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Robertson HE, Sebé-Pedrós A, Saudemont B, Loe-Mie Y, Zakrzewski AC, Grau-Bové X, Mailhe MP, Schiffer P, Telford MJ, Marlow H. Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity. Nat Commun 2024; 15:2469. [PMID: 38503762 PMCID: PMC10951248 DOI: 10.1038/s41467-024-45956-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Phylogenetic analyses over the last two decades have united a few small, and previously orphan clades, the nematodermatids, acoels and xenoturbelids, into the phylum Xenacoelomorpha. Some phylogenetic analyses support a sister relationship between Xenacoelomorpha and Ambulacraria (Xenambulacraria), while others suggest that Xenacoelomorpha may be sister to the rest of the Bilateria (Nephrozoa). An understanding of the cell type complements of Xenacoelomorphs is essential to assessing these alternatives as well as to our broader understanding of bilaterian cell type evolution. Employing whole organism single-cell RNA-seq in the marine xenacoelomorph worm Xenoturbella bocki, we show that Xenambulacrarian nerve nets share regulatory features and a peptidergic identity with those found in cnidarians and protostomes and more broadly share muscle and gland cell similarities with other metazoans. Taken together, these data are consistent with broad homologies of animal gland, muscle, and neurons as well as more specific affinities between Xenoturbella and acoel gut and epidermal tissues, consistent with the monophyly of Xenacoelomorpha.
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Affiliation(s)
- Helen E Robertson
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Anne-C Zakrzewski
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marie-Pierre Mailhe
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Philipp Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Institute of Zoology, Section Developmental Biology, University of Cologne, Köln, Wormlab, Germany
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA.
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.
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2
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Loe-Mie Y, Plançon C, Dubertret C, Yoshikawa T, Yalcin B, Collins SC, Boland A, Deleuze JF, Gorwood P, Benmessaoud D, Simonneau M, Lepagnol-Bestel AM. De Novo Variants Found in Three Distinct Schizophrenia Populations Hit a Common Core Gene Network Related to Microtubule and Actin Cytoskeleton Gene Ontology Classes. Life (Basel) 2024; 14:244. [PMID: 38398753 PMCID: PMC10890674 DOI: 10.3390/life14020244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Schizophrenia (SZ) is a heterogeneous and debilitating psychiatric disorder with a strong genetic component. To elucidate functional networks perturbed in schizophrenia, we analysed a large dataset of whole-genome studies that identified SNVs, CNVs, and a multi-stage schizophrenia genome-wide association study. Our analysis identified three subclusters that are interrelated and with small overlaps: GO:0007017~Microtubule-Based Process, GO:00015629~Actin Cytoskeleton, and GO:0007268~SynapticTransmission. We next analysed three distinct trio cohorts of 75 SZ Algerian, 45 SZ French, and 61 SZ Japanese patients. We performed Illumina HiSeq whole-exome sequencing and identified de novo mutations using a Bayesian approach. We validated 88 de novo mutations by Sanger sequencing: 35 in French, 21 in Algerian, and 32 in Japanese SZ patients. These 88 de novo mutations exhibited an enrichment in genes encoding proteins related to GO:0051015~actin filament binding (p = 0.0011) using David, and enrichments in GO: 0003774~transport (p = 0.019) and GO:0003729~mRNA binding (p = 0.010) using Amigo. One of these de novo variant was found in CORO1C coding sequence. We studied Coro1c haploinsufficiency in a Coro1c+/- mouse and found defects in the corpus callosum. These results could motivate future studies of the mechanisms surrounding genes encoding proteins involved in transport and the cytoskeleton, with the goal of developing therapeutic intervention strategies for a subset of SZ cases.
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Affiliation(s)
- Yann Loe-Mie
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, 75014 Paris, France; (Y.L.-M.); (C.D.); (P.G.); (A.-M.L.-B.)
| | - Christine Plançon
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France; (C.P.); (A.B.); (J.-F.D.)
| | - Caroline Dubertret
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, 75014 Paris, France; (Y.L.-M.); (C.D.); (P.G.); (A.-M.L.-B.)
- AP-HP, Department of Psychiatry, Louis Mourier Hospital, 92700 Colombes, France
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Saitama 351-0106, Japan;
| | - Binnaz Yalcin
- Université de Bourgogne, INSERM Research Center U1231, 21000 Dijon, France; (B.Y.); (S.C.C.)
| | - Stephan C. Collins
- Université de Bourgogne, INSERM Research Center U1231, 21000 Dijon, France; (B.Y.); (S.C.C.)
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France; (C.P.); (A.B.); (J.-F.D.)
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France; (C.P.); (A.B.); (J.-F.D.)
| | - Philip Gorwood
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, 75014 Paris, France; (Y.L.-M.); (C.D.); (P.G.); (A.-M.L.-B.)
