, Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Bram Kuijer
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Ellen P Clark
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Megumi Aita
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Agnieszka Kokot
- Department of Biochemistry and Molecular Genetics, Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sanchita Bhatnagar
- Department of Biochemistry and Molecular Genetics, Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Benjamin D Philpot
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Andrea Cerase
- Blizard Institute, Queen Mary University of London, London, UK.
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23
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The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity. Cell Rep 2020; 28:3182-3198.e11. [PMID: 31533040 PMCID: PMC6859500 DOI: 10.1016/j.celrep.2019.08.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/08/2019] [Accepted: 08/05/2019] [Indexed: 01/17/2023] Open
Abstract
Molecular processes involving lncRNAs regulate cell function. By applying transcriptomics, we identify lncRNAs whose expression is regulated by transforming growth factor β (TGF-β). Upon silencing individual lncRNAs, we identify several that regulate TGF-β signaling. Among these lncRNAs, TGFB2-antisense RNA1 (TGFB2-AS1) is induced by TGF-β through Smad and protein kinase pathways and resides in the nucleus. Depleting TGFB2-AS1 enhances TGF-β/Smad-mediated transcription and expression of hallmark TGF-β-target genes. Increased dose of TGFB2-AS1 reduces expression of these genes, attenuates TGF-β-induced cell growth arrest, and alters BMP and Wnt pathway gene profiles. Mechanistically, TGFB2-AS1, mainly via its 3′ terminal region, binds to the EED adaptor of the Polycomb repressor complex 2 (PRC2), promoting repressive histone H3K27me3 modifications at TGF-β-target gene promoters. Silencing EED or inhibiting PRC2 methylation activity partially rescues TGFB2-AS1-mediated gene repression. Thus, the TGF-β-induced TGFB2-AS1 lncRNA exerts inhibitory functions on TGF-β/BMP signaling output, supporting auto-regulatory negative feedback that balances TGF-β/BMP-mediated responses. TGF-β signaling transcriptionally regulates lncRNAs that regulate TGF-β signaling TGFB2-AS1 is induced by TGF-β to negatively regulate Smad transcriptional output TGFB2-AS1 associates with EED, the Polycomb repressor complex 2 adaptor TGFB2-AS1 promotes repressive histone modifications at TGF-β-target genes
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24
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Javed S, Selliah T, Lee YJ, Huang WH. Dosage-sensitive genes in autism spectrum disorders: From neurobiology to therapy. Neurosci Biobehav Rev 2020; 118:538-567. [PMID: 32858083 DOI: 10.1016/j.neubiorev.2020.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/26/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of heterogenous neurodevelopmental disorders affecting 1 in 59 children. Syndromic ASDs are commonly associated with chromosomal rearrangements or dosage imbalance involving a single gene. Many of these genes are dosage-sensitive and regulate transcription, protein homeostasis, and synaptic function in the brain. Despite vastly different molecular perturbations, syndromic ASDs share core symptoms including social dysfunction and repetitive behavior. However, each ASD subtype has a unique pathogenic mechanism and combination of comorbidities that require individual attention. We have learned a great deal about how these dosage-sensitive genes control brain development and behaviors from genetically-engineered mice. Here we describe the clinical features of eight monogenic neurodevelopmental disorders caused by dosage imbalance of four genes, as well as recent advances in using genetic mouse models to understand their pathogenic mechanisms and develop intervention strategies. We propose that applying newly developed quantitative molecular and neuroscience technologies will advance our understanding of the unique neurobiology of each disorder and enable the development of personalized therapy.
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Affiliation(s)
- Sehrish Javed
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Tharushan Selliah
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.
