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Kukanja P, Langseth CM, Rubio Rodríguez-Kirby LA, Agirre E, Zheng C, Raman A, Yokota C, Avenel C, Tiklová K, Guerreiro-Cacais AO, Olsson T, Hilscher MM, Nilsson M, Castelo-Branco G. Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology. Cell 2024; 187:1990-2009.e19. [PMID: 38513664 DOI: 10.1016/j.cell.2024.02.030] [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: 06/18/2023] [Revised: 12/13/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
Multiple sclerosis (MS) is a neurological disease characterized by multifocal lesions and smoldering pathology. Although single-cell analyses provided insights into cytopathology, evolving cellular processes underlying MS remain poorly understood. We investigated the cellular dynamics of MS by modeling temporal and regional rates of disease progression in mouse experimental autoimmune encephalomyelitis (EAE). By performing single-cell spatial expression profiling using in situ sequencing (ISS), we annotated disease neighborhoods and found centrifugal evolution of active lesions. We demonstrated that disease-associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course. Single-cell spatial mapping of human archival MS spinal cords confirmed the differential distribution of homeostatic and DA-glia, enabled deconvolution of active and inactive lesions into sub-compartments, and identified new lesion areas. By establishing a spatial resource of mouse and human MS neuropathology at a single-cell resolution, our study unveils the intricate cellular dynamics underlying MS.
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Affiliation(s)
- Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177 Stockholm, Sweden.
| | - Christoffer M Langseth
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, 17154 Stockholm, Sweden.
| | - Leslie A Rubio Rodríguez-Kirby
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Chao Zheng
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Amitha Raman
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, 17154 Stockholm, Sweden
| | - Chika Yokota
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, 17154 Stockholm, Sweden
| | - Christophe Avenel
- Department of Information Technology, Uppsala University, 752 37 Uppsala, Sweden; BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, 751 05 Uppsala, Sweden
| | - Katarina Tiklová
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, 17154 Stockholm, Sweden
| | - André O Guerreiro-Cacais
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, 171 76 Solna, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, 171 76 Solna, Sweden
| | - Markus M Hilscher
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, 17154 Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, 17154 Stockholm, Sweden.
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177 Stockholm, Sweden.
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2
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Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature 2023; 616:113-122. [PMID: 36922587 PMCID: PMC10076218 DOI: 10.1038/s41586-023-05795-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [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: 06/06/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context1-5. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly concordant tissue features were identified by either spatial epigenome or spatial transcriptome we also observed distinct patterns, suggesting their differential roles in defining cell states. Linking epigenome to transcriptome pixel by pixel allows the uncovering of new insights in spatial epigenetic priming, differentiation and gene regulation within the tissue architecture. These technologies are of great interest in life science and biomedical research.
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Affiliation(s)
- Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology and Laboratory Medicine, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mingze Dong
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Radiology, Columbia University, New York, NY, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - Liya Wang
- AtlasXomics, Inc., New Haven, CT, USA
| | | | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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3
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Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D, Johnson MR, Corces MR, Montine TJ, Chen X, Chang HY, Malhotra D, Castelo-Branco G. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron 2022; 110:1193-1210.e13. [PMID: 35093191 PMCID: PMC9810341 DOI: 10.1016/j.neuron.2021.12.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 01/14/2021] [Revised: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 01/05/2023]
Abstract
Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and myelin by immune cells, which are thought to be the main drivers of MS susceptibility. We found that immune genes exhibit a primed chromatin state in single mouse and human OLG in a non-disease context, compatible with transitions to immune-competent states in MS. We identified BACH1 and STAT1 as transcription factors involved in immune gene regulation in oligodendrocyte precursor cells (OPCs). A subset of immune genes presents bivalency of H3K4me3/H3K27me3 in OPCs, with Polycomb inhibition leading to their increased activation upon interferon gamma (IFN-γ) treatment. Some MS susceptibility single-nucleotide polymorphisms (SNPs) overlap with these regulatory regions in mouse and human OLG. Treatment of mouse OPCs with IFN-γ leads to chromatin architecture remodeling at these loci and altered expression of interacting genes. Thus, the susceptibility for MS may involve OLG, which therefore constitutes novel targets for immunological-based therapies for MS.