- GHU-Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, 75014 Paris, France
| | - Dalila Benmessaoud
- Etablissement Hospitalo-Universitaire Spécialisé Psychiatrie Frantz FANON, Université Saad DAHLAB, Blida 09000, Algeria;
| | - Michel Simonneau
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, 75014 Paris, France; (Y.L.-M.); (C.D.); (P.G.); (A.-M.L.-B.)
- Laboratoire LuMin, FRE 2036, Universite Paris-Saclay, CNRS, ENS Paris Saclay 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France
- Department of Biology, Ecole Normale Supérieure de Paris-Saclay, Université Paris-Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - Aude-Marie Lepagnol-Bestel
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, 75014 Paris, France; (Y.L.-M.); (C.D.); (P.G.); (A.-M.L.-B.)
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France; (C.P.); (A.B.); (J.-F.D.)
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3
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Boulch M, Cazaux M, Cuffel A, Ruggiu M, Allain V, Corre B, Loe-Mie Y, Hosten B, Cisternino S, Auvity S, Thieblemont C, Caillat-Zucman S, Bousso P. A major role for CD4 + T cells in driving cytokine release syndrome during CAR T cell therapy. Cell Rep Med 2023; 4:101161. [PMID: 37595589 PMCID: PMC10518592 DOI: 10.1016/j.xcrm.2023.101161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/21/2023] [Accepted: 07/26/2023] [Indexed: 08/20/2023]
Abstract
Anti-CD19 chimeric antigen receptor (CAR) T cell therapy represents a breakthrough for the treatment of B cell malignancies. Yet, it can lead to severe adverse events, including cytokine release syndrome (CRS), which may require urgent clinical management. Whether interpatient variability in CAR T cell subsets contributes to CRS is unclear. Here, we show that CD4+ CAR T cells are the main drivers of CRS. Using an immunocompetent model of anti-CD19 CAR T cell therapy, we report that CD4+, but not CD8+, CAR T cells elicit physiological CRS-like manifestations associated with the release of inflammatory cytokines. In CAR T cell-treated patients, CRS occurrence and severity are significantly associated with high absolute values of CD4+ CAR T cells in the blood. CRS in mice occurs independently of CAR T cell-derived interferon γ (IFN-γ) but requires elevated tumor burden. Thus, adjusting the CD4:CD8 CAR T cell ratio to patient tumor load may help mitigate CAR T cell-associated toxicities.
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Affiliation(s)
- Morgane Boulch
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Équipe Labellisée Ligue Contre le Cancer, 75015 Paris, France
| | - Marine Cazaux
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Équipe Labellisée Ligue Contre le Cancer, 75015 Paris, France
| | - Alexis Cuffel
- Université Paris Cité, Hôpital Saint-Louis, AP-HP Nord, Laboratoire d'Immunologie, Paris, France; INSERM UMR976, Institut de Recherche St-Louis, Paris, France
| | - Mathilde Ruggiu
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Équipe Labellisée Ligue Contre le Cancer, 75015 Paris, France
| | - Vincent Allain
- Université Paris Cité, Hôpital Saint-Louis, AP-HP Nord, Laboratoire d'Immunologie, Paris, France; INSERM UMR976, Institut de Recherche St-Louis, Paris, France
| | - Béatrice Corre
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Équipe Labellisée Ligue Contre le Cancer, 75015 Paris, France
| | - Yann Loe-Mie
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, 75015 Paris, France
| | - Benoit Hosten
- Université Paris Cité, INSERM, UMRS-1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; Service de Pharmacie, Unité Claude Kellershohn - Radiopharmacie R&D, AP-HP, Hôpital Saint-Louis, 75475 Paris, France
| | - Salvatore Cisternino
- Université Paris Cité, INSERM, UMRS-1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; Service de Pharmacie, AP-HP, Hôpital Necker, 75015 Paris, France
| | - Sylvain Auvity
- Université Paris Cité, INSERM, UMRS-1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; Service de Pharmacie, AP-HP, Hôpital Necker, 75015 Paris, France
| | - Catherine Thieblemont
- Hémato-Oncologie, Hôpital Saint-Louis, AP-HP, Université Paris Cité, Inserm U1153, Paris, France
| | - Sophie Caillat-Zucman
- Université Paris Cité, Hôpital Saint-Louis, AP-HP Nord, Laboratoire d'Immunologie, Paris, France; INSERM UMR976, Institut de Recherche St-Louis, Paris, France
| | - Philippe Bousso
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Équipe Labellisée Ligue Contre le Cancer, 75015 Paris, France.