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25
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Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment. Dev Cell 2020; 54:21-32.e5. [PMID: 32531209 DOI: 10.1016/j.devcel.2020.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/16/2020] [Accepted: 05/14/2020] [Indexed: 11/20/2022]
Abstract
X chromosome inactivation (XCI) is a global silencing mechanism by which XX and XY mammals equalize X-linked gene dosages. XCI begins with an establishment phase during which Xist RNA spreads and induces de novo heterochromatinization across a female X chromosome and is followed by a maintenance phase when multiple epigenetic pathways lock down the inactive X (Xi) state. Involvement of Polycomb repressive complexes 1 and 2 in XCI has been intensively studied but with conflicting conclusions regarding their recruitment and role in Xi silencing. Here, we reveal that establishment of XCI has two phases and reconcile the roles that Xist repeats A and B play in gene silencing and Polycomb recruitment. Repeat A initiates both processes, whereas repeat B bolsters or stabilizes them thereafter. Once established, XCI no longer requires repeat A during maintenance. These findings integrate disparate studies and present a unified view of Xist's role in Polycomb-mediated silencing.
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26
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Fagiolini M, Patrizi A, LeBlanc J, Jin LW, Maezawa I, Sinnett S, Gray SJ, Molholm S, Foxe JJ, Johnston MV, Naidu S, Blue M, Hossain A, Kadam S, Zhao X, Chang Q, Zhou Z, Zoghbi H. Intellectual and Developmental Disabilities Research Centers: A Multidisciplinary Approach to Understand the Pathogenesis of Methyl-CpG Binding Protein 2-related Disorders. Neuroscience 2020; 445:190-206. [PMID: 32360592 DOI: 10.1016/j.neuroscience.2020.04.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022]
Abstract
Disruptions in the gene encoding methyl-CpG binding protein 2 (MECP2) underlie complex neurodevelopmental disorders including Rett Syndrome (RTT), MECP2 duplication disorder, intellectual disabilities, and autism. Significant progress has been made on the molecular and cellular basis of MECP2-related disorders providing a new framework for understanding how altered epigenetic landscape can derail the formation and refinement of neuronal circuits in early postnatal life and proper neurological function. This review will summarize selected major findings from the past years and particularly highlight the integrated and multidisciplinary work done at eight NIH-funded Intellectual and Developmental Disabilities Research Centers (IDDRC) across the US. Finally, we will outline a path forward with identification of reliable biomarkers and outcome measures, longitudinal preclinical and clinical studies, reproducibility of results across centers as a synergistic effort to decode and treat the pathogenesis of the complex MeCP2 disorders.
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Affiliation(s)
- Michela Fagiolini
- Children's Hospital Intellectual and Developmental Disabilities Research Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Annarita Patrizi
- Children's Hospital Intellectual and Developmental Disabilities Research Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jocelyn LeBlanc
- Children's Hospital Intellectual and Developmental Disabilities Research Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee-Way Jin
- UC Davis MIND Institute, University of California, Sacramento, CA, USA
| | - Izumi Maezawa
- UC Davis MIND Institute, University of California, Sacramento, CA, USA
| | - Sarah Sinnett
- UNC Intellectual and Developmental Disabilities Research Center, University of North Carolina, Gene Therapy Center and Dept. of Ophthalmology, Chapel Hill, NC, USA; Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Steven J Gray
- UNC Intellectual and Developmental Disabilities Research Center, University of North Carolina, Gene Therapy Center and Dept. of Ophthalmology, Chapel Hill, NC, USA; Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sophie Molholm
- The Cognitive Neurophysiology Laboratory, Departments of Pediatrics, Neuroscience, and Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John J Foxe
- The Cognitive Neurophysiology Laboratory, Ernest J. Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Michael V Johnston
- Kennedy Krieger Institute Intellectual and Developmental Disabilities Research Center/Hugo Moser Research Institute at Kennedy Krieger and Johns Hopkins School of Medicine, USA
| | - Sakkubai Naidu
- Kennedy Krieger Institute Intellectual and Developmental Disabilities Research Center/Hugo Moser Research Institute at Kennedy Krieger and Johns Hopkins School of Medicine, USA
| | - Mary Blue
- Kennedy Krieger Institute Intellectual and Developmental Disabilities Research Center/Hugo Moser Research Institute at Kennedy Krieger and Johns Hopkins School of Medicine, USA
| | - Ahamed Hossain
- Kennedy Krieger Institute Intellectual and Developmental Disabilities Research Center/Hugo Moser Research Institute at Kennedy Krieger and Johns Hopkins School of Medicine, USA
| | - Shilpa Kadam
- Kennedy Krieger Institute Intellectual and Developmental Disabilities Research Center/Hugo Moser Research Institute at Kennedy Krieger and Johns Hopkins School of Medicine, USA
