1
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Scala M, Khan K, Beneteau C, Fox RG, von Hardenberg S, Khan A, Joubert M, Fievet L, Musquer M, Le Vaillant C, Holsclaw JK, Lim D, Berking AC, Accogli A, Giacomini T, Nobili L, Striano P, Zara F, Torella A, Nigro V, Cogné B, Salick MR, Kaykas A, Eggan K, Capra V, Bézieau S, Davis EE, Wells MF. Biallelic loss-of-function variants in CACHD1 cause a novel neurodevelopmental syndrome with facial dysmorphism and multisystem congenital abnormalities. Genet Med 2024; 26:101057. [PMID: 38158856 DOI: 10.1016/j.gim.2023.101057] [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: 07/15/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
PURPOSE We established the genetic etiology of a syndromic neurodevelopmental condition characterized by variable cognitive impairment, recognizable facial dysmorphism, and a constellation of extra-neurological manifestations. METHODS We performed phenotypic characterization of 6 participants from 4 unrelated families presenting with a neurodevelopmental syndrome and used exome sequencing to investigate the underlying genetic cause. To probe relevance to the neurodevelopmental phenotype and craniofacial dysmorphism, we established two- and three-dimensional human stem cell-derived neural models and generated a stable cachd1 zebrafish mutant on a transgenic cartilage reporter line. RESULTS Affected individuals showed mild cognitive impairment, dysmorphism featuring oculo-auriculo abnormalities, and developmental defects involving genitourinary and digestive tracts. Exome sequencing revealed biallelic putative loss-of-function variants in CACHD1 segregating with disease in all pedigrees. RNA sequencing in CACHD1-depleted neural progenitors revealed abnormal expression of genes with key roles in Wnt signaling, neurodevelopment, and organ morphogenesis. CACHD1 depletion in neural progenitors resulted in reduced percentages of post-mitotic neurons and enlargement of 3D neurospheres. Homozygous cachd1 mutant larvae showed mandibular patterning defects mimicking human facial dysmorphism. CONCLUSION Our findings support the role of loss-of-function variants in CACHD1 as the cause of a rare neurodevelopmental syndrome with facial dysmorphism and multisystem abnormalities.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy; Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Kamal Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Claire Beneteau
- CHU Nantes, Department of Medical Genetics, CHU Nantes, 9 quai Moncousu, Nantes, France; CHU Nantes, UF of Fœtopathology and Genetics, Nantes, France; CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Rachel G Fox
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | | | - Ayaz Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Madeleine Joubert
- CHU Nantes, UF of Fœtopathology and Genetics, Nantes, France; CHU Nantes, Department of Anatomical Pathology, Nantes, France
| | - Lorraine Fievet
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC
| | - Marie Musquer
- CHU Nantes, UF of Fœtopathology and Genetics, Nantes, France; CHU Nantes, Department of Anatomical Pathology, Nantes, France
| | | | | | - Derek Lim
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust and Birmingham Health Partners, Birmingham, United Kingdom; Department of Medicine, University of Birmingham, Birmingham, United Kingdom
| | | | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Thea Giacomini
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Child Neuropsychiatry Unit, IRCCS G. Gaslini Institute, Genoa, Italy
| | - Lino Nobili
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Child Neuropsychiatry Unit, IRCCS G. Gaslini Institute, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Benjamin Cogné
- CHU Nantes, Department of Medical Genetics, CHU Nantes, 9 quai Moncousu, Nantes, France; Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Valeria Capra
- Medical Genetics Unit, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Stéphane Bézieau
- CHU Nantes, Department of Medical Genetics, CHU Nantes, 9 quai Moncousu, Nantes, France; Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Department of Pediatrics and Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL.
| | - Michael F Wells
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA.
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2
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Baum ML, Wilton DK, Fox RG, Carey A, Hsu YHH, Hu R, Jäntti HJ, Fahey JB, Muthukumar AK, Salla N, Crotty W, Scott-Hewitt N, Bien E, Sabatini DA, Lanser TB, Frouin A, Gergits F, Håvik B, Gialeli C, Nacu E, Lage K, Blom AM, Eggan K, McCarroll SA, Johnson MB, Stevens B. CSMD1 regulates brain complement activity and circuit development. Brain Behav Immun 2024; 119:317-332. [PMID: 38552925 DOI: 10.1016/j.bbi.2024.03.041] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/29/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Complement proteins facilitate synaptic elimination during neurodevelopmental pruning, but neural complement regulation is not well understood. CUB and Sushi Multiple Domains 1 (CSMD1) can regulate complement activity in vitro, is expressed in the brain, and is associated with increased schizophrenia risk. Beyond this, little is known about CSMD1 including whether it regulates complement activity in the brain or otherwise plays a role in neurodevelopment. We used biochemical, immunohistochemical, and proteomic techniques to examine the regional, cellular, and subcellular distribution as well as protein interactions of CSMD1 in the brain. To evaluate whether CSMD1 is involved in complement-mediated synapse elimination, we examined Csmd1-knockout mice and CSMD1-knockout human stem cell-derived neurons. We interrogated synapse and circuit development of the mouse visual thalamus, a process that involves complement pathway activity. We also quantified complement deposition on synapses in mouse visual thalamus and on cultured human neurons. Finally, we assessed uptake of synaptosomes by cultured microglia. We found that CSMD1 is present at synapses and interacts with complement proteins in the brain. Mice lacking Csmd1 displayed increased levels of complement component C3, an increased colocalization of C3 with presynaptic terminals, fewer retinogeniculate synapses, and aberrant segregation of eye-specific retinal inputs to the visual thalamus during the critical period of complement-dependent refinement of this circuit. Loss of CSMD1 in vivo enhanced synaptosome engulfment by microglia in vitro, and this effect was dependent on activity of the microglial complement receptor, CR3. Finally, human stem cell-derived neurons lacking CSMD1 were more vulnerable to complement deposition. These data suggest that CSMD1 can function as a regulator of complement-mediated synapse elimination in the brain during development.
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Affiliation(s)
- Matthew L Baum
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; MD-PhD Program of Harvard & MIT, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel K Wilton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel G Fox
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alanna Carey
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruilong Hu
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Henna J Jäntti
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jaclyn B Fahey
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allie K Muthukumar
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nikkita Salla
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William Crotty
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Nicole Scott-Hewitt
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Bien
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David A Sabatini
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Toby B Lanser
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arnaud Frouin
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick Gergits
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Chrysostomi Gialeli
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, S-214 28 Malmö, Sweden; Cardiovascular Research - Translational Studies Research Group, Department of Clinical Sciences, Lund University, S-214 28 Malmö, Sweden
| | - Eugene Nacu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, S-214 28 Malmö, Sweden
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew B Johnson
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Beth Stevens
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, USA.
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3
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Guss EJ, Sathe L, Dai A, Derebenskiy T, Vega AR, Eggan K, Wells MF. Protocol for neurogenin-2-mediated induction of human stem cell-derived neural progenitor cells. STAR Protoc 2024; 5:102878. [PMID: 38335091 PMCID: PMC10865475 DOI: 10.1016/j.xpro.2024.102878] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/01/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Human pluripotent stem cell-derived neural progenitor cells (NPCs) are an essential tool for the study of brain development and developmental disorders such as autism. Here, we present a protocol to generate NPCs rapidly and reproducibly from human stem cells using dual-SMAD inhibition coupled with a brief pulse of mouse neurogenin-2 (Ngn2) overexpression. We detail the 48-h induction scheme deployed to produce these cells-termed stem cell-derived Ngn2-accelerated progenitor cells-followed by steps for expansion, purification, banking, and quality assessment. For complete details on the use and execution of this protocol, please refer to Wells et al.1.
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Affiliation(s)
- Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Laila Sathe
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Dai
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tim Derebenskiy
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ana Rodriguez Vega
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael F Wells
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.
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4
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Limone F, Couto A, Wang JY, Zhang Y, McCourt B, Huang C, Minkin A, Jani M, McNeer S, Keaney J, Gillet G, Gonzalez RL, Goodman WA, Kadiu I, Eggan K, Burberry A. Myeloid and lymphoid expression of C9orf72 regulates IL-17A signaling in mice. Sci Transl Med 2024; 16:eadg7895. [PMID: 38295187 DOI: 10.1126/scitranslmed.adg7895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
A mutation in C9ORF72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Patients with ALS or FTD often develop autoimmunity and inflammation that precedes or coincides with the onset of neurological symptoms, but the underlying mechanisms are poorly understood. Here, we knocked out murine C9orf72 in seven hematopoietic progenitor compartments by conditional mutagenesis and found that myeloid lineage C9orf72 prevents splenomegaly, loss of tolerance, and premature mortality. Furthermore, we demonstrated that C9orf72 plays a role in lymphoid cells to prevent interleukin-17A (IL-17A) production and neutrophilia. Mass cytometry identified early and sustained elevation of the costimulatory molecule CD80 expressed on C9orf72-deficient mouse macrophages, monocytes, and microglia. Enrichment of CD80 was similarly observed in human spinal cord microglia from patients with C9ORF72-mediated ALS compared with non-ALS controls. Single-cell RNA sequencing of murine spinal cord, brain cortex, and spleen demonstrated coordinated induction of gene modules related to antigen processing and presentation and antiviral immunity in C9orf72-deficient endothelial cells, microglia, and macrophages. Mechanistically, C9ORF72 repressed the trafficking of CD80 to the cell surface in response to Toll-like receptor agonists, interferon-γ, and IL-17A. Deletion of Il17a in C9orf72-deficient mice prevented CD80 enrichment in the spinal cord, reduced neutrophilia, and reduced gut T helper type 17 cells. Last, systemic delivery of an IL-17A neutralizing antibody augmented motor performance and suppressed neuroinflammation in C9orf72-deficient mice. Altogether, we show that C9orf72 orchestrates myeloid costimulatory potency and provide support for IL-17A as a therapeutic target for neuroinflammation associated with ALS or FTD.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Leiden University Medical Center, LUMC, 2333 ZA Leiden, Netherlands
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jin-Yuan Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Yingying Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Blake McCourt
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cerianne Huang
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Adina Minkin
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marghi Jani
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sarah McNeer
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - James Keaney
- Neuroinflammation Focus Area, UCB Biopharma SRL, Braine-l'Alleud 1420, Belgium
| | - Gaëlle Gillet
- Neuroinflammation Focus Area, UCB Biopharma SRL, Braine-l'Alleud 1420, Belgium
| | - Rodrigo Lopez Gonzalez
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
| | - Wendy A Goodman
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Irena Kadiu
- Neuroinflammation Focus Area, UCB Biopharma SRL, Braine-l'Alleud 1420, Belgium
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Aaron Burberry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
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5
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Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, Carpenter AE, Singh S, Nehme R, Raychaudhuri S. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nat Commun 2024; 15:347. [PMID: 38184653 PMCID: PMC10771466 DOI: 10.1038/s41467-023-44045-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/28/2023] [Indexed: 01/08/2024] Open
Abstract
The morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combine genomic sequencing and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identify novel associations between rare protein altering variants in WASF2, TSPAN15, and PRLR with several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirms their role in cell morphology. Analysis of common variants yields one significant association and nominate over 300 variants with suggestive evidence (P < 10-6) of association with one or more morphology traits. We then use these data to make predictions about sample size requirements for increasing discovery in cellular genetic studies. We conclude that, similar to molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.