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Affiliation(s)
- Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mukund Kabbe
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Cassandra A van Tuijn
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Abeer Heskol
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Chao Zheng
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's Associate Laboratory, PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Leslie Kirby
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniela Calini
- Roche Pharma Research and Early Development, 4070 Basel, Switzerland
| | - Michael R Johnson
- Faculty of Medicine, Department of Brain Sciences, Imperial College of London, SW7 2AZ London, UK
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Immunology, Genetics, and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5101, USA
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, 4070 Basel, Switzerland
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, 171 77 Stockholm, Sweden.
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4
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Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, Samudyata, Luginbühl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, de Hoon M, Arner E, Lenhard B, Plessy C, Castelo-Branco G, Orlando V, Carninci P. Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Nat Commun 2021; 12:3128. [PMID: 34011993 PMCID: PMC8134558 DOI: 10.1038/s41467-021-23542-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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5
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Agirre E, Oldfield AJ, Bellora N, Segelle A, Luco RF. Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. Nat Commun 2021; 12:682. [PMID: 33514745 PMCID: PMC7846797 DOI: 10.1038/s41467-021-20979-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary. Chromatin is known to regulate splicing by modulating recruitment of splicing factors. Using machine learning approaches, the authors have underlined a chromatin code for alternative splicing regulation that is conserved amongst cell lines.
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Affiliation(s)
- E Agirre
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France.,Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - A J Oldfield
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France
| | - N Bellora
- Institute of Nuclear Technologies for Health (INTECNUS), National Scientific and Technical Research Council (CONICET), Bariloche, 8400, Argentina
| | - A Segelle
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France
| | - R F Luco
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France.
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6
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Tripathi A, Volsko C, Garcia JP, Agirre E, Allan KC, Tesar PJ, Trapp BD, Castelo-Branco G, Sim FJ, Dutta R. Oligodendrocyte Intrinsic miR-27a Controls Myelination and Remyelination. Cell Rep 2020; 29:904-919.e9. [PMID: 31644912 DOI: 10.1016/j.celrep.2019.09.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 06/12/2019] [Revised: 08/13/2019] [Accepted: 09/06/2019] [Indexed: 12/29/2022] Open
Abstract
Remyelination requires the generation of new oligodendrocytes (OLs), which are derived from oligodendrocyte progenitor cells (OPCs). Maturation of OPCs into OLs is a multi-step process. Here, we describe a microRNA expressed by OLs, miR-27a, as a regulator of OL development and survival. Increased levels of miR-27a were found in OPCs associated with multiple sclerosis (MS) lesions and in animal models of demyelination. Increased levels of miR-27a led to inhibition of OPC proliferation by cell-cycle arrest, as well as impaired differentiation of human OPCs (hOPCs) and myelination by dysregulating the Wnt-β-catenin signaling pathway. In vivo administration of miR-27a led to suppression of myelinogenic signals, leading to loss of endogenous myelination and remyelination. Our findings provide evidence supporting a critical role for a steady-state level of OL-specific miR-27a in supporting multiple steps in the complex process of OPC maturation and remyelination.
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Affiliation(s)
- Ajai Tripathi
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, USA
| | - Christina Volsko
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, USA
| | - Jessie P Garcia
- Jacob's School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Bruce D Trapp
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, USA
| | - Goncalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fraser J Sim
- Jacob's School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
| | - Ranjan Dutta
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, USA; Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA.
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7
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Gómez Acuña LI, Nazer E, Rodríguez-Seguí SA, Pozzi B, Buggiano V, Marasco LE, Agirre E, He C, Alló M, Kornblihtt AR. Nuclear role for human Argonaute-1 as an estrogen-dependent transcription coactivator. J Cell Biol 2020; 219:e201908097. [PMID: 32673398 PMCID: PMC7480116 DOI: 10.1083/jcb.201908097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 08/12/2019] [Revised: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
In mammals, argonaute (AGO) proteins have been characterized for their roles in small RNA-mediated posttranscriptional and also in transcriptional gene silencing. Here, we report a different role for AGO1 in estradiol-triggered transcriptional activation in human cells. We show that in MCF-7 mammary gland cells, AGO1 associates with transcriptional enhancers of estrogen receptor α (ERα) and that this association is up-regulated by treating the cells with estrogen (E2), displaying a positive correlation with the activation of these enhancers. Moreover, we show that AGO1 interacts with ERα and that this interaction is also increased by E2 treatment, but occurs in the absence of RNA. We show that AGO1 acts positively as a coactivator in estradiol-triggered transcription regulation by promoting ERα binding to its enhancers. Consistently, AGO1 depletion decreases long-range contacts between ERα enhancers and their target promoters. Our results point to a role of AGO1 in transcriptional regulation in human cells that is independent from small RNA binding.