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quiang Chang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhaolan Zhou
- Department of Genetic, Epigenetic Institute, University of Pennsylvania Perelman School of Medicine, Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Huda Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
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27
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Halmai JANM, Deng P, Gonzalez CE, Coggins NB, Cameron D, Carter JL, Buchanan FKB, Waldo JJ, Lock SR, Anderson JD, O’Geen H, Segal DJ, Nolta J, Fink KD. Artificial escape from XCI by DNA methylation editing of the CDKL5 gene. Nucleic Acids Res 2020; 48:2372-2387. [PMID: 31925439 PMCID: PMC7049732 DOI: 10.1093/nar/gkz1214] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
A significant number of X-linked genes escape from X chromosome inactivation and are associated with a distinct epigenetic signature. One epigenetic modification that strongly correlates with X-escape is reduced DNA methylation in promoter regions. Here, we created an artificial escape by editing DNA methylation on the promoter of CDKL5, a gene causative for an infantile epilepsy, from the silenced X-chromosomal allele in human neuronal-like cells. We identify that a fusion of the catalytic domain of TET1 to dCas9 targeted to the CDKL5 promoter using three guide RNAs causes significant reactivation of the inactive allele in combination with removal of methyl groups from CpG dinucleotides. Strikingly, we demonstrate that co-expression of TET1 and a VP64 transactivator have a synergistic effect on the reactivation of the inactive allele to levels >60% of the active allele. We further used a multi-omics assessment to determine potential off-targets on the transcriptome and methylome. We find that synergistic delivery of dCas9 effectors is highly selective for the target site. Our findings further elucidate a causal role for reduced DNA methylation associated with escape from X chromosome inactivation. Understanding the epigenetics associated with escape from X chromosome inactivation has potential for those suffering from X-linked disorders.
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MESH Headings
- Alleles
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- Catalytic Domain
- Cell Line, Tumor
- Chromosomes, Human, X/chemistry
- Chromosomes, Human, X/metabolism
- CpG Islands
- Epigenesis, Genetic
- Gene Editing
- Gene Silencing
- Humans
- Mixed Function Oxygenases/genetics
- Mixed Function Oxygenases/metabolism
- Neurons/cytology
- Neurons/metabolism
- Promoter Regions, Genetic
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Trans-Activators/genetics
- Trans-Activators/metabolism
- X Chromosome Inactivation
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Julian A N M Halmai
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Peter Deng
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Casiana E Gonzalez
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Nicole B Coggins
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David Cameron
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Jasmine L Carter
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Fiona K B Buchanan
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Jennifer J Waldo
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Samantha R Lock
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | | | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Jan Nolta
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Kyle D Fink
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
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28
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Widespread organ tolerance to Xist loss and X reactivation except under chronic stress in the gut. Proc Natl Acad Sci U S A 2020; 117:4262-4272. [PMID: 32041873 DOI: 10.1073/pnas.1917203117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Long thought to be dispensable after establishing X chromosome inactivation (XCI), Xist RNA is now known to also maintain the inactive X (Xi). To what extent somatic X reactivation causes physiological abnormalities is an active area of inquiry. Here, we use multiple mouse models to investigate in vivo consequences. First, when Xist is deleted systemically in post-XCI embryonic cells using the Meox2-Cre driver, female pups exhibit no morbidity or mortality despite partial X reactivation. Second, when Xist is conditionally deleted in epithelial cells using Keratin14-Cre or in B cells using CD19-Cre, female mice have a normal life span without obvious illness. Third, when Xist is deleted in gut using Villin-Cre, female mice remain healthy despite significant X-autosome dosage imbalance. Finally, when the gut is acutely stressed by azoxymethane/dextran sulfate (AOM/DSS) exposure, both Xist-deleted and wild-type mice develop gastrointestinal tumors. Intriguingly, however, under prolonged stress, mutant mice develop larger tumors and have a higher tumor burden. The effect is female specific. Altogether, these observations reveal a surprising systemic tolerance to Xist loss but importantly reveal that Xist and XCI are protective to females during chronic stress.