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Affiliation(s)
- Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Centre for Gene Therapy and Regenerative Medicine, King's College, London, UK
| | - Jatin Arora
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samira Asgari
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ajay Nadig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Peirent
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dhara Liyanage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory P Way
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tiffany Amariuta
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California, La Jolla, CA, USA
- Department of Medicine, University of California, La Jolla, CA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Marzieh Haghighi
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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6
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Lakes YB, Moye SL, Mo J, Tegtmeyer M, Nehme R, Charlton M, Salinas G, McKay RM, Eggan K, Le LQ. Econazole selectively induces cell death in NF1-homozygous mutant tumor cells. Cell Rep Med 2023; 4:101309. [PMID: 38086379 PMCID: PMC10772348 DOI: 10.1016/j.xcrm.2023.101309] [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: 06/10/2023] [Revised: 10/06/2023] [Accepted: 11/12/2023] [Indexed: 12/22/2023]
Abstract
Cutaneous neurofibromas (cNFs) are tumors that develop in more than 99% of individuals with neurofibromatosis type 1 (NF1). They develop in the dermis and can number in the thousands. cNFs can be itchy and painful and negatively impact self-esteem. There is no US Food and Drug Administration (FDA)-approved drug for their treatment. Here, we screen a library of FDA-approved drugs using a cNF cell model derived from human induced pluripotent stem cells (hiPSCs) generated from an NF1 patient. We engineer an NF1 mutation in the second allele to mimic loss of heterozygosity, differentiate the NF1+/- and NF1-/- hiPSCs into Schwann cell precursors (SCPs), and use them to screen a drug library to assess for inhibition of NF1-/- but not NF1+/- cell proliferation. We identify econazole nitrate as being effective against NF1-/- hiPSC-SCPs. Econazole cream selectively induces apoptosis in Nf1-/- murine nerve root neurosphere cells and human cNF xenografts. This study supports further testing of econazole for cNF treatment.
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Affiliation(s)
- Yenal B Lakes
- Department of Stem Cell and Regenerative Medicine, Harvard University, Boston, MA, USA
| | - Stefanie L Moye
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Juan Mo
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Maura Charlton
- Department of Stem Cell and Regenerative Medicine, Harvard University, Boston, MA, USA
| | - Gabrielle Salinas
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Renee M McKay
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Medicine, Harvard University, Boston, MA, USA.
| | - Lu Q Le
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; O'Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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7
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Dolan MJ, Therrien M, Jereb S, Kamath T, Gazestani V, Atkeson T, Marsh SE, Goeva A, Lojek NM, Murphy S, White CM, Joung J, Liu B, Limone F, Eggan K, Hacohen N, Bernstein BE, Glass CK, Leinonen V, Blurton-Jones M, Zhang F, Epstein CB, Macosko EZ, Stevens B. Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat Immunol 2023; 24:1382-1390. [PMID: 37500887 PMCID: PMC10382323 DOI: 10.1038/s41590-023-01558-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 04/28/2022] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
Microglia, the macrophages of the brain parenchyma, are key players in neurodegenerative diseases such as Alzheimer's disease. These cells adopt distinct transcriptional subtypes known as states. Understanding state function, especially in human microglia, has been elusive owing to a lack of tools to model and manipulate these cells. Here, we developed a platform for modeling human microglia transcriptional states in vitro. We found that exposure of human stem-cell-differentiated microglia to synaptosomes, myelin debris, apoptotic neurons or synthetic amyloid-beta fibrils generated transcriptional diversity that mapped to gene signatures identified in human brain microglia, including disease-associated microglia, a state enriched in neurodegenerative diseases. Using a new lentiviral approach, we demonstrated that the transcription factor MITF drives a disease-associated transcriptional signature and a highly phagocytic state. Together, these tools enable the manipulation and functional interrogation of human microglial states in both homeostatic and disease-relevant contexts.
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Affiliation(s)
- Michael-John Dolan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Martine Therrien
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Saša Jereb
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tushar Kamath
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Vahid Gazestani
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Trevor Atkeson
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel E Marsh
- Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aleksandrina Goeva
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neal M Lojek
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah Murphy
- Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
| | | | - Julia Joung
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
- Department of Brain and Cognitive Science, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
| | - Bingxu Liu
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
| | - Francesco Limone
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Leiden University Medical Center, LUMC, Leiden, the Netherlands
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ville Leinonen
- Department of Neurosurgery, Kuopio University Hospital and Institute of Clinical Medicine - Neurosurgery, University of Eastern Finland, Kuopio, Finland
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, Sue and Bill Gross Stem Cell Research Center, UCI Institute for Memory Impairments and Neurological Disorders, Institute for Immunology, University of California, Irvine, CA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
- Department of Brain and Cognitive Science, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
| | | | - Evan Z Macosko
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA.
| | - Beth Stevens
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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8
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Wells MF, Nemesh J, Ghosh S, Mitchell JM, Salick MR, Mello CJ, Meyer D, Pietilainen O, Piccioni F, Guss EJ, Raghunathan K, Tegtmeyer M, Hawes D, Neumann A, Worringer KA, Ho D, Kommineni S, Chan K, Peterson BK, Raymond JJ, Gold JT, Siekmann MT, Zuccaro E, Nehme R, Kaykas A, Eggan K, McCarroll SA. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 2023; 30:312-332.e13. [PMID: 36796362 PMCID: PMC10581885 DOI: 10.1016/j.stem.2023.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 09/16/2020] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
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Affiliation(s)
- Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jana M Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA
| | | | - Curtis J Mello
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Karrie Chan
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brant K Peterson
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Joseph J Raymond
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - John T Gold
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Marco T Siekmann
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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9
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Pietiläinen O, Trehan A, Meyer D, Mitchell J, Tegtmeyer M, Valakh V, Gebre H, Chen T, Vartiainen E, Farhi SL, Eggan K, McCarroll SA, Nehme R. Astrocytic cell adhesion genes linked to schizophrenia correlate with synaptic programs in neurons. Cell Rep 2023; 42:111988. [PMID: 36640364 PMCID: PMC10721115 DOI: 10.1016/j.celrep.2022.111988] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
The maturation of neurons and the development of synapses, although emblematic of neurons, also relies on interactions with astrocytes and other glia. Here, to study the role of glia-neuron interactions, we analyze the transcriptomes of human pluripotent stem cell (hPSC)-derived neurons, from 80 human donors, that were cultured with or without contact with glial cells. We find that the presence of astrocytes enhances synaptic gene-expression programs in neurons when in physical contact with astrocytes. These changes in neurons correlate with increased expression, in the cocultured glia, of genes that encode synaptic cell adhesion molecules. Both the neuronal and astrocyte gene-expression programs are enriched for genes associated with schizophrenia risk. Our results suggest that astrocyte-expressed genes with synaptic functions are associated with stronger expression of synaptic genetic programs in neurons, and they suggest a potential role for astrocyte-neuron interactions in schizophrenia.
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Affiliation(s)
- Olli Pietiläinen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA; Neuroscience Center, Helsinki Institute for Life Science, University of Helsinki, 00290 Helsinki, Finland.
| | - Aditi Trehan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jana Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA; Centre for Gene Therapy and Regenerative Medicine, King's College, London WC2R 2LS, UK
| | - Vera Valakh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hilena Gebre
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Theresa Chen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Emilia Vartiainen
- Neuroscience Center, Helsinki Institute for Life Science, University of Helsinki, 00290 Helsinki, Finland
| | - Samouil L Farhi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA.
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10
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Limone F, Guerra San Juan I, Mitchell JM, Smith JLM, Raghunathan K, Meyer D, Ghosh SD, Couto A, Klim JR, Joseph BJ, Gold J, Mello CJ, Nemesh J, Smith BM, Verhage M, McCarroll SA, Pietiläinen O, Nehme R, Eggan K. Efficient generation of lower induced motor neurons by coupling Ngn2 expression with developmental cues. Cell Rep 2023; 42:111896. [PMID: 36596304 PMCID: PMC10117176 DOI: 10.1016/j.celrep.2022.111896] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/01/2022] [Accepted: 12/08/2022] [Indexed: 01/03/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) are a powerful tool for disease modeling of hard-to-access tissues (such as the brain). Current protocols either direct neuronal differentiation with small molecules or use transcription-factor-mediated programming. In this study, we couple overexpression of transcription factor Neurogenin2 (Ngn2) with small molecule patterning to differentiate hPSCs into lower induced motor neurons (liMoNes/liMNs). This approach induces canonical MN markers including MN-specific Hb9/MNX1 in more than 95% of cells. liMNs resemble bona fide hPSC-derived MN, exhibit spontaneous electrical activity, express synaptic markers, and can contact muscle cells in vitro. Pooled, multiplexed single-cell RNA sequencing on 50 hPSC lines reveals reproducible populations of distinct subtypes of cervical and brachial MNs that resemble their in vivo, embryonic counterparts. Combining small molecule patterning with Ngn2 overexpression facilitates high-yield, reproducible production of disease-relevant MN subtypes, which is fundamental in propelling our knowledge of MN biology and its disruption in disease.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Leiden University Medical Center, LUMC, 2333 ZA Leiden, the Netherlands.