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4
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Cossec JC, Traboulsi T, Sart S, Loe-Mie Y, Guthmann M, Hendriks IA, Theurillat I, Nielsen ML, Torres-Padilla ME, Baroud CN, Dejean A. Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures. Cell Rep 2023; 42:112380. [PMID: 37061916 PMCID: PMC10157296 DOI: 10.1016/j.celrep.2023.112380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/08/2023] [Accepted: 03/26/2023] [Indexed: 04/17/2023] Open
Abstract
Recent advances in synthetic embryology have opened new avenues for understanding the complex events controlling mammalian peri-implantation development. Here, we show that mouse embryonic stem cells (ESCs) solely exposed to chemical inhibition of SUMOylation generate embryo-like structures comprising anterior neural and trunk-associated regions. HypoSUMOylation-instructed ESCs give rise to spheroids that self-organize into gastrulating structures containing cell types spatially and functionally related to embryonic and extraembryonic compartments. Alternatively, spheroids cultured in a droplet microfluidic device form elongated structures that undergo axial organization reminiscent of natural embryo morphogenesis. Single-cell transcriptomics reveals various cellular lineages, including properly positioned anterior neuronal cell types and paraxial mesoderm segmented into somite-like structures. Transient SUMOylation suppression gradually increases DNA methylation genome wide and repressive mark deposition at Nanog. Interestingly, cell-to-cell variations in SUMOylation levels occur during early embryogenesis. Our approach provides a proof of principle for potentially powerful strategies to explore early embryogenesis by targeting chromatin roadblocks of cell fate change.
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Affiliation(s)
- Jack-Christophe Cossec
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France.
| | - Tatiana Traboulsi
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | - Sébastien Sart
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France; Physical Microfluidics and Bioengineering Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Yann Loe-Mie
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, 75015 Paris, France
| | - Manuel Guthmann
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ilan Theurillat
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany; Faculty of Biology, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Charles N Baroud
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France; Physical Microfluidics and Bioengineering Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France.
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5
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Bastide S, Chomsky E, Saudemont B, Loe-Mie Y, Schmutz S, Novault S, Marlow H, Tanay A, Spitz F. TATTOO-seq delineates spatial and cell type-specific regulatory programs in the developing limb. Sci Adv 2022; 8:eadd0695. [PMID: 36516250 PMCID: PMC9750149 DOI: 10.1126/sciadv.add0695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The coordinated differentiation of progenitor cells into specialized cell types and their spatial organization into distinct domains is central to embryogenesis. Here, we developed and applied an unbiased spatially resolved single-cell transcriptomics method to identify the genetic programs underlying the emergence of specialized cell types during mouse limb development and their spatial integration. We identify multiple transcription factors whose expression patterns are predominantly associated with cell type specification or spatial position, suggesting two parallel yet highly interconnected regulatory systems. We demonstrate that the embryonic limb undergoes a complex multiscale reorganization upon perturbation of one of its spatial organizing centers, including the loss of specific cell populations, alterations of preexisting cell states' molecular identities, and changes in their relative spatial distribution. Our study shows how multidimensional single-cell, spatially resolved molecular atlases can allow the deconvolution of spatial identity and cell fate and reveal the interconnected genetic networks that regulate organogenesis and its reorganization upon genetic alterations.
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Affiliation(s)
- Sébastien Bastide
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- École Doctorale “Complexité du Vivant”, Sorbonne Université, 75005 Paris, France
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Sandrine Schmutz
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Sophie Novault
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Heather Marlow
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
| | - François Spitz
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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6
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Viard J, Loe-Mie Y, Daudin R, Khelfaoui M, Plancon C, Boland A, Tejedor F, Huganir RL, Kim E, Kinoshita M, Liu G, Haucke V, Moncion T, Yu E, Hindie V, Bléhaut H, Mircher C, Herault Y, Deleuze JF, Rain JC, Simonneau M, Lepagnol-Bestel AM. Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease. Life Sci Alliance 2022; 5:e202101205. [PMID: 35914814 PMCID: PMC9348576 DOI: 10.26508/lsa.202101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
Down syndrome (DS) is caused by human chromosome 21 (HSA21) trisomy. It is characterized by a poorly understood intellectual disability (ID). We studied two mouse models of DS, one with an extra copy of the <i>Dyrk1A</i> gene (189N3) and the other with an extra copy of the mouse Chr16 syntenic region (Dp(16)1Yey). RNA-seq analysis of the transcripts deregulated in the embryonic hippocampus revealed an enrichment in genes associated with chromatin for the 189N3 model, and synapses for the Dp(16)1Yey model. A large-scale yeast two-hybrid screen (82 different screens, including 72 HSA21 baits and 10 rebounds) of a human brain library containing at least 10<sup>7</sup> independent fragments identified 1,949 novel protein-protein interactions. The direct interactors of HSA21 baits and rebounds were significantly enriched in ID-related genes (<i>P</i>-value < 2.29 × 10<sup>-8</sup>). Proximity ligation assays showed that some of the proteins encoded by HSA21 were located at the dendritic spine postsynaptic density, in a protein network at the dendritic spine postsynapse. We located HSA21 DYRK1A and DSCAM, mutations of which increase the risk of autism spectrum disorder (ASD) 20-fold, in this postsynaptic network. We found that an intracellular domain of DSCAM bound either DLGs, which are multimeric scaffolds comprising receptors, ion channels and associated signaling proteins, or DYRK1A. The DYRK1A-DSCAM interaction domain is conserved in <i>Drosophila</i> and humans. The postsynaptic network was found to be enriched in proteins associated with ARC-related synaptic plasticity, ASD, and late-onset Alzheimer's disease. These results highlight links between DS and brain diseases with a complex genetic basis.