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Affiliation(s)
- Luciana I Gómez Acuña
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Ezequiel Nazer
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Santiago A Rodríguez-Seguí
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Valeria Buggiano
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciano E Marasco
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | | | - Cody He
- Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Mariano Alló
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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8
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Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P. An Atlas of Vagal Sensory Neurons and Their Molecular Specialization. Cell Rep 2020; 27:2508-2523.e4. [PMID: 31116992 PMCID: PMC6533201 DOI: 10.1016/j.celrep.2019.04.096] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/25/2019] [Accepted: 04/22/2019] [Indexed: 12/31/2022] Open
Abstract
Sensory functions of the vagus nerve are critical for conscious perceptions and for monitoring visceral functions in the cardio-pulmonary and gastrointestinal systems. Here, we present a comprehensive identification, classification, and validation of the neuron types in the neural crest (jugular) and placode (nodose) derived vagal ganglia by single-cell RNA sequencing (scRNA-seq) transcriptomic analysis. Our results reveal major differences between neurons derived from different embryonic origins. Jugular neurons exhibit fundamental similarities to the somatosensory spinal neurons, including major types, such as C-low threshold mechanoreceptors (C-LTMRs), A-LTMRs, Aδ-nociceptors, and cold-, and mechano-heat C-nociceptors. In contrast, the nodose ganglion contains 18 distinct types dedicated to surveying the physiological state of the internal body. Our results reveal a vast diversity of vagal neuron types, including many previously unanticipated types, as well as proposed types that are consistent with chemoreceptors, nutrient detectors, baroreceptors, and stretch and volume mechanoreceptors of the respiratory, gastrointestinal, and cardiovascular systems. A comprehensive molecular identification of neuronal types in vagal ganglion complex Prdm12+ jugular ganglion neurons share features with spinal somatosensory neurons Phox2b+ viscerosensory nodose neurons are molecularly versatile and highly specialized Nodose neuron types are consistent with chemo-, baro-, stretch-, tension-, and volume-sensors
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Affiliation(s)
- Jussi Kupari
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Häring
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Eneritz Agirre
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Patrik Ernfors
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.
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9
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Falcão AM, Meijer M, Scaglione A, Rinwa P, Agirre E, Liang J, Larsen SC, Heskol A, Frawley R, Klingener M, Varas-Godoy M, Raposo AASF, Ernfors P, Castro DS, Nielsen ML, Casaccia P, Castelo-Branco G. PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination. Cell Rep 2020; 27:1090-1102.e10. [PMID: 31018126 PMCID: PMC6486480 DOI: 10.1016/j.celrep.2019.03.108] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/13/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022] Open
Abstract
Citrullination, the deimination of peptidylarginine residues into peptidylcitrulline, has been implicated in the etiology of several diseases. In multiple sclerosis, citrullination is thought to be a major driver of pathology through hypercitrullination and destabilization of myelin. As such, inhibition of citrullination has been suggested as a therapeutic strategy for MS. Here, in contrast, we show that citrullination by peptidylarginine deiminase 2 (PAD2) contributes to normal oligodendrocyte differentiation, myelination, and motor function. We identify several targets for PAD2, including myelin and chromatin-related proteins, implicating PAD2 in epigenomic regulation. Accordingly, we observe that PAD2 inhibition and its knockdown affect chromatin accessibility and prevent the upregulation of oligodendrocyte differentiation genes. Moreover, mice lacking PAD2 display motor dysfunction and a decreased number of myelinated axons in the corpus callosum. We conclude that citrullination contributes to proper oligodendrocyte lineage progression and myelination. PAD2 is increased upon OL differentiation OL differentiation is facilitated by PAD2-mediated chromatin remodeling in myelin genes PAD2 contributes to efficient myelination and motor and cognitive functions Nuclear and myelin proteins interact and are citrullinated by PAD2
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Affiliation(s)
- Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Antonella Scaglione
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Puneet Rinwa
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jialiang Liang
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Sara C Larsen
- Department of Proteomics, the Novo Nordisk Foundation Center for Protein Research, Faculty of Heath Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Abeer Heskol
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Rebecca Frawley
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Michael Klingener
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Manuel Varas-Godoy
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Cancer Cell Biology Lab, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile
| | | | - Patrik Ernfors
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Diogo S Castro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Michael L Nielsen
- Department of Proteomics, the Novo Nordisk Foundation Center for Protein Research, Faculty of Heath Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Patrizia Casaccia
- Neuroscience Initiative at the Advanced Science Research Center of the Graduate Center of the City University of New York, New York, NY, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 171 77 Stockholm, Sweden.
