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Lam I, Ndayisaba A, Lewis AJ, Fu Y, Sagredo GT, Kuzkina A, Zaccagnini L, Celikag M, Sandoe J, Sanz RL, Vahdatshoar A, Martin TD, Morshed N, Ichihashi T, Tripathi A, Ramalingam N, Oettgen-Suazo C, Bartels T, Boussouf M, Schäbinger M, Hallacli E, Jiang X, Verma A, Tea C, Wang Z, Hakozaki H, Yu X, Hyles K, Park C, Wang X, Theunissen TW, Wang H, Jaenisch R, Lindquist S, Stevens B, Stefanova N, Wenning G, van de Berg WDJ, Luk KC, Sanchez-Pernaute R, Gómez-Esteban JC, Felsky D, Kiyota Y, Sahni N, Yi SS, Chung CY, Stahlberg H, Ferrer I, Schöneberg J, Elledge SJ, Dettmer U, Halliday GM, Bartels T, Khurana V. Rapid iPSC inclusionopathy models shed light on formation, consequence, and molecular subtype of α-synuclein inclusions. Neuron 2024; 112:2886-2909.e16. [PMID: 39079530 PMCID: PMC11377155 DOI: 10.1016/j.neuron.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 10/26/2023] [Accepted: 06/03/2024] [Indexed: 09/07/2024]
Abstract
The heterogeneity of protein-rich inclusions and its significance in neurodegeneration is poorly understood. Standard patient-derived iPSC models develop inclusions neither reproducibly nor in a reasonable time frame. Here, we developed screenable iPSC "inclusionopathy" models utilizing piggyBac or targeted transgenes to rapidly induce CNS cells that express aggregation-prone proteins at brain-like levels. Inclusions and their effects on cell survival were trackable at single-inclusion resolution. Exemplar cortical neuron α-synuclein inclusionopathy models were engineered through transgenic expression of α-synuclein mutant forms or exogenous seeding with fibrils. We identified multiple inclusion classes, including neuroprotective p62-positive inclusions versus dynamic and neurotoxic lipid-rich inclusions, both identified in patient brains. Fusion events between these inclusion subtypes altered neuronal survival. Proteome-scale α-synuclein genetic- and physical-interaction screens pinpointed candidate RNA-processing and actin-cytoskeleton-modulator proteins like RhoA whose sequestration into inclusions could enhance toxicity. These tractable CNS models should prove useful in functional genomic analysis and drug development for proteinopathies.
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Affiliation(s)
- Isabel Lam
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Amanda J Lewis
- École Polytechnique Fédérale de Lausanne and University of Lausanne, Lausanne, Switzerland
| | - YuHong Fu
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health School of Medical Science, Sydney, NSW, Australia
| | - Giselle T Sagredo
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health School of Medical Science, Sydney, NSW, Australia
| | - Anastasia Kuzkina
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | - Meral Celikag
- Dementia Research Institute, University College London, London, UK
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Ricardo L Sanz
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Timothy D Martin
- Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nader Morshed
- Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Boston Children's Hospital, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Arati Tripathi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Charlotte Oettgen-Suazo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Theresa Bartels
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Manel Boussouf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Max Schäbinger
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Xin Jiang
- Yumanity Therapeutics, Cambridge, MA, USA
| | - Amrita Verma
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Challana Tea
- University of California, San Diego, San Diego, CA, USA
| | - Zichen Wang
- University of California, San Diego, San Diego, CA, USA
| | | | - Xiao Yu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Kelly Hyles
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Chansaem Park
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xinyuan Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | - Haoyi Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Beth Stevens
- Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Boston Children's Hospital, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadia Stefanova
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gregor Wenning
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Kelvin C Luk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rosario Sanchez-Pernaute
- BioBizkaia Health Research Institute, Barakaldo, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | | | - Daniel Felsky
- Centre for Addiction and Mental Health, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | | | - Nidhi Sahni
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Baylor College of Medicine, Houston, TX, USA
| | - S Stephen Yi
- The University of Texas at Austin, Austin, TX, USA
| | | | - Henning Stahlberg
- École Polytechnique Fédérale de Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Isidro Ferrer
- The University of Barcelona, Institut d'Investigacio Biomedica de Bellvitge IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Stephen J Elledge
- Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Glenda M Halliday
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health School of Medical Science, Sydney, NSW, Australia; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Tim Bartels
- Dementia Research Institute, University College London, London, UK
| | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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2
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Santhosh Kumar S, Naseri NN, Pather SR, Hallacli E, Ndayisaba A, Buenaventura C, Acosta K, Roof J, Fazelinia H, Spruce LA, Luk K, Khurana V, Rhoades E, Shalem O. Sequential CRISPR screening reveals partial NatB inhibition as a strategy to mitigate alpha-synuclein levels in human neurons. SCIENCE ADVANCES 2024; 10:eadj4767. [PMID: 38335281 PMCID: PMC10857481 DOI: 10.1126/sciadv.adj4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Alpha-synuclein (αSyn) protein levels correlate with the risk and severity of Parkinson's disease and related neurodegenerative diseases. Lowering αSyn is being actively investigated as a therapeutic modality. Here, we systematically map the regulatory network that controls endogenous αSyn using sequential CRISPR-knockout and -interference screens in an αSyn gene (SNCA)-tagged cell line and induced pluripotent stem cell-derived neurons (iNeurons). We uncover αSyn modifiers at multiple regulatory layers, with amino-terminal acetyltransferase B (NatB) enzymes being the most potent endogenous αSyn modifiers in both cell lines. Amino-terminal acetylation protects the cytosolic αSyn from rapid degradation by the proteasome in a Ube2w-dependent manner. Moreover, we show that pharmacological inhibition of methionyl-aminopeptidase 2, a regulator of NatB complex formation, attenuates endogenous αSyn in iNeurons carrying SNCA triplication. Together, our study reveals several gene networks that control endogenous αSyn, identifies mechanisms mediating the degradation of nonacetylated αSyn, and illustrates potential therapeutic pathways for decreasing αSyn levels in synucleinopathies.