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Affiliation(s)
- Julia Viard
- Centre Psychiatrie and Neurosciences, INSERM U894, Paris, France
- Laboratoire de Génomique Fonctionnelle, CNG, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Evry, France
| | - Yann Loe-Mie
- Centre Psychiatrie and Neurosciences, INSERM U894, Paris, France
| | - Rachel Daudin
- Centre Psychiatrie and Neurosciences, INSERM U894, Paris, France
| | - Malik Khelfaoui
- Centre Psychiatrie and Neurosciences, INSERM U894, Paris, France
| | - Christine Plancon
- Laboratoire de Génomique Fonctionnelle, CNG, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Evry, France
| | - Anne Boland
- Laboratoire de Génomique Fonctionnelle, CNG, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Evry, France
| | - Francisco Tejedor
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández (CSIC-UMH), Universidad Miguel Hernandez-Campus de San Juan, San Juan, Spain
| | - Richard L Huganir
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Makoto Kinoshita
- Department of Molecular Biology, Division of Biological Science, Nagoya University Graduate School of Science, Nagoya, Japan
| | - Guofa Liu
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA
| | - Volker Haucke
- Department of Molecular Pharmacology and Cell Biology, Leibniz Institut für Molekulare Pharmakologie (FMP) and Freie Universität Berlin, Berlin, Germany
| | | | - Eugene Yu
- Department of Cellular and Molecular Biology, Roswell Park Division of Graduate School, State University of New York at Buffalo, Buffalo, NY, USA
| | | | | | | | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, Illkirch, France
- INSERM, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- PHENOMIN, Institut Clinique de la Souris, ICS, GIE CERBM, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Jean-François Deleuze
- Laboratoire de Génomique Fonctionnelle, CNG, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Evry, France
| | | | - Michel Simonneau
- Centre Psychiatrie and Neurosciences, INSERM U894, Paris, France
- Université Paris-Saclay, CNRS, ENS Paris-Saclay, CentraleSupélec, LuMIn, Gif sur Yvette, France
- Department of Biology, Ecole Normale Supérieure Paris-Saclay Université Paris-Saclay, Gif sur Yvette, France
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7
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Lepagnol-Bestel AM, Zvara A, Maussion G, Quignon F, Ngimbous B, Ramoz N, Imbeaud S, Loe-Mie Y, Benihoud K, Agier N, Salin PA, Cardona A, Khung-Savatovsky S, Kallunki P, Delabar JM, Puskas LG, Delacroix H, Aggerbeck L, Delezoide AL, Delattre O, Gorwood P, Moalic JM, Simonneau M. Corrigendum to: DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to deregulate gene clusters involved in the neuronal phenotypic traits of Down syndrome. Hum Mol Genet 2021; 31:2106-2107. [PMID: 34918050 DOI: 10.1093/hmg/ddab346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Agnes Zvara
- Laboratory for Functional Genomics, Biological Research Center, HAS, Szeged, Hungary
| | - Gilles Maussion
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | | | - Bedel Ngimbous
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Nicolas Ramoz
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Sandrine Imbeaud
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | - Yann Loe-Mie
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Karim Benihoud
- CNRS UMR 8121 Vectorologie et Transfert de Génes, Institut Gustave Roussy, 39, rue Camille Desmoulins, 94805 Villejuif Cedex, France; Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Nicolas Agier
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | | | | | - Suonavy Khung-Savatovsky
- Service de Biologie du Développement/Foetopathologie, Hôpital Robert Debré , AP-HP, Université Paris Diderot-Paris 7, Paris, France
| | | | | | - Laszlo G Puskas
- Laboratory for Functional Genomics, Biological Research Center, HAS, Szeged, Hungary
| | - Hervé Delacroix
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | - Lawrence Aggerbeck
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | - Anne-Lise Delezoide
- Service de Biologie du Développement/Foetopathologie, Hôpital Robert Debré , AP-HP, Université Paris Diderot-Paris 7, Paris, France
| | | | - Philip Gorwood
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Jean-Marie Moalic
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Michel Simonneau
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
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8
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Boulch M, Cazaux M, Loe-Mie Y, Thibaut R, Corre B, Lemaître F, Grandjean CL, Garcia Z, Bousso P. A cross-talk between CAR T cell subsets and the tumor microenvironment is essential for sustained cytotoxic activity. Sci Immunol 2021; 6:6/57/eabd4344. [PMID: 33771887 DOI: 10.1126/sciimmunol.abd4344] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 12/29/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy relies on the activity of a large pool of tumor-targeting cytotoxic effectors. Whether CAR T cells act autonomously or require interactions with the tumor microenvironment (TME) remains incompletely understood. Here, we report an essential cross-talk between CAR T cell subsets and the TME for tumor control in an immunocompetent mouse B cell lymphoma model of anti-CD19 CAR T cell therapy. Using single-cell RNA sequencing, we revealed substantial modification of the TME during CAR T cell therapy. Interferon-γ (IFN-γ) produced by CAR T cells not only enhanced endogenous T and natural killer cell activity but was also essential for sustaining CAR T cell cytotoxicity, as revealed by intravital imaging. CAR T cell-derived IFN-γ facilitated host interleukin-12 production that supported host immune and CAR T cell responses. Compared with CD8+ CAR T cells, CD4+ CAR T cells were more efficient at host immune activation but less capable of direct tumor killing. In summary, CAR T cells do not act independently in vivo but rely instead on cytokine-mediated cross-talk with the TME for optimal activity. Invigorating CAR T cell interplay with the host represents an attractive strategy to prevent relapses after therapy.