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10
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Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, Samudyata, Luginbühl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, Hoon MD, Arner E, Lenhard B, Plessy C, Castelo-Branco G, Orlando V, Carninci P. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun 2020; 11:1018. [PMID: 32094342 PMCID: PMC7039879 DOI: 10.1038/s41467-020-14337-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [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: 11/12/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA–chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type–specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure. Mammalian genomes encode tens of thousands of ncRNAs that have important roles in regulation of gene expression and chromatin organization. Here, the authors present RADICLseq to map RNA-chromatin interactions in intact nuclei to shed light on these fine-tuned processes.
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Affiliation(s)
- Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan. .,Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | | | - Ana Maria Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,Department of Medicine (H7), Karolinska Institutet, Stockholm, 141 86, Sweden
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Giovanni Pascarella
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Leonie Roos
- Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, W12 0NN, UK.,MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Alex J Nash
- Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, W12 0NN, UK.,MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Marco Ghilotti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Christopher J F Cameron
- School of Computer Science, McGill University, Montréal, QC, Canada.,Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC, Canada
| | - Matthew Valentine
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Science, 117312, Moscow, Russia.,Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, 119991, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Region, Russia
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kaori Kashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Samudyata
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Riccardo Cazzoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Okinawa Institute of Science and Technology, Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | | | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Boris Lenhard
- Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, W12 0NN, UK.,MRC London Institute of Medical Sciences, London, W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, 5008, Bergen, Norway
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Valerio Orlando
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy. .,KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), Division of Biological Environmental Sciences and Engineering, 23955-6900, Thuwal, Saudi Arabia.
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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11
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Gauchier M, Kan S, Barral A, Sauzet S, Agirre E, Bonnell E, Saksouk N, Barth TK, Ide S, Urbach S, Wellinger RJ, Luco RF, Imhof A, Déjardin J. SETDB1-dependent heterochromatin stimulates alternative lengthening of telomeres. Sci Adv 2019; 5:eaav3673. [PMID: 31086817 PMCID: PMC6506250 DOI: 10.1126/sciadv.aav3673] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
Alternative lengthening of telomeres, or ALT, is a recombination-based process that maintains telomeres to render some cancer cells immortal. The prevailing view is that ALT is inhibited by heterochromatin because heterochromatin prevents recombination. To test this model, we used telomere-specific quantitative proteomics on cells with heterochromatin deficiencies. In contrast to expectations, we found that ALT does not result from a lack of heterochromatin; rather, ALT is a consequence of heterochromatin formation at telomeres, which is seeded by the histone methyltransferase SETDB1. Heterochromatin stimulates transcriptional elongation at telomeres together with the recruitment of recombination factors, while disrupting heterochromatin had the opposite effect. Consistently, loss of SETDB1, disrupts telomeric heterochromatin and abrogates ALT. Thus, inhibiting telomeric heterochromatin formation in ALT cells might offer a new therapeutic approach to cancer treatment.