| | - Irune Guerra San Juan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, the Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jana M Mitchell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Janell L M Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Dia Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian J Joseph
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Departments of Pathology and Cell Biology, Columbia University Irving Medical Centre, New York, NY 10032, USA
| | - John Gold
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Curtis J Mello
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Nemesh
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brittany M Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthijs Verhage
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, the Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Steven A McCarroll
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietiläinen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ralda Nehme
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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11
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Wang AY, Sheng Y, Li W, Jung D, Junek GV, Liu H, Park J, Lee D, Wang M, Maharjan S, Kumashi S, Hao J, Zhang YS, Eggan K, Wang H. A Multimodal and Multifunctional CMOS Cellular Interfacing Array for Digital Physiology and Pathology Featuring an Ultra Dense Pixel Array and Reconfigurable Sampling Rate. IEEE Trans Biomed Circuits Syst 2022; 16:1057-1074. [PMID: 36417722 DOI: 10.1109/tbcas.2022.3224064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The article presents a fully integrated multimodal and multifunctional CMOS biosensing/actuating array chip and system for multi-dimensional cellular/tissue characterization. The CMOS chip supports up to 1,568 simultaneous parallel readout channels across 21,952 individually addressable multimodal pixels with 13 μm × 13 μm 2-D pixel pitch along with 1,568 Pt reference electrodes. These features allow the CMOS array chip to perform multimodal physiological measurements on living cell/tissue samples with both high throughput and single-cell resolution. Each pixel supports three sensing and one actuating modalities, each reconfigurable for different functionalities, in the form of full array (FA) or fast scan (FS) voltage recording schemes, bright/dim optical detection, 2-/4-point impedance sensing (ZS), and biphasic current stimulation (BCS) with adjustable stimulation area for single-cell or tissue-level stimulation. Each multi-modal pixel contains an 8.84 μm × 11 μm Pt electrode, 4.16 μm × 7.2 μm photodiode (PD), and in-pixel circuits for PD measurements and pixel selection. The chip is fabricated in a standard 130nm BiCMOS process as a proof of concept. The on-chip electrodes are constructed by unique design and in-house post-CMOS fabrication processes, including a critical Al shorting of all pixels during fabrication and Al etching after fabrication that ensures a high-yield planar electrode array on CMOS with high biocompatibility and long-term measurement reliability. For demonstration, extensive biological testing is performed with human and mouse progenitor cells, in which multidimensional biophysiological data are acquired for comprehensive cellular characterization.
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12
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Nehme R, Pietiläinen O, Artomov M, Tegtmeyer M, Valakh V, Lehtonen L, Bell C, Singh T, Trehan A, Sherwood J, Manning D, Peirent E, Malik R, Guss EJ, Hawes D, Beccard A, Bara AM, Hazelbaker DZ, Zuccaro E, Genovese G, Loboda AA, Neumann A, Lilliehook C, Kuismin O, Hamalainen E, Kurki M, Hultman CM, Kähler AK, Paulo JA, Ganna A, Madison J, Cohen B, McPhie D, Adolfsson R, Perlis R, Dolmetsch R, Farhi S, McCarroll S, Hyman S, Neale B, Barrett LE, Harper W, Palotie A, Daly M, Eggan K. The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia. Nat Commun 2022; 13:3690. [PMID: 35760976 PMCID: PMC9237031 DOI: 10.1038/s41467-022-31436-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 06/08/2022] [Indexed: 12/30/2022] Open
Abstract
It is unclear how the 22q11.2 deletion predisposes to psychiatric disease. To study this, we generated induced pluripotent stem cells from deletion carriers and controls and utilized CRISPR/Cas9 to introduce the heterozygous deletion into a control cell line. Here, we show that upon differentiation into neural progenitor cells, the deletion acted in trans to alter the abundance of transcripts associated with risk for neurodevelopmental disorders including autism. In excitatory neurons, altered transcripts encoded presynaptic factors and were associated with genetic risk for schizophrenia, including common and rare variants. To understand how the deletion contributed to these changes, we defined the minimal protein-protein interaction network that best explains gene expression alterations. We found that many genes in 22q11.2 interact in presynaptic, proteasome, and JUN/FOS transcriptional pathways. Our findings suggest that the 22q11.2 deletion impacts genes that may converge with psychiatric risk loci to influence disease manifestation in each deletion carrier.
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Affiliation(s)
- Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Olli Pietiläinen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Mykyta Artomov
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Vera Valakh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Leevi Lehtonen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Christina Bell
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Aditi Trehan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - John Sherwood
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Danielle Manning
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Emily Peirent
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Rhea Malik
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Anne M Bara
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Alexander A Loboda
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Christina Lilliehook
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Outi Kuismin
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- PEDEGO Research Unit, University of Oulu, FI-90014, Oulu, Finland
- Medical Research Center, Oulu University Hospital, FI-90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, 90220, Oulu, Finland
| | - Eija Hamalainen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Mitja Kurki
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - Andrea Ganna
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Jon Madison
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Bruce Cohen
- Department of Psychiatry, McLean Hospital, Belmont, MA, 02478, USA
| | - Donna McPhie
- Department of Psychiatry, McLean Hospital, Belmont, MA, 02478, USA
| | - Rolf Adolfsson
- Umea University, Faculty of Medicine, Department of Clinical Sciences, Psychiatry, 901 85, Umea, Sweden
| | - Roy Perlis
- Psychiatry Dept., Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ricardo Dolmetsch
- Novartis Institutes for Biomedical Research, Novartis, Cambridge, MA, 02139, USA
| | - Samouil Farhi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Steven Hyman
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ben Neale
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Stem Cell and Regenerative Biology, and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA, 02138, USA.
- BioMarin Pharmaceutical, San Rafael, CA, 94901, USA.
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13
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Wang M, Li W, Hao J, Gonzales A, Zhao Z, Flores RS, Kuang X, Mu X, Ching T, Tang G, Luo Z, Garciamendez-Mijares CE, Sahoo JK, Wells MF, Niu G, Agrawal P, Quiñones-Hinojosa A, Eggan K, Zhang YS. Molecularly cleavable bioinks facilitate high-performance digital light processing-based bioprinting of functional volumetric soft tissues. Nat Commun 2022; 13:3317. [PMID: 35680907 PMCID: PMC9184597 DOI: 10.1038/s41467-022-31002-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/30/2022] [Indexed: 12/12/2022] Open
Abstract
Digital light processing bioprinting favors biofabrication of tissues with improved structural complexity. However, soft-tissue fabrication with this method remains a challenge to balance the physical performances of the bioinks for high-fidelity bioprinting and suitable microenvironments for the encapsulated cells to thrive. Here, we propose a molecular cleavage approach, where hyaluronic acid methacrylate (HAMA) is mixed with gelatin methacryloyl to achieve high-performance bioprinting, followed by selectively enzymatic digestion of HAMA, resulting in tissue-matching mechanical properties without losing the structural complexity and fidelity. Our method allows cellular morphological and functional improvements across multiple bioprinted tissue types featuring a wide range of mechanical stiffness, from the muscles to the brain, the softest organ of the human body. This platform endows us to biofabricate mechanically precisely tunable constructs to meet the biological function requirements of target tissues, potentially paving the way for broad applications in tissue and tissue model engineering. Soft tissue fabrication using digital light processing remains challenging. Here the authors present a molecular cleavage approach to achieve high-performance bioprinting of constructs with tissue-matching mechanical properties and structural complexity.
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Affiliation(s)
- Mian Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Wanlu Li
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Jin Hao
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arthur Gonzales
- University of the Philippines Diliman, Quezon City, Metro Manila, Philippines
| | - Zhibo Zhao
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Regina Sanchez Flores
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Xiao Kuang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Xuan Mu
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Terry Ching
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA.,Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore.,Digital Manufacturing and Design Centre, Singapore University of Technology and Design, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Guosheng Tang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Zeyu Luo
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | - Carlos Ezio Garciamendez-Mijares
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | | | - Michael F Wells
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gengle Niu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Prajwal Agrawal
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
| | | | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA. .,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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14
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Boivin B, Roet KCD, Huang X, Karhohs KW, Rohban MH, Sandoe J, Wiskow O, Maeda R, Grantham A, Dornon MK, Shao J, Frost D, Baker D, Eggan K, Carpenter AE, Woolf CJ. A multiparametric activity profiling platform for neuron disease phenotyping and drug screening. Mol Biol Cell 2022; 33:ar54. [PMID: 34910584 PMCID: PMC9265164 DOI: 10.1091/mbc.e21-10-0481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 11/22/2022] Open
Abstract
Patient stem cell-derived models enable imaging of complex disease phenotypes and the development of scalable drug discovery platforms. Current preclinical methods for assessing cellular activity do not, however, capture the full intricacies of disease-induced disturbances and instead typically focus on a single parameter, which impairs both the understanding of disease and the discovery of effective therapeutics. Here, we describe a cloud-based image processing and analysis platform that captures the intricate activity profile revealed by GCaMP fluorescence recordings of intracellular calcium changes and enables the discovery of molecules that correct 153 parameters that define the amyotrophic lateral sclerosis motor neuron disease phenotype. In a high-throughput screen, we identified compounds that revert the multiparametric disease profile to that found in healthy cells, a novel and robust measure of therapeutic potential quite distinct from unidimensional screening. This platform can guide the development of therapeutics that counteract the multifaceted pathological features of diseased cellular activity.