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Affiliation(s)
- Morgane Boulch
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Marine Cazaux
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France. .,University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Yann Loe-Mie
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Ronan Thibaut
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Béatrice Corre
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France
| | - Fabrice Lemaître
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France
| | - Capucine L Grandjean
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France
| | - Zacarias Garcia
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France
| | - Philippe Bousso
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, INSERM U1223, 75015 Paris, France.
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9
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Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, Vilo J, Simonneau M, Peterson H. HENA, heterogeneous network-based data set for Alzheimer's disease. Sci Data 2019; 6:151. [PMID: 31413325 PMCID: PMC6694132 DOI: 10.1038/s41597-019-0152-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease and other types of dementia are the top cause for disabilities in later life and various types of experiments have been performed to understand the underlying mechanisms of the disease with the aim of coming up with potential drug targets. These experiments have been carried out by scientists working in different domains such as proteomics, molecular biology, clinical diagnostics and genomics. The results of such experiments are stored in the databases designed for collecting data of similar types. However, in order to get a systematic view of the disease from these independent but complementary data sets, it is necessary to combine them. In this study we describe a heterogeneous network-based data set for Alzheimer's disease (HENA). Additionally, we demonstrate the application of state-of-the-art graph convolutional networks, i.e. deep learning methods for the analysis of such large heterogeneous biological data sets. We expect HENA to allow scientists to explore and analyze their own results in the broader context of Alzheimer's disease research.
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Affiliation(s)
- Elena Sügis
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
| | - Jerome Dauvillier
- Swiss Institute of Bioinformatics, Vital-IT group, Unil Quartier Sorge, Genopode building, CH-1015, Lausanne, Switzerland
| | - Anna Leontjeva
- CSIRO Data 61, 5/13 Garden St, Eveleigh, NSW, 2015, Australia
| | - Priit Adler
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
| | - Valerie Hindie
- Hybrigenics SA, 3-5 Impasse Reille, 75014, Paris, France
| | - Thomas Moncion
- Hybrigenics SA, 3-5 Impasse Reille, 75014, Paris, France
| | | | - Rachel Daudin
- Institut national de la santé et de la recherche médicale, INSERM U894 2 ter rue d'Alésia, 75014, Paris, France
- Laboratoire Aimé Cotton, Centre National Recherche Scientifique, Université Paris-Sud, Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, 91405, Orsay, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Institut Pasteur, CNRS UMR3738, Paris, 75015, France
| | - Yann Herault
- Centre Européen de Recherche en Biologie et Médecine, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Jean-Charles Lambert
- Institut Pasteur de Lille, UMR 744 1 rue du Pr. Calmette BP 245, 59019, Lille cedex, France
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, United Kingdom
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | | | - Ioannis Xenarios
- Center for Integrative Genomics University of Lausanne, Genopode, 1015, Lausanne, Switzerland
- Genome Center Health 2030, Analytical Platform Department, Chemin des Mines 9, 1202, Genève, Switzerland
- DFR CHUV, Rue du Bugnon 21, 1011, Lausanne, Switzerland
- Agora Center, LICR/Department of Oncology, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
| | - Jaak Vilo
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
| | - Michel Simonneau
- Institut national de la santé et de la recherche médicale, INSERM U894 2 ter rue d'Alésia, 75014, Paris, France.
- Laboratoire Aimé Cotton, Centre National Recherche Scientifique, Université Paris-Sud, Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, 91405, Orsay, France.
| | - Hedi Peterson
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia.