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Affiliation(s)
- Saranya Santhosh Kumar
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nima N. Naseri
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarshan R. Pather
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erinc Hallacli
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Buenaventura
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen Acosta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Roof
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A. Spruce
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelvin Luk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Ndayisaba A, Pitaro AT, Willett AS, Jones KA, de Gusmao CM, Olsen AL, Kim J, Rissanen E, Woods JK, Srinivasan SR, Nagy A, Nagy A, Mesidor M, Cicero S, Patel V, Oakley DH, Tuncali I, Taglieri-Noble K, Clark EC, Paulson J, Krolewski RC, Ho GP, Hung AY, Wills AM, Hayes MT, Macmore JP, Warren L, Bower PG, Langer CB, Kellerman LR, Humphreys CW, Glanz BI, Dielubanza EJ, Frosch MP, Freeman RL, Gibbons CH, Stefanova N, Chitnis T, Weiner HL, Scherzer CR, Scholz SW, Vuzman D, Cox LM, Wenning G, Schmahmann JD, Gupta AS, Novak P, Young GS, Feany MB, Singhal T, Khurana V. Clinical Trial-Ready Patient Cohorts for Multiple System Atrophy: Coupling Biospecimen and iPSC Banking to Longitudinal Deep-Phenotyping. CEREBELLUM (LONDON, ENGLAND) 2024; 23:31-51. [PMID: 36190676 PMCID: PMC9527378 DOI: 10.1007/s12311-022-01471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
Multiple system atrophy (MSA) is a fatal neurodegenerative disease of unknown etiology characterized by widespread aggregation of the protein alpha-synuclein in neurons and glia. Its orphan status, biological relationship to Parkinson's disease (PD), and rapid progression have sparked interest in drug development. One significant obstacle to therapeutics is disease heterogeneity. Here, we share our process of developing a clinical trial-ready cohort of MSA patients (69 patients in 2 years) within an outpatient clinical setting, and recruiting 20 of these patients into a longitudinal "n-of-few" clinical trial paradigm. First, we deeply phenotype our patients with clinical scales (UMSARS, BARS, MoCA, NMSS, and UPSIT) and tests designed to establish early differential diagnosis (including volumetric MRI, FDG-PET, MIBG scan, polysomnography, genetic testing, autonomic function tests, skin biopsy) or disease activity (PBR06-TSPO). Second, we longitudinally collect biospecimens (blood, CSF, stool) and clinical, biometric, and imaging data to generate antecedent disease-progression scores. Third, in our Mass General Brigham SCiN study (stem cells in neurodegeneration), we generate induced pluripotent stem cell (iPSC) models from our patients, matched to biospecimens, including postmortem brain. We present 38 iPSC lines derived from MSA patients and relevant disease controls (spinocerebellar ataxia and PD, including alpha-synuclein triplication cases), 22 matched to whole-genome sequenced postmortem brain. iPSC models may facilitate matching patients to appropriate therapies, particularly in heterogeneous diseases for which patient-specific biology may elude animal models. We anticipate that deeply phenotyped and genotyped patient cohorts matched to cellular models will increase the likelihood of success in clinical trials for MSA.