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29
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Sinden DS, Holman CD, Bare CJ, Sun X, Gade AR, Cohen DE, Pitt GS. Knockout of the X-linked Fgf13 in the hypothalamic paraventricular nucleus impairs sympathetic output to brown fat and causes obesity. FASEB J 2019; 33:11579-11594. [PMID: 31339804 PMCID: PMC6994920 DOI: 10.1096/fj.201901178r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022]
Abstract
Fibroblast growth factor (FGF)13, a nonsecreted, X-linked, FGF homologous factor, is differentially expressed in adipocytes in response to diet, yet Fgf13's role in metabolism has not been explored. Heterozygous Fgf13 knockouts fed normal chow and housed at 22°C showed hyperactivity accompanying reduced core temperature and obesity when housed at 30°C. Those heterozygous knockouts showed defects in thermogenesis even at 30°C and an inability to protect core temperature. Surprisingly, we detected trivial FGF13 in adipose of wild-type mice fed normal chow and no obesity in adipose-specific heterozygous knockouts housed at 30°C, and we detected an intact brown fat response through exogenous β3 agonist stimulation, suggesting a defect in sympathetic drive to brown adipose tissue. In contrast, hypothalamic-specific ablation of Fgf13 recapitulated weight gain at 30°C. Norepinephrine turnover in brown fat was reduced at both housing temperatures. Thus, our data suggest that impaired CNS regulation of sympathetic activation of brown fat underlies obesity and thermogenesis in Fgf13 heterozygous knockouts fed normal chow.-Sinden, D. S., Holman, C. D., Bare, C. J., Sun, X., Gade, A. R., Cohen, D. E., Pitt, G. S. Knockout of the X-linked Fgf13 in the hypothalamic paraventricular nucleus impairs sympathetic output to brown fat and causes obesity.
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Affiliation(s)
- Daniel S. Sinden
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, New York, USA
| | - Corey D. Holman
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, New York, USA
| | - Curtis J. Bare
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, New York, USA
| | - Xiaolu Sun
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, New York, USA
| | - Aravind R. Gade
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, New York, USA
| | - David E. Cohen
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, New York, USA
| | - Geoffrey S. Pitt
- Cardiovascular Research Institute, Weill Cornell Medical College, New York, New York, USA
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30
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Talon I, Janiszewski A, Chappell J, Vanheer L, Pasque V. Recent Advances in Understanding the Reversal of Gene Silencing During X Chromosome Reactivation. Front Cell Dev Biol 2019; 7:169. [PMID: 31552244 PMCID: PMC6733891 DOI: 10.3389/fcell.2019.00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Dosage compensation between XX female and XY male cells is achieved by a process known as X chromosome inactivation (XCI) in mammals. XCI is initiated early during development in female cells and is subsequently stably maintained in most somatic cells. Despite its stability, the robust transcriptional silencing of XCI is reversible, in the embryo and also in a number of reprogramming settings. Although XCI has been intensively studied, the dynamics, factors, and mechanisms of X chromosome reactivation (XCR) remain largely unknown. In this review, we discuss how new sequencing technologies and reprogramming approaches have enabled recent advances that revealed the timing of transcriptional activation during XCR. We also discuss the factors and chromatin features that might be important to understand the dynamics and mechanisms of the erasure of transcriptional gene silencing on the inactive X chromosome (Xi).
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Affiliation(s)
| | | | | | | | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
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31
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Abstract
Rett syndrome (RTT) is a severe neurological disorder caused by mutations in the gene encoding methyl-CpG-binding protein 2 (MeCP2). Almost two decades of research into RTT have greatly advanced our understanding of the function and regulation of the multifunctional protein MeCP2. Here, we review recent advances in understanding how loss of MeCP2 impacts different stages of brain development, discuss recent findings demonstrating the molecular role of MeCP2 as a transcriptional repressor, assess primary and secondary effects of MeCP2 loss and examine how loss of MeCP2 can result in an imbalance of neuronal excitation and inhibition at the circuit level along with dysregulation of activity-dependent mechanisms. These factors present challenges to the search for mechanism-based therapeutics for RTT and suggest specific approaches that may be more effective than others.