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia.
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10
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Sebé-Pedrós A, Saudemont B, Chomsky E, Plessier F, Mailhé MP, Renno J, Loe-Mie Y, Lifshitz A, Mukamel Z, Schmutz S, Novault S, Steinmetz PRH, Spitz F, Tanay A, Marlow H. Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. Cell 2018; 173:1520-1534.e20. [PMID: 29856957 DOI: 10.1016/j.cell.2018.05.019] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/22/2018] [Accepted: 05/09/2018] [Indexed: 01/19/2023]
Abstract
The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.
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Affiliation(s)
- Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Flora Plessier
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France; Département de Biologie, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Marie-Pierre Mailhé
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Justine Renno
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zohar Mukamel
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sandrine Schmutz
- Cytometry & Biomarkers UtechS, Cytometry Platform, Institut Pasteur, 75015 Paris, France
| | - Sophie Novault
- Cytometry & Biomarkers UtechS, Cytometry Platform, Institut Pasteur, 75015 Paris, France
| | - Patrick R H Steinmetz
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen 5006, Norway
| | - François Spitz
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Heather Marlow
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; CNRS, UMR3738, 25 Rue du Dr Roux, 75015 Paris, France.
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11
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Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature 2017; 551:51-56. [PMID: 29094699 PMCID: PMC5687303 DOI: 10.1038/nature24281] [Citation(s) in RCA: 670] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
Abstract
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.
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Affiliation(s)
- Wibke Schwarzer
- Developmental Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
| | - Nezar Abdennur
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Aleksandra Pekowska
- Genome Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Yann Loe-Mie
- Institut Pasteur, (Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department. Institut Pasteur. 75015 Paris, France
- CNRS, UMR3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Nuno A Fonseca
- European Bioinformatics Institute. European Molecular Biology Laboratory. Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wolfgang Huber
- Genome Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Leonid Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Francois Spitz
- Developmental Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
- Genome Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
- Institut Pasteur, (Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department. Institut Pasteur. 75015 Paris, France
- CNRS, UMR3738, 25 rue du Dr Roux, 75015 Paris, France
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12
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Haziza S, Mohan N, Loe-Mie Y, Lepagnol-Bestel AM, Massou S, Adam MP, Le XL, Viard J, Plancon C, Daudin R, Koebel P, Dorard E, Rose C, Hsieh FJ, Wu CC, Potier B, Herault Y, Sala C, Corvin A, Allinquant B, Chang HC, Treussart F, Simonneau M. Fluorescent nanodiamond tracking reveals intraneuronal transport abnormalities induced by brain-disease-related genetic risk factors. Nat Nanotechnol 2017; 12:322-328. [PMID: 27893730 DOI: 10.1038/nnano.2016.260] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 10/24/2016] [Indexed: 05/24/2023]
Abstract
Brain diseases such as autism and Alzheimer's disease (each inflicting >1% of the world population) involve a large network of genes displaying subtle changes in their expression. Abnormalities in intraneuronal transport have been linked to genetic risk factors found in patients, suggesting the relevance of measuring this key biological process. However, current techniques are not sensitive enough to detect minor abnormalities. Here we report a sensitive method to measure the changes in intraneuronal transport induced by brain-disease-related genetic risk factors using fluorescent nanodiamonds (FNDs). We show that the high brightness, photostability and absence of cytotoxicity allow FNDs to be tracked inside the branches of dissociated neurons with a spatial resolution of 12 nm and a temporal resolution of 50 ms. As proof of principle, we applied the FND tracking assay on two transgenic mouse lines that mimic the slight changes in protein concentration (∼30%) found in the brains of patients. In both cases, we show that the FND assay is sufficiently sensitive to detect these changes.