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Affiliation(s)
- Alain Ndayisaba
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
- Division of Clinical Neurobiology, Department of Neurology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - Ariana T Pitaro
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Andrew S Willett
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Kristie A Jones
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Claudio Melo de Gusmao
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Abby L Olsen
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Jisoo Kim
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Eero Rissanen
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Jared K Woods
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sharan R Srinivasan
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI , 48103, USA
| | - Anna Nagy
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Amanda Nagy
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Merlyne Mesidor
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Steven Cicero
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Viharkumar Patel
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Idil Tuncali
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Katherine Taglieri-Noble
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Emily C Clark
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Jordan Paulson
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Richard C Krolewski
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Gary P Ho
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Albert Y Hung
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Michael T Hayes
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Jason P Macmore
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | | | - Pamela G Bower
- The Multiple System Atrophy Coalition, Inc., 7918 Jones Branch Drive, Suite 300, McLean, VA, 22102, USA
| | - Carol B Langer
- The Multiple System Atrophy Coalition, Inc., 7918 Jones Branch Drive, Suite 300, McLean, VA, 22102, USA
| | - Lawrence R Kellerman
- The Multiple System Atrophy Coalition, Inc., 7918 Jones Branch Drive, Suite 300, McLean, VA, 22102, USA
| | - Christopher W Humphreys
- Department of Pulmonary, Sleep and Critical Care Medicine, Salem Hospital, MassGeneral Brigham, Salem, MA, 01970, USA
| | - Bonnie I Glanz
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Elodi J Dielubanza
- Department of Urology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew P Frosch
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Roy L Freeman
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher H Gibbons
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Nadia Stefanova
- Division of Clinical Neurobiology, Department of Neurology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - Tanuja Chitnis
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Howard L Weiner
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Clemens R Scherzer
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Sonja W Scholz
- Laboratory of Neurogenetics, Disorders and Stroke, National Institute of Neurological, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, 21287, USA
| | - Dana Vuzman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Laura M Cox
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Gregor Wenning
- Division of Clinical Neurobiology, Department of Neurology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - Jeremy D Schmahmann
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Anoopum S Gupta
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Peter Novak
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Geoffrey S Young
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Tarun Singhal
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA
| | - Vikram Khurana
- Department of Neurology, Building for Transformative Medicine Room 10016L, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Road, Boston, 02115, USA.
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4
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Regenerating Damaged Myocardium: A Review of Stem-Cell Therapies for Heart Failure. Cells 2021; 10:cells10113125. [PMID: 34831347 PMCID: PMC8625160 DOI: 10.3390/cells10113125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022] Open
Abstract
Cardiovascular disease (CVD) is one of the contributing factors to more than one-third of human mortality and the leading cause of death worldwide. The death of cardiac myocyte is a fundamental pathological process in cardiac pathologies caused by various heart diseases, including myocardial infarction. Thus, strategies for replacing fibrotic tissue in the infarcted region with functional myocardium have long been a goal of cardiovascular research. This review begins by briefly discussing a variety of somatic stem- and progenitor-cell populations that were frequently studied in early investigations of regenerative myocardial therapy and then focuses primarily on pluripotent stem cells (PSCs), especially induced-pluripotent stem cells (iPSCs), which have emerged as perhaps the most promising source of cardiomyocytes for both therapeutic applications and drug testing. We also describe attempts to generate cardiomyocytes directly from cardiac fibroblasts (i.e., transdifferentiation), which, if successful, may enable the pool of endogenous cardiac fibroblasts to be used as an in-situ source of cardiomyocytes for myocardial repair.
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5
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Malik V, Zimmer D, Jauch R. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming. Cell Mol Life Sci 2018; 75:1587-1612. [PMID: 29335749 PMCID: PMC11105716 DOI: 10.1007/s00018-018-2748-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite 'two-in-one' DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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6
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Jerabek S, Ng CK, Wu G, Arauzo-Bravo MJ, Kim KP, Esch D, Malik V, Chen Y, Velychko S, MacCarthy CM, Yang X, Cojocaru V, Schöler HR, Jauch R. Changing POU dimerization preferences converts Oct6 into a pluripotency inducer. EMBO Rep 2016; 18:319-333. [PMID: 28007765 PMCID: PMC5286379 DOI: 10.15252/embr.201642958] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022] Open
Abstract
The transcription factor Oct4 is a core component of molecular cocktails inducing pluripotent stem cells (iPSCs), while other members of the POU family cannot replace Oct4 with comparable efficiency. Rather, group III POU factors such as Oct6 induce neural lineages. Here, we sought to identify molecular features determining the differential DNA‐binding and reprogramming activity of Oct4 and Oct6. In enhancers of pluripotency genes, Oct4 cooperates with Sox2 on heterodimeric SoxOct elements. By re‐analyzing ChIP‐Seq data and performing dimerization assays, we found that Oct6 homodimerizes on palindromic OctOct more cooperatively and more stably than Oct4. Using structural and biochemical analyses, we identified a single amino acid directing binding to the respective DNA elements. A change in this amino acid decreases the ability of Oct4 to generate iPSCs, while the reverse mutation in Oct6 does not augment its reprogramming activity. Yet, with two additional amino acid exchanges, Oct6 acquires the ability to generate iPSCs and maintain pluripotency. Together, we demonstrate that cell type‐specific POU factor function is determined by select residues that affect DNA‐dependent dimerization.
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Affiliation(s)
- Stepan Jerabek
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Calista Kl Ng
- Institute of Medical Biology, Singapore City, Singapore
| | - Guangming Wu
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marcos J Arauzo-Bravo
- Biodonostia Health Research Institute, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Kee-Pyo Kim
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Daniel Esch
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Vikas Malik
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanpu Chen
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | | | - Xiaoxiao Yang
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Vlad Cojocaru
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Center for Multiscale Theory and Computation, University of Münster, Münster, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster, Germany .,Medical Faculty, University of Münster, Münster, Germany
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China .,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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