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Affiliation(s)
- Bruno Boivin
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Kasper C D Roet
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Xuan Huang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Kyle W Karhohs
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA 02142
| | - Mohammad H Rohban
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA 02142
| | - Jack Sandoe
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Rie Maeda
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Alyssa Grantham
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Mary K Dornon
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Jenny Shao
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Devlin Frost
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Dylan Baker
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Anne E Carpenter
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA 02142
| | - Clifford J Woolf
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
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15
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Bazarek S, Johnston BR, Sten M, Mandeville R, Eggan K, Wainger BJ, Brown JM. Spinal motor neuron transplantation to enhance nerve reconstruction strategies: Towards a cell therapy. Exp Neurol 2022; 353:114054. [PMID: 35341748 DOI: 10.1016/j.expneurol.2022.114054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/06/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/19/2022]
Abstract
Nerve transfers have become a powerful intervention to restore function following devastating paralyzing injuries. A major limitation to peripheral nerve repair and reconstructive strategies is the progressive, fibrotic degeneration of the distal nerve and denervated muscle, eventually precluding recovery of these targets and thus defining a time window within which reinnervation must occur. One proven strategy in the clinic has been the sacrifice and transfer of an adjacent distal motor nerve to provide axons to occupy, and thus preserve (or "babysit"), the target muscle. However, available nearby nerves are limited in severe brachial plexus or spinal cord injury. An alternative and novel proposition is the transplantation of spinal motor neurons (SMNs) derived from human induced pluripotent stem cells (iPSCs) into the target nerve to extend their axons to occupy and preserve the targets. These cells could potentially be delivered through minimally invasive or percutaneous techniques. Several reports have demonstrated survival, functional innervation, and muscular preservation following transplantation of SMNs into rodent nerves. Advances in the generation, culture, and differentiation of human iPSCs now offer the possibility for an unlimited supply of clinical grade SMNs. This review will discuss the previous reports of peripheral SMN transplantation, outline key considerations, and propose next steps towards advancing this approach to clinic. Stem cells have garnered great enthusiasm for their potential to revolutionize medicine. However, this excitement has often led to premature clinical studies with ill-defined cell products and mechanisms of action, particularly in spinal cord injury. We believe the peripheral transplantation of a defined SMN population to address neuromuscular degeneration will be transformative in augmenting current reconstructive strategies. By thus removing the current barriers of time and distance, this strategy would dramatically enhance the potential for reconstruction and functional recovery in otherwise hopeless paralyzing injuries. Furthermore, this strategy may be used as a permanent axon replacement following destruction of lower motor neurons and would enable exogenous stimulation options, such as pacing of transplanted SMN axons in the phrenic nerve to avoid mechanical ventilation in high cervical cord injury or amyotrophic lateral sclerosis.
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Affiliation(s)
- Stanley Bazarek
- Department of Neurosurgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, United States of America; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Benjamin R Johnston
- Department of Neurosurgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, United States of America; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Margaret Sten
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ross Mandeville
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
| | - Kevin Eggan
- BioMarin Pharmaceutical Inc., San Rafael, CA, United States of America
| | - Brian J Wainger
- Departments of Neurology and Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America.
| | - Justin M Brown
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America.
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16
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Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O'Dushlaine C, Pato C, Pato M, MacArthur DG, McCarroll SA, Eggan K. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell 2022; 29:472-486.e7. [PMID: 35176222 PMCID: PMC8900618 DOI: 10.1016/j.stem.2022.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.
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Affiliation(s)
- Florian T Merkle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome - MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Colm O'Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Michele Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Daniel G MacArthur
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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17
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Ashoti A, Limone F, van Kranenburg M, Alemany A, Baak M, Vivié J, Piccioni F, Dijkers PF, Creyghton M, Eggan K, Geijsen N. Considerations and practical implications of performing a phenotypic CRISPR/Cas survival screen. PLoS One 2022; 17:e0263262. [PMID: 35176052 PMCID: PMC8853573 DOI: 10.1371/journal.pone.0263262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/12/2021] [Accepted: 01/17/2022] [Indexed: 12/26/2022] Open
Abstract
Genome-wide screens that have viability as a readout have been instrumental to identify essential genes. The development of gene knockout screens with the use of CRISPR-Cas has provided a more sensitive method to identify these genes. Here, we performed an exhaustive genome-wide CRISPR/Cas9 phenotypic rescue screen to identify modulators of cytotoxicity induced by the pioneer transcription factor, DUX4. Misexpression of DUX4 due to a failure in epigenetic repressive mechanisms underlies facioscapulohumeral muscular dystrophy (FHSD), a complex muscle disorder that thus far remains untreatable. As the name implies, FSHD generally starts in the muscles of the face and shoulder girdle. Our CRISPR/Cas9 screen revealed no key effectors other than DUX4 itself that could modulate DUX4 cytotoxicity, suggesting that treatment efforts in FSHD should be directed towards direct modulation of DUX4 itself. Our screen did however reveal some rare and unexpected genomic events, that had an important impact on the interpretation of our data. Our findings may provide important considerations for planning future CRISPR/Cas9 phenotypic survival screens.
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MESH Headings
- CRISPR-Cas Systems
- Cell Survival
- Gene Expression Regulation
- Homeodomain Proteins/antagonists & inhibitors
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Muscle Cells/metabolism
- Muscle Cells/pathology
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Myoblasts/metabolism
- Myoblasts/pathology
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Affiliation(s)
- Ator Ashoti
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
- * E-mail: (AA); (FL); (NG); (KE)
| | - Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University Cambridge, MA, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- * E-mail: (AA); (FL); (NG); (KE)
| | - Melissa van Kranenburg
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Anna Alemany
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Mirna Baak
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Judith Vivié
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
- Single Cell Discoveries, Utrecht, The Netherlands
| | | | - Pascale F. Dijkers
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Menno Creyghton
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University Cambridge, MA, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- * E-mail: (AA); (FL); (NG); (KE)
| | - Niels Geijsen
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
- * E-mail: (AA); (FL); (NG); (KE)
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18
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Fukuda A, Hazelbaker DZ, Motosugi N, Hao J, Limone F, Beccard A, Mazzucato P, Messana A, Okada C, San Juan IG, Qian M, Umezawa A, Akutsu H, Barrett LE, Eggan K. De novo DNA methyltransferases DNMT3A and DNMT3B are essential for XIST silencing for erosion of dosage compensation in pluripotent stem cells. Stem Cell Reports 2021; 16:2138-2148. [PMID: 34416176 PMCID: PMC8452533 DOI: 10.1016/j.stemcr.2021.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 12/31/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have proven to be valuable tools for both drug discovery and the development of cell-based therapies. However, the long non-coding RNA XIST, which is essential for the establishment and maintenance of X chromosome inactivation, is repressed during culture, thereby causing erosion of dosage compensation in female hPSCs. Here, we report that the de novo DNA methyltransferases DNMT3A/3B are necessary for XIST repression in female hPSCs. We found that the deletion of both genes, but not the individual genes, inhibited XIST silencing, maintained the heterochromatin mark of H3K27me3, and did not cause global overdosage in X-linked genes. Meanwhile, DNMT3A/3B deletion after XIST repression failed to restore X chromosome inactivation. Our findings revealed that de novo DNA methyltransferases are primary factors responsible for initiating erosion of dosage compensation in female hPSCs, and XIST silencing is stably maintained in a de novo DNA-methylation-independent manner.
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Affiliation(s)
- Atsushi Fukuda
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan; The Institute of Medical Science, Tokai University, Kanagawa, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan.
| | - Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nami Motosugi
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Jin Hao
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francesco Limone
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrizia Mazzucato
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angelica Messana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chisa Okada
- Support Center for Medical Research and Education, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Irune Guerra San Juan
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Menglu Qian
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Lindy E Barrett
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Eggan
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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19
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Huang X, Roet KCD, Zhang L, Brault A, Berg AP, Jefferson AB, Klug-McLeod J, Leach KL, Vincent F, Yang H, Coyle AJ, Jones LH, Frost D, Wiskow O, Chen K, Maeda R, Grantham A, Dornon MK, Klim JR, Siekmann MT, Zhao D, Lee S, Eggan K, Woolf CJ. Human amyotrophic lateral sclerosis excitability phenotype screen: Target discovery and validation. Cell Rep 2021; 35:109224. [PMID: 34107252 PMCID: PMC8209673 DOI: 10.1016/j.celrep.2021.109224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/14/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Drug development is hampered by poor target selection. Phenotypic screens using neurons differentiated from patient stem cells offer the possibility to validate known and discover novel disease targets in an unbiased fashion. To identify targets for managing hyperexcitability, a pathological feature of amyotrophic lateral sclerosis (ALS), we design a multi-step screening funnel using patient-derived motor neurons. High-content live cell imaging is used to evaluate neuronal excitability, and from a screen against a chemogenomic library of 2,899 target-annotated compounds, 67 reduce the hyperexcitability of ALS motor neurons carrying the SOD1(A4V) mutation, without cytotoxicity. Bioinformatic deconvolution identifies 13 targets that modulate motor neuron excitability, including two known ALS excitability modulators, AMPA receptors and Kv7.2/3 ion channels, constituting target validation. We also identify D2 dopamine receptors as modulators of ALS motor neuron excitability. This screen demonstrates the power of human disease cell-based phenotypic screens for identifying clinically relevant targets for neurological disorders. Motor neuron hyperexcitability is observed in both ALS patients and their iPSC-derived neurons. Combining a high-content live imaging excitability phenotypic assay, high-throughput screening against a cross-annotated chemogenomic library, and bioinformatic enrichment analysis, Huang et al. identify targets modulating the hyperexcitability of ALS patient-derived motor neurons in an unbiased manner.
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Affiliation(s)
- Xuan Huang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Kasper C D Roet
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Liying Zhang
- Medicine Design, Pfizer, Cambridge, MA 02139, USA
| | - Amy Brault
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Allison P Berg
- Rare Disease Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Anne B Jefferson
- Pfizer Centers for Therapeutic Innovation (CTI), San Francisco, CA 94080, USA
| | | | - Karen L Leach
- Pfizer Centers for Therapeutic Innovation (CTI), Cambridge, MA 02139, USA
| | | | - Hongying Yang
- Pfizer Centers for Therapeutic Innovation (CTI), Cambridge, MA 02139, USA
| | - Anthony J Coyle
- Pfizer Centers for Therapeutic Innovation (CTI), Cambridge, MA 02139, USA
| | - Lyn H Jones
- Medicine Design, Pfizer, Cambridge, MA 02139, USA
| | - Devlin Frost
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Kuchuan Chen
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Rie Maeda
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Alyssa Grantham
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mary K Dornon
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Marco T Siekmann
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Dongyi Zhao
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Seungkyu Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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20
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Klim JR, Pintacuda G, Nash LA, Guerra San Juan I, Eggan K. Connecting TDP-43 Pathology with Neuropathy. Trends Neurosci 2021; 44:424-440. [PMID: 33832769 DOI: 10.1016/j.tins.2021.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 10/01/2020] [Revised: 02/04/2021] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
Transactive response DNA-binding protein 43 kDa (TDP-43), a multifunctional nucleic acid-binding protein, is a primary component of insoluble aggregates associated with several devastating nervous system disorders; mutations in TARDBP, its encoding gene, are a cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we review established and emerging roles of TDP-43 and consider how its dysfunction impinges on RNA homeostasis in the nervous system, thereby contributing to neural degeneration. Notably, improper splicing of the axonal growth-associated factor STMN2 has recently been connected to TDP-43 dysfunction, providing a mechanistic link between TDP-43 proteinopathies and neuropathy. This review highlights how a deep understanding of the function of TDP-43 in the brain might be leveraged to develop new targeted therapies for several neurological disorders.