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Affiliation(s)
- Mathilde Gauchier
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Sophie Kan
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Amandine Barral
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Sandrine Sauzet
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Eneritz Agirre
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Erin Bonnell
- Department of Microbiology and Infectious Diseases, PRAC-Université de Sherbrooke 3201 Jean-Mignault, Sherbrooke, Qc J1E 4K8, Canada
| | - Nehmé Saksouk
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Teresa K. Barth
- Munich Centre of Integrated Protein Science and Division of Molecular Biology Biomedical Center, Faculty of Medicine, LMU Munich, Großhaderner Str.9 82152 Planegg, Martinsried, Germany
| | - Satoru Ide
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Serge Urbach
- Functional Proteomics Facility, Institute of Functional Genomics, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, PRAC-Université de Sherbrooke 3201 Jean-Mignault, Sherbrooke, Qc J1E 4K8, Canada
| | - Reini F. Luco
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
| | - Axel Imhof
- Munich Centre of Integrated Protein Science and Division of Molecular Biology Biomedical Center, Faculty of Medicine, LMU Munich, Großhaderner Str.9 82152 Planegg, Martinsried, Germany
| | - Jérôme Déjardin
- Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier 34000, France
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12
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Falcão AM, van Bruggen D, Marques S, Meijer M, Jäkel S, Agirre E, Samudyata, Floriddia EM, Vanichkina DP, Ffrench-Constant C, Williams A, Guerreiro-Cacais AO, Castelo-Branco G. Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis. Nat Med 2018; 24:1837-1844. [PMID: 30420755 PMCID: PMC6544508 DOI: 10.1038/s41591-018-0236-y] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [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: 01/21/2018] [Accepted: 09/14/2018] [Indexed: 11/22/2022]
Abstract
Multiple sclerosis (MS) is characterized by an immune system attack targeting myelin, which is produced by oligodendrocytes (OLs). We performed single-cell transcriptomic analysis of OL lineage cells from the spinal cord of mice induced with experimental autoimmune encephalomyelitis (EAE), which mimics several aspects of MS. We found unique OLs and OL precursor cells (OPCs) in EAE and uncovered several genes specifically alternatively spliced in these cells. Surprisingly, EAE-specific OL lineage populations expressed genes involved in antigen processing and presentation via major histocompatibility complex class I and II (MHC-I and -II), and in immunoprotection, suggesting alternative functions of these cells in a disease context. Importantly, we found that disease-specific oligodendroglia are also present in human MS brains and that a substantial number of genes known to be susceptibility genes for MS, so far mainly associated with immune cells, are expressed in the OL lineage cells. Finally, we demonstrate that OPCs can phagocytose and that MHC-II-expressing OPCs can activate memory and effector CD4-positive T cells. Our results suggest that OLs and OPCs are not passive targets but instead active immunomodulators in MS. The disease-specific OL lineage cells, for which we identify several biomarkers, may represent novel direct targets for immunomodulatory therapeutic approaches in MS.
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Affiliation(s)
- Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden.
| | - David van Bruggen
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Sueli Marques
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Sarah Jäkel
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Samudyata
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Elisa M Floriddia
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Darya P Vanichkina
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, New South Wales , Australia
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Charles Ffrench-Constant
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
| | - Anna Williams
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
| | | | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Stockholm, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
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13
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van Bruggen D, Agirre E, Castelo-Branco G. Single-cell transcriptomic analysis of oligodendrocyte lineage cells. Curr Opin Neurobiol 2017; 47:168-175. [PMID: 29126015 DOI: 10.1016/j.conb.2017.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 11/16/2022]
Abstract
Oligodendrocytes (OLs) are glial cells in the central nervous system (CNS), which produce myelin, a lipid-rich membrane that insulates neuronal axons. The main function ascribed to OLs is to regulate the speed of electric pulse transmission, and as such OLs have been widely considered as a single and discrete population. Nevertheless, OLs and their precursor cells (OPCs) throughout the CNS have different morphologies and regional functional differences have been observed. Moreover, OLs have recently been involved in other functional processes such as metabolic coupling with axons. In this review, we focus on recent advances in single-cell transcriptomics suggesting that OLs are more heterogeneous than previously thought, with defined subpopulations and cell states that are associated with different stages of lineage progression and might also represent distinct functional states.