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32
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Treating Rett syndrome: from mouse models to human therapies. Mamm Genome 2019; 30:90-110. [PMID: 30820643 PMCID: PMC6606665 DOI: 10.1007/s00335-019-09793-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023]
Abstract
Rare diseases are very difficult to study mechanistically and to develop therapies for because of the scarcity of patients. Here, the rare neuro-metabolic disorder Rett syndrome (RTT) is discussed as a prototype for precision medicine, demonstrating how mouse models have led to an understanding of the development of symptoms. RTT is caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2). Mecp2-mutant mice are being used in preclinical studies that target the MECP2 gene directly, or its downstream pathways. Importantly, this work may improve the health of RTT patients. Clinical presentation may vary widely among individuals based on their mutation, but also because of the degree of X chromosome inactivation and the presence of modifier genes. Because it is a complex disorder involving many organ systems, it is likely that recovery of RTT patients will involve a combination of treatments. Precision medicine is warranted to provide the best efficacy to individually treat RTT patients.
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33
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Kumari D, Gazy I, Usdin K. Pharmacological Reactivation of the Silenced FMR1 Gene as a Targeted Therapeutic Approach for Fragile X Syndrome. Brain Sci 2019; 9:brainsci9020039. [PMID: 30759772 PMCID: PMC6406686 DOI: 10.3390/brainsci9020039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
More than ~200 CGG repeats in the 5′ untranslated region of the FMR1 gene results in transcriptional silencing and the absence of the FMR1 encoded protein, FMRP. FMRP is an RNA-binding protein that regulates the transport and translation of a variety of brain mRNAs in an activity-dependent manner. The loss of FMRP causes dysregulation of many neuronal pathways and results in an intellectual disability disorder, fragile X syndrome (FXS). Currently, there is no effective treatment for FXS. In this review, we discuss reactivation of the FMR1 gene as a potential approach for FXS treatment with an emphasis on the use of small molecules to inhibit the pathways important for gene silencing.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Inbal Gazy
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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34
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Jégu T, Blum R, Cochrane JC, Yang L, Wang CY, Gilles ME, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT. Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. Nat Struct Mol Biol 2019; 26:96-109. [PMID: 30664740 PMCID: PMC6421574 DOI: 10.1038/s41594-018-0176-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023]
Abstract
The noncoding RNA Xist recruits silencing factors to the inactive X chromosome (Xi) and facilitates re-organization of Xi structure. Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion triggers a gain of accessibility of selective chromatin regions that is regulated by BRG1, an ATPase subunit of the SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits nucleosome remodeling and ATPase activities of BRG1, while in cell culture Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, starting from pre-existing BRG1 sites that are free of Xist. BRG1 re-association correlates with cohesin binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi “superloops.” Thus, Xist binding inhibits BRG1’s nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi.