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Affiliation(s)
- Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Greta Pintacuda
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Leslie A Nash
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Irune Guerra San Juan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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21
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Wainger BJ, Macklin EA, Vucic S, McIlduff CE, Paganoni S, Maragakis NJ, Bedlack R, Goyal NA, Rutkove SB, Lange DJ, Rivner MH, Goutman SA, Ladha SS, Mauricio EA, Baloh RH, Simmons Z, Pothier L, Kassis SB, La T, Hall M, Evora A, Klements D, Hurtado A, Pereira JD, Koh J, Celnik PA, Chaudhry V, Gable K, Juel VC, Phielipp N, Marei A, Rosenquist P, Meehan S, Oskarsson B, Lewis RA, Kaur D, Kiskinis E, Woolf CJ, Eggan K, Weiss MD, Berry JD, David WS, Davila-Perez P, Camprodon JA, Pascual-Leone A, Kiernan MC, Shefner JM, Atassi N, Cudkowicz ME. Effect of Ezogabine on Cortical and Spinal Motor Neuron Excitability in Amyotrophic Lateral Sclerosis: A Randomized Clinical Trial. JAMA Neurol 2021; 78:186-196. [PMID: 33226425 DOI: 10.1001/jamaneurol.2020.4300] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Importance Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of the motor nervous system. Clinical studies have demonstrated cortical and spinal motor neuron hyperexcitability using transcranial magnetic stimulation and threshold tracking nerve conduction studies, respectively, although metrics of excitability have not been used as pharmacodynamic biomarkers in multi-site clinical trials. Objective To ascertain whether ezogabine decreases cortical and spinal motor neuron excitability in ALS. Design, Setting, and Participants This double-blind, placebo-controlled phase 2 randomized clinical trial sought consent from eligible participants from November 3, 2015, to November 9, 2017, and was conducted at 12 US sites within the Northeast ALS Consortium. Participants were randomized in equal numbers to a higher or lower dose of ezogabine or to an identical matched placebo, and they completed in-person visits at screening, baseline, week 6, and week 8 for clinical assessment and neurophysiological measurements. Interventions Participants were randomized to receive 600 mg/d or 900 mg/d of ezogabine or a matched placebo for 10 weeks. Main Outcomes and Measures The primary outcome was change in short-interval intracortical inhibition (SICI; SICI-1 was used in analysis to reflect stronger inhibition from an increase in amplitude) from pretreatment mean at screening and baseline to the full-dose treatment mean at weeks 6 and 8. The secondary outcomes included levels of cortical motor neuron excitability (including resting motor threshold) measured by transcranial magnetic stimulation and spinal motor neuron excitability (including strength-duration time constant) measured by threshold tracking nerve conduction studies. Results A total of 65 participants were randomized to placebo (23), 600 mg/d of ezogabine (23), and 900 mg/d of ezogabine (19 participants); 45 were men (69.2%) and the mean (SD) age was 58.3 (8.8) years. The SICI-1 increased by 53% (mean ratio, 1.53; 95% CI, 1.12-2.09; P = .009) in the 900-mg/d ezogabine group vs placebo group. The SICI-1 did not change in the 600-mg/d ezogabine group vs placebo group (mean ratio, 1.15; 95% CI, 0.87-1.52; P = .31). The resting motor threshold increased in the 600-mg/d ezogabine group vs placebo group (mean ratio, 4.61; 95% CI, 0.21-9.01; P = .04) but not in the 900-mg/d ezogabine group vs placebo group (mean ratio, 1.95; 95% CI, -2.64 to 6.54; P = .40). Ezogabine caused a dose-dependent decrease in excitability by several other metrics, including strength-duration time constant in the 900-mg/d ezogabine group vs placebo group (mean ratio, 0.73; 95% CI, 0.60 to 0.87; P < .001). Conclusions and Relevance Ezogabine decreased cortical and spinal motor neuron excitability in participants with ALS, suggesting that such neurophysiological metrics may be used as pharmacodynamic biomarkers in multisite clinical trials. Trial Registration ClinicalTrials.gov Identifier: NCT02450552.
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Affiliation(s)
- Brian J Wainger
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Department of Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA.,Harvard Stem Cell Institute, Cambridge.,Broad Institute of MIT and Harvard, Cambridge
| | - Eric A Macklin
- Harvard Medical School, Boston MA.,Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Steve Vucic
- Department of Neurology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Courtney E McIlduff
- Harvard Medical School, Boston MA.,Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Sabrina Paganoni
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA.,Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Boston, Massachusetts
| | | | - Richard Bedlack
- Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Namita A Goyal
- Department of Neurology, University of California Irvine, Irvine
| | - Seward B Rutkove
- Harvard Medical School, Boston MA.,Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Dale J Lange
- Department of Neurology, Hospital for Special Surgery, New York, New York
| | - Michael H Rivner
- Department of Neurology, Augusta University Medical Center, Augusta, Georgia
| | | | - Shafeeq S Ladha
- Department of Neurology, Barrow Neurological Institute, Phoenix, Arizona
| | | | - Robert H Baloh
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, California
| | - Zachary Simmons
- Department of Neurology, Penn State Hershey Medical Center, Hershey, Pennsylvania
| | - Lindsay Pothier
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston
| | - Sylvia Baedorf Kassis
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston
| | - Thuong La
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston
| | - Meghan Hall
- Department of Neurology, Barrow Neurological Institute, Phoenix, Arizona
| | - Armineuza Evora
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston
| | - David Klements
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston
| | - Aura Hurtado
- Harvard Medical School, Boston MA.,Department of Psychiatry, Massachusetts General Hospital, Boston
| | - Joao D Pereira
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA
| | - Joan Koh
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston
| | - Pablo A Celnik
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Vinay Chaudhry
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Karissa Gable
- Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Vern C Juel
- Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Nicolas Phielipp
- Department of Neurology, University of California Irvine, Irvine
| | - Adel Marei
- Department of Neurology, Hospital for Special Surgery, New York, New York
| | - Peter Rosenquist
- Department of Psychiatry, Augusta University Medical Center, Augusta, Georgia
| | - Sean Meehan
- School of Kinesiology, University of Michigan, Ann Arbor
| | | | - Richard A Lewis
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, California
| | - Divpreet Kaur
- Department of Neurology, Penn State Hershey Medical Center, Hershey, Pennsylvania
| | | | - Clifford J Woolf
- Harvard Medical School, Boston MA.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Kevin Eggan
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA.,Harvard Stem Cell Institute, Cambridge.,Broad Institute of MIT and Harvard, Cambridge.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | | | - James D Berry
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA
| | - William S David
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA
| | - Paula Davila-Perez
- Harvard Medical School, Boston MA.,Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Joan A Camprodon
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA.,Department of Psychiatry, Massachusetts General Hospital, Boston
| | - Alvaro Pascual-Leone
- Harvard Medical School, Boston MA.,Marcus Institute and Center for Memory Health, Hebrew SeniorLife, Boston, Massachusetts.,Institut Guttmann, Universitat Autonoma, Barcelona, Spain
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia.,Department of Neurology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Jeremy M Shefner
- Department of Neurology, Barrow Neurological Institute, Phoenix, Arizona
| | - Nazem Atassi
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA
| | - Merit E Cudkowicz
- The Sean M. Healey and AMG Center for ALS and the Neurological Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Boston.,Harvard Medical School, Boston MA
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22
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Dobrindt K, Zhang H, Das D, Abdollahi S, Prorok T, Ghosh S, Weintraub S, Genovese G, Powell SK, Lund A, Akbarian S, Eggan K, McCarroll S, Duan J, Avramopoulos D, Brennand KJ. Publicly Available hiPSC Lines with Extreme Polygenic Risk Scores for Modeling Schizophrenia. Complex Psychiatry 2021; 6:68-82. [PMID: 34883504 PMCID: PMC7923934 DOI: 10.1159/000512716] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/27/2020] [Indexed: 07/23/2023] Open
Abstract
Schizophrenia (SZ) is a common and debilitating psychiatric disorder with limited effective treatment options. Although highly heritable, risk for this polygenic disorder depends on the complex interplay of hundreds of common and rare variants. Translating the growing list of genetic loci significantly associated with disease into medically actionable information remains an important challenge. Thus, establishing platforms with which to validate the impact of risk variants in cell-type-specific and donor-dependent contexts is critical. Towards this, we selected and characterized a collection of 12 human induced pluripotent stem cell (hiPSC) lines derived from control donors with extremely low and high SZ polygenic risk scores (PRS). These hiPSC lines are publicly available at the California Institute for Regenerative Medicine (CIRM). The suitability of these extreme PRS hiPSCs for CRISPR-based isogenic comparisons of neurons and glia was evaluated across 3 independent laboratories, identifying 9 out of 12 meeting our criteria. We report a standardized resource of publicly available hiPSCs on which we hope to perform genome engineering and generate diverse kinds of functional data, with comparisons across studies facilitated by the use of a common set of genetic backgrounds.
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Affiliation(s)
- Kristina Dobrindt
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Debamitra Das
- Department of Genetic Medicine and Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sara Abdollahi
- Department of Genetic Medicine and Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tim Prorok
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Weintraub
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel K. Powell
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anina Lund
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kevin Eggan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine and Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kristen J. Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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23
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Affiliation(s)
- Yishai Avior
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel
| | - Elyad Lezmi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, and The Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel.