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Affiliation(s)
- David van Bruggen
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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14
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Lopez-Gazpio I, Maritxalar M, Gonzalez-Agirre A, Rigau G, Uria L, Agirre E. Interpretable semantic textual similarity: Finding and explaining differences between sentences. Knowl Based Syst 2017. [DOI: 10.1016/j.knosys.2016.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Agirre E, Bellora N, Alló M, Pagès A, Bertucci P, Kornblihtt AR, Eyras E. A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins. BMC Biol 2015; 13:31. [PMID: 25934638 PMCID: PMC4446157 DOI: 10.1186/s12915-015-0141-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [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: 11/25/2014] [Accepted: 04/22/2015] [Indexed: 12/20/2022] Open
Abstract
Background Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing regulation involving chromatin, transcription and multiple protein factors. In particular, the CCCTC-binding factor (CTCF), the Argonaute protein AGO1, and members of the heterochromatin protein 1 (HP1) family have been implicated in the regulation of splicing associated with chromatin and the elongation of RNAPII. These results raise the question of whether these proteins may associate at the chromatin level to modulate alternative splicing. Results Using chromatin immunoprecipitation sequencing (ChIP-Seq) data for CTCF, AGO1, HP1α, H3K27me3, H3K9me2, H3K36me3, RNAPII, total H3 and 5metC and alternative splicing arrays from two cell lines, we have analyzed the combinatorial code of their binding to chromatin in relation to the alternative splicing patterns between two cell lines, MCF7 and MCF10. Using Machine Learning techniques, we identified the changes in chromatin signals that are most significantly associated with splicing regulation between these two cell lines. Moreover, we have built a map of the chromatin signals on the pre-mRNA, that is, a chromatin-based RNA-map, which can explain 606 (68.55%) of the regulated events between MCF7 and MCF10. This chromatin code involves the presence of HP1α, CTCF, AGO1, RNAPII and histone marks around regulated exons and can differentiate patterns of skipping and inclusion. Additionally, we found a significant association of HP1α and CTCF activities around the regulated exons and a putative DNA binding site for HP1α. Conclusions Our results show that a considerable number of alternative splicing events could have a chromatin-dependent regulation involving the association of HP1α and CTCF near regulated exons. Additionally, we find further evidence for the involvement of HP1α and AGO1 in chromatin-related splicing regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0141-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eneritz Agirre
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Present address: Institute of Human Genetics, CNRS UPR 1142, Montpellier, France.
| | - Nicolás Bellora
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Present address: INIBIOMA, CONICET-UNComahue, Bariloche, Río Negro, Argentina.
| | - Mariano Alló
- IFIBYNE-UBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C1428EHA), Buenos Aires, Argentina. .,Present address: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Amadís Pagès
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Centre for Genomic Regulation, E08003, Barcelona, Spain.
| | - Paola Bertucci
- IFIBYNE-UBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C1428EHA), Buenos Aires, Argentina. .,Present address: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Alberto R Kornblihtt
- IFIBYNE-UBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C1428EHA), Buenos Aires, Argentina.
| | - Eduardo Eyras
- Universitat Pompeu Fabra, E08003, Barcelona, Spain. .,Catalan Institution of Research and Advanced Studies (ICREA), E08010, Barcelona, Spain.
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16
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Abstract
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data, which could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.
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Affiliation(s)
- Gael P Alamancos
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
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17
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Abstract
Recent advances in high-throughput sequencing have facilitated the genome-wide studies of small non-coding RNAs (sRNAs). Numerous studies have highlighted the role of various classes of sRNAs at different levels of gene regulation and disease. The fast growth of sequence data and the diversity of sRNA species have prompted the need to organise them in annotation databases. There are currently several databases that collect sRNA data. Various tools are provided for access, with special emphasis on the well-characterised family of micro-RNAs. The striking heterogeneity of the new classes of sRNAs and the lack of sufficient functional annotation, however, make integration of these datasets a difficult task. This review describes the currently available databases for human sRNAs that are accessible via the internet, and some of the large datasets for human sRNAs from high-throughput sequencing experiments that are so far only available as supplementary data in publications. Some of the main issues related to the integration and annotation of sRNA datasets are also discussed.
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Affiliation(s)
- Eneritz Agirre
- Department of Computational Genomics, Universitat Pompeu Fabra, Dr. Aiguader 88, E08003 Barcelona, Spain
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18
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Alló M, Schor IE, Muñoz MJ, de la Mata M, Agirre E, Valcárcel J, Eyras E, Kornblihtt AR. Chromatin and alternative splicing. Cold Spring Harb Symp Quant Biol 2011; 75:103-11. [PMID: 21289049 DOI: 10.1101/sqb.2010.75.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alternative splicing affects more than 90% of human genes. Coupling between transcription and splicing has become crucial in the complex network underlying alternative splicing regulation. Because chromatin is the real template for nuclear transcription, changes in its structure, but also in the "reading" and "writing" of the histone code, could modulate splicing choices. Here, we discuss the evidence supporting these ideas, from the first proposal of chromatin affecting alternative splicing, performed 20 years ago, to the latest findings including genome-wide evidence that nucleosomes are preferentially positioned in exons. We focus on two recent reports from our laboratories that add new evidence to this field. The first report shows that a physiological stimulus such as neuron depolarization promotes intragenic histone acetylation (H3K9ac) and chromatin relaxation, causing the skipping of exon 18 of the neural cell adhesion molecule gene. In the second report, we show how specific histone modifications can be created at targeted gene regions as a way to affect alternative splicing: Using small interfering RNAs (siRNAs), we increased the levels of H3K9me2 and H3K27me3 in the proximity of alternative exon 33 of the human fibronectin gene, favoring its inclusion into mature messenger RNA (mRNA) through a mechanism that recalls RNA-mediated transcriptional gene silencing.