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Affiliation(s)
- Teddy Jégu
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roy Blum
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jesse C Cochrane
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Yang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chen-Yu Wang
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maud-Emmanuelle Gilles
- Institute for RNA Medicine, Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David Colognori
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Attila Szanto
- Howard Hughes Medical Institute, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Boston, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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35
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Adrianse RL, Smith K, Gatbonton-Schwager T, Sripathy SP, Lao U, Foss EJ, Boers RG, Boers JB, Gribnau J, Bedalov A. Perturbed maintenance of transcriptional repression on the inactive X-chromosome in the mouse brain after Xist deletion. Epigenetics Chromatin 2018; 11:50. [PMID: 30170615 PMCID: PMC6118007 DOI: 10.1186/s13072-018-0219-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/16/2018] [Indexed: 01/22/2023] Open
Abstract
Background The long noncoding RNA Xist is critical for initiation and establishment of X-chromosome inactivation during embryogenesis in mammals, but it is unclear whether its continued expression is required for maintaining X-inactivation in vivo. Results By using an inactive X-chromosome-linked MeCP2-GFP reporter, which allowed us to enumerate reactivation events in the mouse brain even when they occur in very few cells, we found that deletion of Xist in the brain after establishment of X-chromosome inactivation leads to reactivation in 2–5% of neurons and in a smaller fraction of astrocytes. In contrast to global loss of both H3 lysine 27 trimethylation (H3K27m3) and histone H2A lysine 119 monoubiquitylation (H2AK119ub1) we observed upon Xist deletion, alterations in CpG methylation were subtle, and this was mirrored by only minor alterations in X-chromosome-wide gene expression levels, with highly expressed genes more prone to both derepression and demethylation compared to genes with low expression level. Conclusion Our results demonstrate that Xist plays a role in the maintenance of histone repressive marks, DNA methylation and transcriptional repression on the inactive X-chromosome, but that partial loss of X-dosage compensation in the absence of Xist in the brain is well tolerated. Electronic supplementary material The online version of this article (10.1186/s13072-018-0219-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robin L Adrianse
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA
| | - Kaleb Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA
| | - Tonibelle Gatbonton-Schwager
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA
| | - Smitha P Sripathy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA
| | - Eric J Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus MC, 3015 CN, Rotterdam, The Netherlands.,Department of Obstetrics and Gynaecology, Erasmus MC, 3015 CN, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus MC, 3015 CN, Rotterdam, The Netherlands.,Delft Diagnostic Laboratories, 2288 ER, Rijswijk, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015 CN, Rotterdam, The Netherlands
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA, 98109, USA. .,Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, University of Washington, Seattle, WA, 98195, USA.
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36
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Tsix-Mecp2 female mouse model for Rett syndrome reveals that low-level MECP2 expression extends life and improves neuromotor function. Proc Natl Acad Sci U S A 2018; 115:8185-8190. [PMID: 30038001 DOI: 10.1073/pnas.1800931115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by a mutation in the X-linked methyl-CpG-binding protein 2 (MECP2). There is currently no disease-specific treatment, but MECP2 restoration through reactivation of the inactive X (Xi) has been of considerable interest. Progress toward an Xi-reactivation therapy has been hampered by a lack of suitable female mouse models. Because of cellular mosaicism due to random X-chromosome inactivation (XCI), Mecp2+/- heterozygous females develop only mild RTT. Here, we create an improved female mouse model by introducing a mutation in Tsix, the antisense regulator of XCI allelic choice. Tsix-Mecp2 mice show reduced MECP2 mosaicism and closely phenocopy the severely affected Mecp2-null males. Tsix-Mecp2 females demonstrate shortened lifespan, motor weakness, tremors, and gait disturbance. Intriguingly, they also exhibit repetitive behaviors, as is often seen in human RTT, including excessive grooming and biting that result in self-injury. With a Tsix allelic series, we vary MECP2 levels in brain and demonstrate a direct, but nonlinear correlation between MECP2 levels and phenotypic improvement. As little as 5-10% MECP2 restoration improves neuromotor function and extends lifespan five- to eightfold. Our study thus guides future pharmacological strategies and suggests that partial MECP2 restoration could have disproportionate therapeutic benefit.