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Affiliation(s)
- Simon Haziza
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Nitin Mohan
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
| | - Yann Loe-Mie
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | | | - Sophie Massou
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
| | - Marie-Pierre Adam
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
| | - Xuan Loc Le
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
| | - Julia Viard
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Christine Plancon
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Centre National de Génotypage, 91057 Evry, France
| | - Rachel Daudin
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Pascale Koebel
- Institut de génétique et de biologie moléculaire et cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67400 Illkirch-Graffenstaden, France
| | - Emilie Dorard
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Christiane Rose
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Feng-Jen Hsieh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Chih-Che Wu
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou Hsien 545, Taiwan
| | - Brigitte Potier
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Yann Herault
- Institut de génétique et de biologie moléculaire et cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67400 Illkirch-Graffenstaden, France
| | - Carlo Sala
- Neuroscience Institute, CNR, 20129 Milano, Italy
| | - Aiden Corvin
- Department of Psychiatry, Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Bernadette Allinquant
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
| | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - François Treussart
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
| | - Michel Simonneau
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France
- Centre de Psychiatrie et Neurosciences, INSERM U894, Université Paris-Descartes, 75014 Paris, France
- Department of Biology, ENS Cachan, Université Paris-Saclay, 94235 Cachan, France
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13
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Viollet C, Simon A, Tolle V, Labarthe A, Grouselle D, Loe-Mie Y, Simonneau M, Martel G, Epelbaum J. Somatostatin-IRES-Cre Mice: Between Knockout and Wild-Type? Front Endocrinol (Lausanne) 2017; 8:131. [PMID: 28674519 PMCID: PMC5474965 DOI: 10.3389/fendo.2017.00131] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/29/2017] [Indexed: 01/24/2023] Open
Abstract
The neuropeptide somatostatin (SOM) is widely expressed in rodent brain and somatostatin-IRES-Cre (SOM-cre) mouse strains are increasingly used to unravel the physiology of SOM-containing neurons. However, while knock-in targeting strategy greatly improves Cre-Lox system accuracy, recent reports have shown that genomic insertion of Cre construct per se can markedly affect physiological function. We show that Cre transgene insertion into the 3'UTR of the somatostatin gene leads to the selective and massive depletion of endogenous SOM in all tested brain regions. It also strongly impacts SOM-related neuroendocrine responses in a similar manner to what has been reported for SST KO mice: increased corticosterone levels after 30-min restraint stress, decreased amplitude and regularity of ultradian growth hormone secretory patterns accompanied by changes in sexually dimorphic liver gene expression (serpina1, Cyp2b9, Cyp2a4, Cyp2d9, and Cyp7b1). In addition to demonstrating the need for examination of the consequences of Cre transgenesis, these results also reveal how this SOM-cre strain may be a useful tool in studying the functional consequences of moderate to low SOM levels as reported in neurological and psychiatric disorders.
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Affiliation(s)
- Cécile Viollet
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
- *Correspondence: Cécile Viollet, ; Jacques Epelbaum,
| | - Axelle Simon
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Virginie Tolle
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Alexandra Labarthe
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Dominique Grouselle
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Yann Loe-Mie
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Michel Simonneau
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
- Laboratoire Aimé Cotton, CNRS, Université Paris-Sud, ENS Paris-Saclay, Université Paris-Saclay, Orsay, France
| | - Guillaume Martel
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Jacques Epelbaum
- INSERM U894, Centre de Psychiatrie et Neurosciences, Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
- MECADEV UMR 7179 CNRS, Muséum National d’Histoire Naturelle, Brunoy, France
- *Correspondence: Cécile Viollet, ; Jacques Epelbaum,
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Loe-Mie Y, Lepagnol-Bestel AM, Maussion G, Doron-Faigenboim A, Imbeaud S, Delacroix H, Aggerbeck L, Pupko T, Gorwood P, Simonneau M, Moalic JM. SMARCA2 and other genome-wide supported schizophrenia-associated genes: regulation by REST/NRSF, network organization and primate-specific evolution. Hum Mol Genet 2010; 19:2841-57. [PMID: 20457675 DOI: 10.1093/hmg/ddq184] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The SMARCA2 gene, which encodes BRM in the SWI/SNF chromatin-remodeling complex, was recently identified as being associated with schizophrenia (SZ) in a genome-wide approach. Polymorphisms in SMARCA2, associated with the disease, produce changes in the expression of the gene and/or in the encoded amino acid sequence. We show here that an SWI/SNF-centered network including the Smarca2 gene is modified by the down-regulation of REST/NRSF in a mouse neuronal cell line. REST/NRSF down-regulation also modifies the levels of Smarce1, Smarcd3 and SWI/SNF interactors (Hdac1, RcoR1 and Mecp2). Smarca2 down-regulation generates an abnormal dendritic spine morphology that is an intermediate phenotype of SZ. We further found that 8 (CSF2RA, HIST1H2BJ, NOTCH4, NRGN, SHOX, SMARCA2, TCF4 and ZNF804A) out of 10 genome-wide supported SZ-associated genes are part of an interacting network (including SMARCA2), 5 members of which encode transcription regulators. The expression of 3 (TCF4, SMARCA2 and CSF2RA) of the 10 genome-wide supported SZ-associated genes is modified when the REST/NRSF-SWI/SNF chromatin-remodeling complex is experimentally manipulated in mouse cell lines and in transgenic mouse models. The REST/NRSF-SWI/SNF deregulation also results in the differential expression of genes that are clustered in chromosomes suggesting the induction of genome-wide epigenetic changes. Finally, we found that SMARCA2 interactors and the genome-wide supported SZ-associated genes are considerably enriched in genes displaying positive selection in primates and in the human lineage which suggests the occurrence of novel protein interactions in primates. Altogether, these data identify the SWI/SNF chromatin-remodeling complex as a key component of the genetic architecture of SZ.