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24
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Avior Y, Eggan K, Benvenisty N. Retraction Notice to: Cancer-Related Mutations Identified in Primed and Naive Human Pluripotent Stem Cells. Cell Stem Cell 2020; 28:173. [PMID: 33433329 DOI: 10.1016/j.stem.2020.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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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25
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Burberry A, Wells MF, Limone F, Couto A, Smith KS, Keaney J, Gillet G, van Gastel N, Wang JY, Pietilainen O, Qian M, Eggan P, Cantrell C, Mok J, Kadiu I, Scadden DT, Eggan K. C9orf72 suppresses systemic and neural inflammation induced by gut bacteria. Nature 2020; 582:89-94. [PMID: 32483373 PMCID: PMC7416879 DOI: 10.1038/s41586-020-2288-7] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/09/2020] [Indexed: 12/11/2022]
Abstract
A hexanucleotide-repeat expansion in C9ORF72 is the most common genetic variant that contributes to amyotrophic lateral sclerosis and frontotemporal dementia1,2. The C9ORF72 mutation acts through gain- and loss-of-function mechanisms to induce pathways that are implicated in neural degeneration3-9. The expansion is transcribed into a long repetitive RNA, which negatively sequesters RNA-binding proteins5 before its non-canonical translation into neural-toxic dipeptide proteins3,4. The failure of RNA polymerase to read through the mutation also reduces the abundance of the endogenous C9ORF72 gene product, which functions in endolysosomal pathways and suppresses systemic and neural inflammation6-9. Notably, the effects of the repeat expansion act with incomplete penetrance in families with a high prevalence of amyotrophic lateral sclerosis or frontotemporal dementia, indicating that either genetic or environmental factors modify the risk of disease for each individual. Identifying disease modifiers is of considerable translational interest, as it could suggest strategies to diminish the risk of developing amyotrophic lateral sclerosis or frontotemporal dementia, or to slow progression. Here we report that an environment with reduced abundance of immune-stimulating bacteria10,11 protects C9orf72-mutant mice from premature mortality and significantly ameliorates their underlying systemic inflammation and autoimmunity. Consistent with C9orf72 functioning to prevent microbiota from inducing a pathological inflammatory response, we found that reducing the microbial burden in mutant mice with broad spectrum antibiotics-as well as transplanting gut microflora from a protective environment-attenuated inflammatory phenotypes, even after their onset. Our studies provide further evidence that the microbial composition of our gut has an important role in brain health and can interact in surprising ways with well-known genetic risk factors for disorders of the nervous system.
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Affiliation(s)
- Aaron Burberry
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael F Wells
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francesco Limone
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
| | - Alexander Couto
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin S Smith
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Keaney
- Neuroscience Therapeutic Area, New Medicines, UCB Biopharma SPRL, Braine-l'Alleud, Belgium
| | - Gaëlle Gillet
- Neuroscience Therapeutic Area, New Medicines, UCB Biopharma SPRL, Braine-l'Alleud, Belgium
| | - Nick van Gastel
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jin-Yuan Wang
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olli Pietilainen
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Menglu Qian
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Pierce Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher Cantrell
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joanie Mok
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Irena Kadiu
- Neuroscience Therapeutic Area, New Medicines, UCB Biopharma SPRL, Braine-l'Alleud, Belgium
| | - David T Scadden
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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26
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Hazelbaker DZ, Beccard A, Angelini G, Mazzucato P, Messana A, Lam D, Eggan K, Barrett LE. A multiplexed gRNA piggyBac transposon system facilitates efficient induction of CRISPRi and CRISPRa in human pluripotent stem cells. Sci Rep 2020; 10:635. [PMID: 31959800 PMCID: PMC6971260 DOI: 10.1038/s41598-020-57500-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/30/2019] [Indexed: 12/18/2022] Open
Abstract
CRISPR-Cas9-mediated gene interference (CRISPRi) and activation (CRISPRa) approaches hold promise for functional gene studies and genome-wide screens in human pluripotent stem cells (hPSCs). However, in contrast to CRISPR-Cas9 nuclease approaches, the efficiency of CRISPRi/a depends on continued expression of the dead Cas9 (dCas9) effector and guide RNA (gRNA), which can vary substantially depending on transgene design and delivery. Here, we design and generate new fluorescently labeled piggyBac (PB) vectors to deliver uniform and sustained expression of multiplexed gRNAs. In addition, we generate hPSC lines harboring AAVS1-integrated, inducible and fluorescent dCas9-KRAB and dCas9-VPR transgenes to allow for accurate quantification and tracking of cells that express both the dCas9 effectors and gRNAs. We then employ these systems to target the TCF4 gene in hPSCs and assess expression levels of the dCas9 effectors, individual gRNAs and targeted gene. We also assess the performance of our PB system for single gRNA delivery, confirming its utility for library format applications. Collectively, our results provide proof-of-principle application of a stable, multiplexed PB gRNA delivery system that can be widely exploited to further enable genome engineering studies in hPSCs. Paired with diverse CRISPR tools including our dual fluorescence CRISPRi/a cell lines, this system can facilitate functional dissection of individual genes and pathways as well as larger-scale screens for studies of development and disease.
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Affiliation(s)
- Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gabriella Angelini
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Patrizia Mazzucato
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Angelica Messana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daisy Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
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27
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Farhan SMK, Howrigan DP, Abbott LE, Klim JR, Topp SD, Byrnes AE, Churchhouse C, Phatnani H, Smith BN, Rampersaud E, Wu G, Wuu J, Shatunov A, Iacoangeli A, Khleifat AA, Mordes DA, Ghosh S, Eggan K, Rademakers R, McCauley JL, Schüle R, Züchner S, Benatar M, Taylor JP, Nalls M, Gotkine M, Shaw PJ, Morrison KE, Al-Chalabi A, Traynor B, Shaw CE, Goldstein DB, Harms MB, Daly MJ, Neale BM. Publisher Correction: Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein. Nat Neurosci 2019; 23:295. [PMID: 31857710 DOI: 10.1038/s41593-019-0570-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Sali M K Farhan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Daniel P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liam E Abbott
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute Harvard University, Cambridge, MA, USA
| | - Simon D Topp
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Andrea E Byrnes
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Claire Churchhouse
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Bradley N Smith
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Evadnie Rampersaud
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami, Miami, FL, USA
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute King's College London, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute King's College London, London, UK.,Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience King's College London, London, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute King's College London, London, UK
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute Harvard University, Cambridge, MA, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute Harvard University, Cambridge, MA, USA
| | | | | | | | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute Harvard University, Cambridge, MA, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Rebecca Schüle
- Center for Neurology and Hertie Institute für Clinical Brain Research, University of Tübingen, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Stephan Züchner
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Michael Benatar
- Department of Neurology, University of Miami, Miami, FL, USA
| | - J Paul Taylor
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA.,Data Tecnica International, Glen Echo, MD, USA
| | - Marc Gotkine
- Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Karen E Morrison
- Faculty of Medicine, University of Southampton and Department of Neurology, University Hospital Southampton, Southampton, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute King's College London, London, UK.,Department of Neurology, King's College Hospital, London, UK
| | - Bryan Traynor
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA.,Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher E Shaw
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.,Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Matthew B Harms
- Department of Neurology, Columbia University, New York, NY, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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28
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Nehme R, Zuccaro E, Ghosh SD, Li C, Sherwood JL, Pietilainen O, Barrett LE, Limone F, Worringer KA, Kommineni S, Zang Y, Cacchiarelli D, Meissner A, Adolfsson R, Haggarty S, Madison J, Muller M, Arlotta P, Fu Z, Feng G, Eggan K. Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. Cell Rep 2019; 23:2509-2523. [PMID: 29791859 PMCID: PMC6003669 DOI: 10.1016/j.celrep.2018.04.066] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/07/2018] [Accepted: 04/14/2018] [Indexed: 11/05/2022] Open
Abstract
Transcription factor programming of pluripotent stem cells (PSCs) has emerged as an approach to generate human neurons for disease modeling. However, programming schemes produce a variety of cell types, and those neurons that are made often retain an immature phenotype, which limits their utility in modeling neuronal processes, including synaptic transmission. We report that combining NGN2 programming with SMAD and WNT inhibition generates human patterned induced neurons (hpiNs). Single-cell analyses showed that hpiN cultures contained cells along a developmental continuum, ranging from poorly differentiated neuronal progenitors to well-differentiated, excitatory glutamatergic neurons. The most differentiated neurons could be identified using a CAMK2A::GFP reporter gene and exhibited greater functionality, including NMDAR-mediated synaptic transmission. We conclude that utilizing single-cell and reporter gene approaches for selecting successfully programmed cells for study will greatly enhance the utility of hpiNs and other programmed neuronal populations in the modeling of nervous system disorders.
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Affiliation(s)
- Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sulagna Dia Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chenchen Li
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - John L Sherwood
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Francesco Limone
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Sravya Kommineni
- Novartis Institutes for Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Ying Zang
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Davide Cacchiarelli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alex Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rolf Adolfsson
- Umea University, Faculty of Medicine, Department of Clinical Sciences, Psychiatry, 901 85 Umea, Sweden
| | - Stephen Haggarty
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jon Madison
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthias Muller
- Novartis Institutes for Biomedical Research, Novartis, 4056 Basel, Switzerland
| | - Paola Arlotta
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zhanyan Fu
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; McGovern Institute for Brain Research in the Department of Brain and Cognitive Sciences at MIT, Cambridge, MA 02139, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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29
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Farhan SMK, Howrigan DP, Abbott LE, Klim JR, Topp SD, Byrnes AE, Churchhouse C, Phatnani H, Smith BN, Rampersaud E, Wu G, Wuu J, Shatunov A, Iacoangeli A, Al Khleifat A, Mordes DA, Ghosh S, Eggan K, Rademakers R, McCauley JL, Schüle R, Züchner S, Benatar M, Taylor JP, Nalls M, Gotkine M, Shaw PJ, Morrison KE, Al-Chalabi A, Traynor B, Shaw CE, Goldstein DB, Harms MB, Daly MJ, Neale BM. Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein. Nat Neurosci 2019; 22:1966-1974. [PMID: 31768050 PMCID: PMC6919277 DOI: 10.1038/s41593-019-0530-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
To discover novel genes underlying amyotrophic lateral sclerosis (ALS), we aggregated exomes from 3,864 cases and 7,839 ancestry-matched controls. We observed a significant excess of rare protein-truncating variants among ALS cases, and these variants were concentrated in constrained genes. Through gene level analyses, we replicated known ALS genes including SOD1, NEK1 and FUS. We also observed multiple distinct protein-truncating variants in a highly constrained gene, DNAJC7. The signal in DNAJC7 exceeded genome-wide significance, and immunoblotting assays showed depletion of DNAJC7 protein in fibroblasts in a patient with ALS carrying the p.Arg156Ter variant. DNAJC7 encodes a member of the heat-shock protein family, HSP40, which, along with HSP70 proteins, facilitates protein homeostasis, including folding of newly synthesized polypeptides and clearance of degraded proteins. When these processes are not regulated, misfolding and accumulation of aberrant proteins can occur and lead to protein aggregation, which is a pathological hallmark of neurodegeneration. Our results highlight DNAJC7 as a novel gene for ALS.