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Pharmacological reactivation of inactive X-linked Mecp2 in cerebral cortical neurons of living mice. Proc Natl Acad Sci U S A 2018; 115:7991-7996. [PMID: 30012595 DOI: 10.1073/pnas.1803792115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rett syndrome (RTT) is a genetic disorder resulting from a loss-of-function mutation in one copy of the X-linked gene methyl-CpG-binding protein 2 (MECP2). Typical RTT patients are females and, due to random X chromosome inactivation (XCI), ∼50% of cells express mutant MECP2 and the other ∼50% express wild-type MECP2. Cells expressing mutant MECP2 retain a wild-type copy of MECP2 on the inactive X chromosome (Xi), the reactivation of which represents a potential therapeutic approach for RTT. Previous studies have demonstrated reactivation of Xi-linked MECP2 in cultured cells by biological or pharmacological inhibition of factors that promote XCI (called "XCI factors" or "XCIFs"). Whether XCIF inhibitors in living animals can reactivate Xi-linked MECP2 in cerebral cortical neurons, the cell type most therapeutically relevant to RTT, remains to be determined. Here, we show that pharmacological inhibitors targeting XCIFs in the PI3K/AKT and bone morphogenetic protein signaling pathways reactivate Xi-linked MECP2 in cultured mouse fibroblasts and human induced pluripotent stem cell-derived postmitotic RTT neurons. Notably, reactivation of Xi-linked MECP2 corrects characteristic defects of human RTT neurons including reduced soma size and branch points. Most importantly, we show that intracerebroventricular injection of the XCIF inhibitors reactivates Xi-linked Mecp2 in cerebral cortical neurons of adult living mice. In support of these pharmacological results, we also demonstrate genetic reactivation of Xi-linked Mecp2 in cerebral cortical neurons of living mice bearing a homozygous XCIF deletion. Collectively, our results further establish the feasibility of pharmacological reactivation of Xi-linked MECP2 as a therapeutic approach for RTT.
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38
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Shah TA, Rogers MB. Unanswered Questions Regarding Sex and BMP/TGF-β Signaling. J Dev Biol 2018; 6:jdb6020014. [PMID: 29914150 PMCID: PMC6027345 DOI: 10.3390/jdb6020014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/02/2018] [Accepted: 06/14/2018] [Indexed: 01/23/2023] Open
Abstract
Crosstalk between the BMP and TGF-β signaling pathways regulates many complex developmental processes from the earliest stages of embryogenesis throughout adult life. In many situations, the two signaling pathways act reciprocally. For example, TGF-β signaling is generally pro-fibrotic, whereas BMP signaling is anti-fibrotic and pro-calcific. Sex-specific differences occur in many diseases including cardiovascular pathologies. Differing ratios of fibrosis and calcification in stenotic valves suggests that BMP/TGF-β signaling may vary in men and women. In this review, we focus on the current understanding of the interplay between sex and BMP/TGF-β signaling and pose several unanswered questions.
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Affiliation(s)
- Tapan A Shah
- Rutgers-New Jersey Medical School, Microbiology, Biochemistry, & Molecular Genetics, Newark, NJ 07103, USA.
| | - Melissa B Rogers
- Rutgers-New Jersey Medical School, Microbiology, Biochemistry, & Molecular Genetics, Newark, NJ 07103, USA.
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39
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Rajpathak SN, Deobagkar DD. Aneuploidy: an important model system to understand salient aspects of functional genomics. Brief Funct Genomics 2018; 17:181-190. [PMID: 29228117 DOI: 10.1093/bfgp/elx041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Maintaining a balance in gene dosage and protein activity is essential to sustain normal cellular functions. Males and females have a wide range of genetic as well as epigenetic differences, where X-linked gene dosage is an essential regulatory factor. Basic understanding of gene dosage maintenance has emerged from the studies carried out using mouse models with FCG (four core genotype) and chromosomal aneuploidy as well as from mono-chromosomal hybrid cells. In mammals, aneuploidy often leads to embryonic lethality particularly in early development with major developmental and structural abnormalities. Thus, in-depth analysis of the causes and consequences of gene dosage alterations is needed to unravel its effects on basic cellular and developmental functions as well as in understanding its medical implications. Cells isolated from individuals with naturally occurring chromosomal aneuploidy can be considered as true representatives, as these cells have stable chromosomal alterations/gene dosage imbalance, which have occurred by modulation of the basic molecular machinery. Therefore, innovative use of these natural aneuploidy cells/organisms with recent molecular and high-throughput techniques will provide an understanding of the basic mechanisms involved in gene dosage balance and the related consequences for functional genomics.