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Affiliation(s)
- Yann Loe-Mie
- INSERM U675/U894, Centre Psychiatrie & Neurosciences, Université Paris-Descartes, 75014 Paris, France
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Moalic J, Le Strat Y, Lepagnol-Bestel A, Ramoz N, Loe-Mie Y, Maussion G, Gorwood P, Simonneau M. Primate-Accelerated Evolutionary Genes: Novel Routes to Drug Discovery in Psychiatric Disorders. Curr Med Chem 2010; 17:1300-16. [DOI: 10.2174/092986710790936338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 02/10/2010] [Indexed: 11/22/2022]
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Lepagnol-Bestel AM, Zvara A, Maussion G, Quignon F, Ngimbous B, Ramoz N, Imbeaud S, Loe-Mie Y, Benihoud K, Agier N, Salin PA, Cardona A, Khung-Savatovsky S, Kallunki P, Delabar JM, Puskas LG, Delacroix H, Aggerbeck L, Delezoide AL, Delattre O, Gorwood P, Moalic JM, Simonneau M. DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to deregulate gene clusters involved in the neuronal phenotypic traits of Down syndrome. Hum Mol Genet 2009; 18:1405-14. [PMID: 19218269 DOI: 10.1093/hmg/ddp047] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The molecular mechanisms that lead to the cognitive defects characteristic of Down syndrome (DS), the most frequent cause of mental retardation, have remained elusive. Here we use a transgenic DS mouse model (152F7 line) to show that DYRK1A gene dosage imbalance deregulates chromosomal clusters of genes located near neuron-restrictive silencer factor (REST/NRSF) binding sites. We found that Dyrk1a binds the SWI/SNF complex known to interact with REST/NRSF. The mutation of a REST/NRSF binding site in the promoter of the REST/NRSF target gene L1cam modifies the transcriptional effect of Dyrk1a-dosage imbalance on L1cam. Dyrk1a dosage imbalance perturbs Rest/Nrsf levels with decreased Rest/Nrsf expression in embryonic neurons and increased expression in adult neurons. Using transcriptome analysis of embryonic brain subregions of transgenic 152F7 mouse line, we identified a coordinated deregulation of multiple genes that are responsible for dendritic growth impairment present in DS. Similarly, Dyrk1a overexpression in primary mouse cortical neurons induced severe reduction of the dendritic growth and dendritic complexity. We propose that DYRK1A overexpression-related neuronal gene deregulation via disturbance of REST/NRSF levels, and the REST/NRSF-SWI/SNF chromatin remodelling complex, significantly contributes to the neural phenotypic changes that characterize DS.
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Maussion G, Carayol J, Lepagnol-Bestel AM, Tores F, Loe-Mie Y, Milbreta U, Rousseau F, Fontaine K, Renaud J, Moalic JM, Philippi A, Chedotal A, Gorwood P, Ramoz N, Hager J, Simonneau M. Convergent evidence identifying MAP/microtubule affinity-regulating kinase 1 (MARK1) as a susceptibility gene for autism. Hum Mol Genet 2008; 17:2541-51. [PMID: 18492799 DOI: 10.1093/hmg/ddn154] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autism spectrum disorders (ASDs) are common, heritable, but genetically heterogeneous neurodevelopmental conditions. We recently defined a susceptibility locus for ASDs on chromosome 1q41-q42. High-resolution single-nucleotide polymorphisms (126 SNPs) genotyping across the chromosome 1q41-q42 region, followed by a MARK1 (microtubule affinity-regulating kinase 1)-tagged-SNP association study in 276 families with autism from the Autism Genetic Research Exchange, showed that several SNPs within the MARK1 gene were significantly associated with ASDs by transmission disequilibrium tests. Haplotype rs12740310*C-rs3737296*G-rs12410279*A was overtransmitted (P(corrected)= 0.0016), with a relative risk for autism of 1.8 in homozygous carriers. Furthermore, ASD-associated SNP rs12410279 modulates the level of transcription of MARK1. We found that MARK1 was overexpressed in the prefrontal cortex (BA46) but not in cerebellar granule cells, on postmortem brain tissues from patients. MARK1 displayed an accelerated evolution along the lineage leading to humans, suggesting possible involvement of this gene in cognition. MARK1 encodes a kinase-regulating microtubule-dependent transport in axons and dendrites. Both overexpression and silencing of MARK1 resulted in significantly shorter dendrite length in mouse neocortical neurons and modified dendritic transport speed. As expected for a gene encoding a key polarity determinant Par-1 protein kinase, MARK1 is involved in axon-dendrite specification. Thus, MARK1 overexpression in humans may be responsible for subtle changes in dendritic functioning.
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Affiliation(s)
- Gilles Maussion
- INSERM U675, IFR2, Faculté de Médecine Xavier Bichat, Université Denis Diderot-Paris 7, Paris, France
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