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Kubasova N, Alves-Pereira CF, Gupta S, Vinogradova S, Gimelbrant A, Barreto VM. In Vivo Clonal Analysis Reveals Random Monoallelic Expression in Lymphocytes That Traces Back to Hematopoietic Stem Cells. Front Cell Dev Biol 2022; 10:827774. [PMID: 36003148 PMCID: PMC9393635 DOI: 10.3389/fcell.2022.827774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Evaluating the epigenetic landscape in the stem cell compartment at the single-cell level is essential to assess the cells’ heterogeneity and predict their fate. Here, using a genome-wide transcriptomics approach in vivo, we evaluated the allelic expression imbalance in the progeny of single hematopoietic cells (HSCs) as a read-out of epigenetic marking. After 4 months of extensive proliferation and differentiation, we found that X-chromosome inactivation (XCI) is tightly maintained in all single-HSC derived hematopoietic cells. In contrast, the vast majority of the autosomal genes did not show clonal patterns of random monoallelic expression (RME). However, a persistent allele-specific autosomal transcription in HSCs and their progeny was found in a rare number of cases, none of which has been previously reported. These data show that: 1) XCI and RME in the autosomal chromosomes are driven by different mechanisms; 2) the previously reported high frequency of genes under RME in clones expanded in vitro (up to 15%) is not found in clones undergoing multiple differentiation steps in vivo; 3) prior to differentiation, HSCs have stable patterns of autosomal RME. We propose that most RME patterns in autosomal chromosomes are erased and established de novo during cell lineage differentiation.
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Affiliation(s)
- Nadiya Kubasova
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- Genetagus, Egas Moniz – Cooperativa de Ensino Superior, CRL, Monte de Caparica, Portugal
| | - Clara F. Alves-Pereira
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Saumya Gupta
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Svetlana Vinogradova
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Alexander Gimelbrant
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
| | - Vasco M. Barreto
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Costa da Caparica, Portugal
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
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Barreto VM, Kubasova N, Alves-Pereira CF, Gendrel AV. X-Chromosome Inactivation and Autosomal Random Monoallelic Expression as "Faux Amis". Front Cell Dev Biol 2021; 9:740937. [PMID: 34631717 PMCID: PMC8495168 DOI: 10.3389/fcell.2021.740937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
X-chromosome inactivation (XCI) and random monoallelic expression of autosomal genes (RMAE) are two paradigms of gene expression regulation where, at the single cell level, genes can be expressed from either the maternal or paternal alleles. X-chromosome inactivation takes place in female marsupial and placental mammals, while RMAE has been described in mammals and also other species. Although the outcome of both processes results in random monoallelic expression and mosaicism at the cellular level, there are many important differences. We provide here a brief sketch of the history behind the discovery of XCI and RMAE. Moreover, we review some of the distinctive features of these two phenomena, with respect to when in development they are established, their roles in dosage compensation and cellular phenotypic diversity, and the molecular mechanisms underlying their initiation and stability.
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Affiliation(s)
- Vasco M Barreto
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Nadiya Kubasova
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Clara F Alves-Pereira
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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Mahú I, Barateiro A, Rial-Pensado E, Martinéz-Sánchez N, Vaz SH, Cal PMSD, Jenkins B, Rodrigues T, Cordeiro C, Costa MF, Mendes R, Seixas E, Pereira MMA, Kubasova N, Gres V, Morris I, Temporão C, Olivares M, Sanz Y, Koulman A, Corzana F, Sebastião AM, López M, Bernardes GJL, Domingos AI. Brain-Sparing Sympathofacilitators Mitigate Obesity without Adverse Cardiovascular Effects. Cell Metab 2020; 31:1120-1135.e7. [PMID: 32402266 PMCID: PMC7671941 DOI: 10.1016/j.cmet.2020.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 03/03/2020] [Accepted: 04/14/2020] [Indexed: 02/02/2023]
Abstract
Anti-obesity drugs in the amphetamine (AMPH) class act in the brain to reduce appetite and increase locomotion. They are also characterized by adverse cardiovascular effects with origin that, despite absence of any in vivo evidence, is attributed to a direct sympathomimetic action in the heart. Here, we show that the cardiac side effects of AMPH originate from the brain and can be circumvented by PEGylation (PEGyAMPH) to exclude its central action. PEGyAMPH does not enter the brain and facilitates SNS activity via theβ2-adrenoceptor, protecting mice against obesity by increasing lipolysis and thermogenesis, coupled to higher heat dissipation, which acts as an energy sink to increase energy expenditure without altering food intake or locomotor activity. Thus, we provide proof-of-principle for a novel class of exclusively peripheral anti-obesity sympathofacilitators that are devoid of any cardiovascular and brain-related side effects.