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40
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Abstract
Rett Syndrome is a severe neurological disorder mainly due to
de novo mutations in the methyl-CpG-binding protein 2 gene (
MECP2). Mecp2 is known to play a role in chromatin organization and transcriptional regulation. In this review, we report the latest advances on the molecular function of Mecp2 and the new animal and cellular models developed to better study Rett syndrome. Finally, we present the latest innovative therapeutic approaches, ranging from classical pharmacology to correct symptoms to more innovative approaches intended to cure the pathology.
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Affiliation(s)
- Yann Ehinger
- Aix Marseille Univ, INSERM, MMG, 13385 Marseille, France
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41
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Leko V, Sripathy S, Adrianse RL, Loe T, Park A, Lao U, Foss EJ, Bartolomei MS, Bedalov A. Pooled shRNA Screen for Reactivation of MeCP2 on the Inactive X Chromosome. J Vis Exp 2018. [PMID: 29553562 DOI: 10.3791/56398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi). Reactivation of the construct in the reporter cell line conferred survival advantage under hygromycin B selection, enabling us to screen a large shRNA library and identify hairpins that reactivated the reporter by measuring their post-selection enrichment using next-generation sequencing. The enriched hairpins were then individually validated by testing their ability to activate the luciferase reporter on Xi.
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Affiliation(s)
- Vid Leko
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health
| | - Smitha Sripathy
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Robin L Adrianse
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Taylor Loe
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Angela Park
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Eric J Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Marisa S Bartolomei
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center; Departments of Medicine and Biochemistry, University of Washington;
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A mixed modality approach towards Xi reactivation for Rett syndrome and other X-linked disorders. Proc Natl Acad Sci U S A 2017; 115:E668-E675. [PMID: 29282321 DOI: 10.1073/pnas.1715124115] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The X-chromosome harbors hundreds of disease genes whose associated diseases predominantly affect males. However, a subset, including neurodevelopmental disorders, Rett syndrome (RTT), fragile X syndrome, and CDKL5 syndrome, also affects females. These disorders lack disease-specific treatment. Because female cells carry two X chromosomes, an emerging treatment strategy has been to reawaken the healthy allele on the inactive X (Xi). Here, we focus on methyl-CpG binding protein 2 (MECP2) restoration for RTT and combinatorially target factors in the interactome of Xist, the noncoding RNA responsible for X inactivation. We identify a mixed modality approach combining an Xist antisense oligonucleotide and a small-molecule inhibitor of DNA methylation, which, together, achieve 30,000-fold MECP2 up-regulation from the Xi in cultured cells. Combining a brain-specific genetic Xist ablation with short-term 5-aza-2'-deoxycytidine (Aza) treatment models the synergy in vivo without evident toxicity. The Xi is selectively reactivated. These experiments provide proof of concept for a mixed modality approach for treating X-linked disorders in females.
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43
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Carrel L, Brown CJ. When the Lyon(ized chromosome) roars: ongoing expression from an inactive X chromosome. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160355. [PMID: 28947654 PMCID: PMC5627157 DOI: 10.1098/rstb.2016.0355] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 12/21/2022] Open
Abstract
A tribute to Mary Lyon was held in October 2016. Many remarked about Lyon's foresight regarding many intricacies of the X-chromosome inactivation process. One such example is that a year after her original 1961 hypothesis she proposed that genes with Y homologues should escape from X inactivation to achieve dosage compensation between males and females. Fifty-five years later we have learned many details about these escapees that we attempt to summarize in this review, with a particular focus on recent findings. We now know that escapees are not rare, particularly on the human X, and that most lack functionally equivalent Y homologues, leading to their increasingly recognized role in sexually dimorphic traits. Newer sequencing technologies have expanded profiling of primary tissues that will better enable connections to sex-biased disorders as well as provide additional insights into the X-inactivation process. Chromosome organization, nuclear location and chromatin environments distinguish escapees from other X-inactivated genes. Nevertheless, several big questions remain, including what dictates their distinct epigenetic environment, the underlying basis of species differences in escapee regulation, how different classes of escapees are distinguished, and the roles that local sequences and chromosome ultrastructure play in escapee regulation.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Mail code H171, Hershey, PA 17033, USA
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada BC V6T 1Z3
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