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Affiliation(s)
- Sali M K Farhan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Daniel P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liam E Abbott
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Simon D Topp
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Andrea E Byrnes
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Claire Churchhouse
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Bradley N Smith
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Evadnie Rampersaud
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami, Miami, FL, USA
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Rebecca Schüle
- Center for Neurology and Hertie Institute für Clinical Brain Research, University of Tübingen, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Stephan Züchner
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Michael Benatar
- Department of Neurology, University of Miami, Miami, FL, USA
| | - J Paul Taylor
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Marc Gotkine
- Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Karen E Morrison
- Faculty of Medicine, University of Southampton and Department of Neurology, University Hospital Southampton, Southampton, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Neurology, King's College Hospital, London, UK
| | - Bryan Traynor
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher E Shaw
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Matthew B Harms
- Department of Neurology, Columbia University, New York, NY, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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30
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Avior Y, Eggan K, Benvenisty N. RETRACTED: Cancer-Related Mutations Identified in Primed and Naive Human Pluripotent Stem Cells. Cell Stem Cell 2019; 25:456-461. [DOI: 10.1016/j.stem.2019.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Groff AF, Resetkova N, DiDomenico F, Sakkas D, Penzias A, Rinn JL, Eggan K. RNA-seq as a tool for evaluating human embryo competence. Genome Res 2019; 29:1705-1718. [PMID: 31548358 PMCID: PMC6771404 DOI: 10.1101/gr.252981.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 05/23/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023]
Abstract
The majority of embryos created through in vitro fertilization (IVF) do not implant. It seems plausible that rates of implantation would improve if we had a better understanding of molecular factors affecting embryo competence. Currently, the process of selecting an embryo for uterine transfer uses an ad hoc combination of morphological criteria, the kinetics of development, and genetic testing for aneuploidy. However, no single criterion can ensure selection of a viable embryo. In contrast, RNA-sequencing (RNA-seq) of embryos could yield high-dimensional data, which may provide additional insight and illuminate the discrepancies among current selection criteria. Recent advances enabling the production of RNA-seq libraries from single cells have facilitated the application of this technique to the study of transcriptional events in early human development. However, these studies have not assessed the quality of their constituent embryos relative to commonly used embryological criteria. Here, we perform proof-of-principle advancement to embryo selection procedures by generating RNA-seq libraries from a trophectoderm biopsy as well as the remaining whole embryo. We combine state-of-the-art embryological methods with low-input RNA-seq to develop the first transcriptome-wide approach for assessing embryo competence. Specifically, we show the capacity of RNA-seq as a promising tool in preimplantation screening by showing that biopsies of an embryo can capture valuable information available in the whole embryo from which they are derived. Furthermore, we show that this technique can be used to generate a RNA-based digital karyotype and to identify candidate competence-associated genes. Together, these data establish the foundation for a future RNA-based diagnostic in IVF.
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Affiliation(s)
- Abigail F Groff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nina Resetkova
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Boston IVF, Waltham, Massachusetts 02451, USA.,Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Francesca DiDomenico
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | | | - Alan Penzias
- Boston IVF, Waltham, Massachusetts 02451, USA.,Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Biochemistry, BioFrontiers, University of Colorado Boulder, Boulder, Colorado 80301, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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32
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Klim JR, Williams LA, Limone F, Guerra San Juan I, Davis-Dusenbery BN, Mordes DA, Burberry A, Steinbaugh MJ, Gamage KK, Kirchner R, Moccia R, Cassel SH, Chen K, Wainger BJ, Woolf CJ, Eggan K. ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. Nat Neurosci 2019; 22:167-179. [PMID: 30643292 PMCID: PMC7153761 DOI: 10.1038/s41593-018-0300-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [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: 05/25/2018] [Accepted: 11/13/2018] [Indexed: 01/18/2023]
Abstract
The findings that amyotrophic lateral sclerosis (ALS) patients almost universally display pathological mislocalization of the RNA-binding protein TDP-43 and that mutations in its gene cause familial ALS have nominated altered RNA metabolism as a disease mechanism. However, the RNAs regulated by TDP-43 in motor neurons and their connection to neuropathy remain to be identified. Here we report transcripts whose abundances in human motor neurons are sensitive to TDP-43 depletion. Notably, expression of STMN2, which encodes a microtubule regulator, declined after TDP-43 knockdown and TDP-43 mislocalization as well as in patient-specific motor neurons and postmortem patient spinal cord. STMN2 loss upon reduced TDP-43 function was due to altered splicing, which is functionally important, as we show STMN2 is necessary for normal axonal outgrowth and regeneration. Notably, post-translational stabilization of STMN2 rescued neurite outgrowth and axon regeneration deficits induced by TDP-43 depletion. We propose that restoring STMN2 expression warrants examination as a therapeutic strategy for ALS.
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Affiliation(s)
- Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luis A Williams
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Q-State Biosciences, Cambridge, MA, USA
| | - Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
| | - Irune Guerra San Juan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brandi N Davis-Dusenbery
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Seven Bridges Genomics, Cambridge, MA, USA
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron Burberry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Kanchana K Gamage
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Amgen Research, Amgen, Inc., Cambridge, MA, USA
| | - Rory Kirchner
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Rob Moccia
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Pfizer, Inc., Cambridge, MA, USA
| | - Seth H Cassel
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Medical Scientist Training Program, Harvard Medical School, Boston, MA, USA
| | - Kuchuan Chen
- FM Kirby Neurobiology Center, Boston Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Brian J Wainger
- FM Kirby Neurobiology Center, Boston Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Massachusetts General Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Clifford J Woolf
- FM Kirby Neurobiology Center, Boston Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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33
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Thams S, Lowry ER, Larraufie MH, Spiller KJ, Li H, Williams DJ, Hoang P, Jiang E, Williams LA, Sandoe J, Eggan K, Lieberam I, Kanning KC, Stockwell BR, Henderson CE, Wichterle H. A Stem Cell-Based Screening Platform Identifies Compounds that Desensitize Motor Neurons to Endoplasmic Reticulum Stress. Mol Ther 2019; 27:87-101. [PMID: 30446391 PMCID: PMC6318783 DOI: 10.1016/j.ymthe.2018.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 05/08/2018] [Revised: 10/07/2018] [Accepted: 10/16/2018] [Indexed: 02/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease selectively targeting motor neurons in the brain and spinal cord. The reasons for differential motor neuron susceptibility remain elusive. We developed a stem cell-based motor neuron assay to study cell-autonomous mechanisms causing motor neuron degeneration, with implications for ALS. A small-molecule screen identified cyclopiazonic acid (CPA) as a stressor to which stem cell-derived motor neurons were more sensitive than interneurons. CPA induced endoplasmic reticulum stress and the unfolded protein response. Furthermore, CPA resulted in an accelerated degeneration of motor neurons expressing human superoxide dismutase 1 (hSOD1) carrying the ALS-causing G93A mutation, compared to motor neurons expressing wild-type hSOD1. A secondary screen identified compounds that alleviated CPA-mediated motor neuron degeneration: three kinase inhibitors and tauroursodeoxycholic acid (TUDCA), a bile acid derivative. The neuroprotective effects of these compounds were validated in human stem cell-derived motor neurons carrying a mutated SOD1 allele (hSOD1A4V). Moreover, we found that the administration of TUDCA in an hSOD1G93A mouse model of ALS reduced muscle denervation. Jointly, these results provide insights into the mechanisms contributing to the preferential susceptibility of ALS motor neurons, and they demonstrate the utility of stem cell-derived motor neurons for the discovery of new neuroprotective compounds.
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Affiliation(s)
- Sebastian Thams
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.
| | - Emily Rhodes Lowry
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Marie-Hélène Larraufie
- Department of Biological Sciences and Department of Chemistry, Columbia University, Northwest Corner Building, MC4846, 550 West 120th Street, New York, NY 10027, USA
| | - Krista J Spiller
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Hai Li
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Damian J Williams
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, 650 West 168th Street, New York, NY, USA
| | - Phuong Hoang
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Elise Jiang
- Department of Biological Sciences and Department of Chemistry, Columbia University, Northwest Corner Building, MC4846, 550 West 120th Street, New York, NY 10027, USA
| | - Luis A Williams
- Department of Stem Cell and Regenerative Biology, Harvard University, MA 02138, USA
| | - Jackson Sandoe
- Department of Stem Cell and Regenerative Biology, Harvard University, MA 02138, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, MA 02138, USA
| | - Ivo Lieberam
- Centre for Stem Cells and Regenerative Medicine and MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 9RT, UK
| | - Kevin C Kanning
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, Northwest Corner Building, MC4846, 550 West 120th Street, New York, NY 10027, USA
| | - Christopher E Henderson
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA; Departments of Neuroscience, Rehabilitation and Regenerative Medicine, and Neurology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.
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34
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Ichida JK, Staats KA, Davis-Dusenbery BN, Clement K, Galloway KE, Babos KN, Shi Y, Son EY, Kiskinis E, Atwater N, Gu H, Gnirke A, Meissner A, Eggan K. Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons. Development 2018; 145:dev.168617. [PMID: 30337375 DOI: 10.1242/dev.168617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/15/2018] [Indexed: 01/11/2023]
Abstract
Advances in stem cell science allow the production of different cell types in vitro either through the recapitulation of developmental processes, often termed 'directed differentiation', or the forced expression of lineage-specific transcription factors. Although cells produced by both approaches are increasingly used in translational applications, their quantitative similarity to their primary counterparts remains largely unresolved. To investigate the similarity between in vitro-derived and primary cell types, we harvested and purified mouse spinal motor neurons and compared them with motor neurons produced by transcription factor-mediated lineage conversion of fibroblasts or directed differentiation of pluripotent stem cells. To enable unbiased analysis of these motor neuron types and their cells of origin, we then subjected them to whole transcriptome and DNA methylome analysis by RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS). Despite major differences in methodology, lineage conversion and directed differentiation both produce cells that closely approximate the primary motor neuron state. However, we identify differences in Fas signaling, the Hox code and synaptic gene expression between lineage-converted and directed differentiation motor neurons that affect their utility in translational studies.