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Affiliation(s)
- M Alló
- Departamento de Fisiología, Biología Molecular y Celular, Laboratorio de Fisiología y Biología Molecular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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Alló M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B, Kornblihtt AR. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol 2009; 16:717-24. [PMID: 19543290 DOI: 10.1038/nsmb.1620] [Citation(s) in RCA: 257] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 05/15/2009] [Indexed: 02/07/2023]
Abstract
When targeting promoter regions, small interfering RNAs (siRNAs) trigger a previously proposed pathway known as transcriptional gene silencing by promoting heterochromatin formation. Here we show that siRNAs targeting intronic or exonic sequences close to an alternative exon regulate the splicing of that exon. The effect occurred in hepatoma and HeLa cells with siRNA antisense strands designed to enter the silencing pathway, suggesting hybridization with nascent pre-mRNA. Unexpectedly, in HeLa cells the sense strands were also effective, suggesting that an endogenous antisense transcript, detectable in HeLa but not in hepatoma cells, acts as a target. The effect depends on Argonaute-1 and is counterbalanced by factors favoring chromatin opening or transcriptional elongation. The increase in heterochromatin marks (dimethylation at Lys9 and trimethylation at Lys27 of histone H3) at the target site, the need for the heterochromatin-associated protein HP1alpha and the reduction in RNA polymerase II processivity suggest a mechanism involving the kinetic coupling of transcription and alternative splicing.
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Affiliation(s)
- Mariano Alló
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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Plass M, Agirre E, Reyes D, Camara F, Eyras E. Co-evolution of the branch site and SR proteins in eukaryotes. Trends Genet 2008; 24:590-4. [PMID: 18992956 DOI: 10.1016/j.tig.2008.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 09/19/2008] [Accepted: 10/02/2008] [Indexed: 11/15/2022]
Abstract
Serine-arginine-rich (SR) proteins are essential for splicing in metazoans but are absent in yeast. By contrast, many fungi have SR protein homologs with variable arginine-rich regions analogous to the arginine-serine-rich (RS) domain in metazoans. The density of RS repeats in these regions correlates with the conservation of the branch site signal, providing evidence for an ancestral origin of SR proteins and indicating that the SR proteins and the branch site co-evolved.
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Affiliation(s)
- Mireya Plass
- Computational Genomics Group, Universitat Pompeu Fabra, PRBB, Dr. Aiguader 88 E08003, Barcelona, Spain
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Martinez D, Lopez de Lacalle O, Agirre E. On the Use of Automatically Acquired Examples for All-Nouns Word Sense Disambiguation. J ARTIF INTELL RES 2008. [DOI: 10.1613/jair.2395] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
This article focuses on Word Sense Disambiguation (WSD), which is a Natural Language Processing task that is thought to be important for many Language Technology applications, such as Information Retrieval, Information Extraction, or Machine Translation. One of the main issues preventing the deployment of WSD technology is the lack of training examples for Machine Learning systems, also known as the Knowledge Acquisition Bottleneck. A method which has been shown to work for small samples of words is the automatic acquisition of examples. We have previously shown that one of the most promising example acquisition methods scales up and produces a freely available database of 150 million examples from Web snippets for all polysemous nouns in WordNet. This paper focuses on the issues that arise when using those examples, all alone or in addition to manually tagged examples, to train a supervised WSD system for all nouns. The extensive evaluation on both lexical-sample and all-words Senseval benchmarks shows that we are able to improve over commonly used baselines and to achieve top-rank performance. The good use of the prior distributions from the senses proved to be a crucial factor.
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Makhmudov U, Tcherekaev V, Shimansky V, Tanyashin S, Mamin R, Mukhametjanov D, Agirre E. Surgical treatment of posterior fossa cholesteatomas. Clin Neurol Neurosurg 1997. [DOI: 10.1016/s0303-8467(97)82446-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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