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Affiliation(s)
- Inês Mahú
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Andreia Barateiro
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; Neuron Glia Biology in Health and Disease, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Eva Rial-Pensado
- NeurObesity Group, Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña 15782, Spain
| | - Noelia Martinéz-Sánchez
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - Sandra H Vaz
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof., Egas Moniz, Lisbon 1649-028, Portugal; Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal
| | - Pedro M S D Cal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof., Egas Moniz, Lisbon 1649-028, Portugal
| | - Benjamin Jenkins
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, Wellcome Trust, MRL Institute of Metabolic Science, University of Cambridge, Pathology building Level 4, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof., Egas Moniz, Lisbon 1649-028, Portugal
| | - Carlos Cordeiro
- Laboratório de FT-ICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisbon 1749-016, Portugal
| | - Miguel F Costa
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Raquel Mendes
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Elsa Seixas
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Mafalda M A Pereira
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Nadiya Kubasova
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Vitka Gres
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Imogen Morris
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Carolina Temporão
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Marta Olivares
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, National Research Council, Valencia (IATA-CSIC), Catedratico Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, National Research Council, Valencia (IATA-CSIC), Catedratico Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Albert Koulman
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, Wellcome Trust, MRL Institute of Metabolic Science, University of Cambridge, Pathology building Level 4, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Ana M Sebastião
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof., Egas Moniz, Lisbon 1649-028, Portugal; Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal
| | - Miguel López
- NeurObesity Group, Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña 15782, Spain
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof., Egas Moniz, Lisbon 1649-028, Portugal; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Ana I Domingos
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK; Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; Howard Hughes Medical Institute, IGC, Oeiras, Portugal.
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Pereira MMA, Mahú I, Seixas E, Martinéz-Sánchez N, Kubasova N, Pirzgalska RM, Cohen P, Dietrich MO, López M, Bernardes GJL, Domingos AI. A brain-sparing diphtheria toxin for chemical genetic ablation of peripheral cell lineages. Nat Commun 2017; 8:14967. [PMID: 28367972 PMCID: PMC5382263 DOI: 10.1038/ncomms14967] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/16/2017] [Indexed: 01/03/2023] Open
Abstract
Conditional expression of diphtheria toxin receptor (DTR) is widely used for tissue-specific ablation of cells. However, diphtheria toxin (DT) crosses the blood-brain barrier, which limits its utility for ablating peripheral cells using Cre drivers that are also expressed in the central nervous system (CNS). Here we report the development of a brain-sparing DT, termed BRAINSPAReDT, for tissue-specific genetic ablation of cells outside the CNS. We prevent blood-brain barrier passage of DT through PEGylation, which polarizes the molecule and increases its size. We validate BRAINSPAReDT with regional genetic sympathectomy: BRAINSPAReDT ablates peripheral but not central catecholaminergic neurons, thus avoiding the Parkinson-like phenotype associated with full dopaminergic depletion. Regional sympathectomy compromises adipose tissue thermogenesis, and renders mice susceptible to obesity. We provide a proof of principle that BRAINSPAReDT can be used for Cre/DTR tissue-specific ablation outside the brain using CNS drivers, while consolidating the link between adiposity and the sympathetic nervous system.
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Affiliation(s)
| | - Inês Mahú
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Elsa Seixas
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | - Noelia Martinéz-Sánchez
- NeurObesity Group, Department of Physiology, CIMUS, University of Santiago de Compostela—Instituto de Investigación Sanitaria, Santiago de Compostela (A Coruña) 15782, Spain,CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela 15706, Spain
| | - Nadiya Kubasova
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
| | | | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Marcelo O Dietrich
- Section of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, USA,Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Miguel López
- NeurObesity Group, Department of Physiology, CIMUS, University of Santiago de Compostela—Instituto de Investigación Sanitaria, Santiago de Compostela (A Coruña) 15782, Spain,CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela 15706, Spain
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Ana I. Domingos
- Obesity Laboratory, Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal,
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