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Affiliation(s)
- Justin K Ichida
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA.,Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kim A Staats
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brandi N Davis-Dusenbery
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Kendell Clement
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kate E Galloway
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kimberly N Babos
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yingxiao Shi
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esther Y Son
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Evangelos Kiskinis
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Nicholas Atwater
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA .,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
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35
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Srikanth P, Lagomarsino VN, Pearse RV, Liao M, Ghosh S, Nehme R, Seyfried N, Eggan K, Young-Pearse TL. Convergence of independent DISC1 mutations on impaired neurite growth via decreased UNC5D expression. Transl Psychiatry 2018; 8:245. [PMID: 30410030 PMCID: PMC6224395 DOI: 10.1038/s41398-018-0281-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022] Open
Abstract
The identification of convergent phenotypes in different models of psychiatric illness highlights robust phenotypes that are more likely to be implicated in disease pathophysiology. Here, we utilize human iPSCs harboring distinct mutations in DISC1 that have been found in families with major mental illness. One mutation was engineered to mimic the consequences on DISC1 protein of a balanced translocation linked to mental illness in a Scottish pedigree; the other mutation was identified in an American pedigree with a high incidence of mental illness. Directed differentiation of these iPSCs using NGN2 expression shows rapid conversion to a homogenous population of mature excitatory neurons. Both DISC1 mutations result in reduced DISC1 protein expression, and show subtle effects on certain presynaptic proteins. In addition, RNA sequencing and qPCR showed decreased expression of UNC5D, DPP10, PCDHA6, and ZNF506 in neurons with both DISC1 mutations. Longitudinal analysis of neurite outgrowth revealed decreased neurite outgrowth in neurons with each DISC1 mutation, which was mimicked by UNC5D knockdown and rescued by transient upregulation of endogenous UNC5D. This study shows a narrow range of convergent phenotypes of two mutations found in families with major mental illness, and implicates dysregulated netrin signaling in DISC1 biology.
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Affiliation(s)
- Priya Srikanth
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Valentina N. Lagomarsino
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Richard V. Pearse
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Meichen Liao
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Sulagna Ghosh
- 000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Ralda Nehme
- 000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Nicholas Seyfried
- 0000 0001 0941 6502grid.189967.8Department of Biochemistry, Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Kevin Eggan
- 000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Tracy L. Young-Pearse
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
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36
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McPhie DL, Nehme R, Ravichandran C, Babb SM, Ghosh SD, Staskus A, Kalinowski A, Kaur R, Douvaras P, Du F, Ongur D, Fossati V, Eggan K, Cohen BM. Oligodendrocyte differentiation of induced pluripotent stem cells derived from subjects with schizophrenias implicate abnormalities in development. Transl Psychiatry 2018; 8:230. [PMID: 30352993 PMCID: PMC6199264 DOI: 10.1038/s41398-018-0284-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022] Open
Abstract
Abnormalities of brain connectivity and signal transduction are consistently observed in individuals with schizophrenias (SZ). Underlying these anomalies, convergent in vivo, post mortem, and genomic evidence suggest abnormal oligodendrocyte (OL) development and function and lower myelination in SZ. Our primary hypothesis was that there would be abnormalities in the number of induced pluripotent stem (iPS) cell-derived OLs from subjects with SZ. Our secondary hypothesis was that these in vitro abnormalities would correlate with measures of white matter (WM) integrity and myelination in the same subjects in vivo, estimated from magnetic resonance imaging. Six healthy control (HC) and six SZ iPS cell lines, derived from skin fibroblasts from well-characterized subjects, were differentiated into OLs. FACS analysis of the oligodendrocyte-specific surface, glycoprotein O4, was performed at three time points of development (days 65, 75, and 85) to quantify the number of late oligodendrocyte progenitor cells (OPCs) and OLs in each line. Significantly fewer O4-positive cells developed from SZ versus HC lines (95% CI 1.0: 8.6, F1,10 = 8.06, p = 0.02). The difference was greater when corrected for age (95% CI 5.4:10.4, F1,8 = 53.6, p < 0.001). A correlation between myelin content in WM in vivo, estimated by magnetization transfer ratio (MTR) and number of O4-positive cells in vitro was also observed across all time points (F1,9 = 4.3, p = 0.07), reaching significance for mature OLs at day 85 in culture (r = 0.70, p < 0.02). Low production of OPCs may be a contributing mechanism underlying WM reduction in SZ.
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Affiliation(s)
- Donna L. McPhie
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Ralda Nehme
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA
| | - Caitlin Ravichandran
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Suzann M. Babb
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Sulagna Dia Ghosh
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA
| | - Alexandra Staskus
- 0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Amy Kalinowski
- 0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Rupinderjit Kaur
- 0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Panagiotis Douvaras
- Blue Rock Therapeutics, Alexandria Center for Life Science, 450 E 29th Street, Suite 504, New York, NY 10016 USA
| | - Fei Du
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Dost Ongur
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
| | - Valentina Fossati
- 0000 0004 5906 3313grid.430819.7The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019 USA
| | - Kevin Eggan
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Bruce M. Cohen
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,0000 0000 8795 072Xgrid.240206.2McLean Hospital, 115 Mill St., Belmont, MA 02478 USA
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37
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Fan LZ, Nehme R, Adam Y, Jung ES, Wu H, Eggan K, Arnold DB, Cohen AE. All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition. Nat Methods 2018; 15:823-831. [PMID: 30275587 PMCID: PMC6204345 DOI: 10.1038/s41592-018-0142-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 07/15/2018] [Indexed: 02/02/2023]
Abstract
Optical assays of synaptic strength would greatly facilitate studies of neuronal transmission and its dysregulation in disease. Here we introduce a genetic toolbox for all-optical interrogation of synaptic electrophysiology (‘synOptopatch’) via mutually exclusive expression of a channelrhodopsin actuator and an archaerhodopsin-derived voltage indicator. Optically induced activity in the channelrhodopsin-expressing neurons generated excitatory and inhibitory post-synaptic potentials which were optically resolved in the reporter-expressing neurons. We further developed a yellow spine-targeted Ca2+ indicator to localize optogenetically triggered synaptic inputs. We demonstrated synOptopatch recordings in cultured rodent neurons and in acute rodent brain slice. In synOptopatch measurements of primary rodent cultures, acute ketamine administration suppressed disynaptic inhibitory feedbacks, mimicking the effect of this drug on network function in both rodents and humans. We localized this action of ketamine to excitatory synapses onto interneurons. These results establish an in vitro all-optical model of disynaptic disinhibition, a synaptic defect hypothesized in schizophrenia-associated psychosis.
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Affiliation(s)
- Linlin Z Fan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ralda Nehme
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Eun Sun Jung
- Department of Biology, Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Hao Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Don B Arnold
- Department of Biology, Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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38
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Mordes DA, Prudencio M, Goodman LD, Klim JR, Moccia R, Limone F, Pietilainen O, Chowdhary K, Dickson DW, Rademakers R, Bonini NM, Petrucelli L, Eggan K. Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients. Acta Neuropathol Commun 2018; 6:55. [PMID: 29973287 PMCID: PMC6031111 DOI: 10.1186/s40478-018-0555-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 06/17/2018] [Indexed: 01/07/2023] Open
Abstract
A hexanucleotide (GGGGCC) repeat expansion in C9ORF72 is the most common genetic contributor to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Reduced expression of the C9ORF72 gene product has been proposed as a potential contributor to disease pathogenesis. Additionally, repetitive RNAs and dipeptide repeat proteins (DPRs), such as poly-GR, can be produced by this hexanucleotide expansion that disrupt a number of cellular processes, potentially contributing to neural degeneration. To better discern which of these mechanisms leads to disease-associated changes in patient brains, we analyzed gene expression data generated from the cortex and cerebellum. We found that transcripts encoding heat shock proteins (HSPs) regulated by the HSF1 transcription factor were significantly induced in C9ORF72-ALS/FTLD patients relative to both sporadic ALS/FTLD cases and controls. Treatment of human neurons with chemically synthesized DPRs was sufficient to activate a similar transcriptional response. Expression of GGGGCC repeats and also poly-GR in the brains of Drosophila lead to the upregulation of HSF1 and the same highly-conserved HSPs. Additionally, HSF1 was a modifier of poly-GR toxicity in Drosophila. Our results suggest that the expression of DPRs are associated with upregulation of HSF1 and activation of a heat shock response in C9ORF72-ALS/FTLD.
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Affiliation(s)
- Daniel A. Mordes
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,0000 0004 0386 9924grid.32224.35Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Lindsey D. Goodman
- 0000 0004 1936 8972grid.25879.31Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Joseph R. Klim
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Rob Moccia
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,Present address: Pfizer, Cambridge, MA 02139 USA
| | - Francesco Limone
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Olli Pietilainen
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Kaitavjeet Chowdhary
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Nancy M. Bonini
- 0000 0004 1936 8972grid.25879.31Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | | | - Kevin Eggan
- 000000041936754Xgrid.38142.3cDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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39
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Zhang Y, Burberry A, Wang JY, Sandoe J, Ghosh S, Udeshi ND, Svinkina T, Mordes DA, Mok J, Charlton M, Li QZ, Carr SA, Eggan K. The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis. Genes Dev 2018; 32:929-943. [PMID: 29950492 PMCID: PMC6075033 DOI: 10.1101/gad.313932.118] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/21/2018] [Indexed: 12/13/2022]
Abstract
A mutation in C9ORF72 is the most common genetic contributor to ALS. Zhang et al. found that C9ORF72's long isoform complexes with and stabilizes SMCR8. Smcr8 loss-of-function mutant mice exhibit a loss of tolerance for many nervous system autoantigens and increased lysosomal exocytosis in mutant macrophages. While a mutation in C9ORF72 is the most common genetic contributor to amyotrophic lateral sclerosis (ALS), much remains to be learned concerning the function of the protein normally encoded at this locus. To elaborate further on functions for C9ORF72, we used quantitative mass spectrometry-based proteomics to identify interacting proteins in motor neurons and found that its long isoform complexes with and stabilizes SMCR8, which further enables interaction with WDR41. To study the organismal and cellular functions for this tripartite complex, we generated Smcr8 loss-of-function mutant mice and found that they developed phenotypes also observed in C9orf72 loss-of-function animals, including autoimmunity. Along with a loss of tolerance for many nervous system autoantigens, we found increased lysosomal exocytosis in Smcr8 mutant macrophages. In addition to elevated surface Lamp1 (lysosome-associated membrane protein 1) expression, we also observed enhanced secretion of lysosomal components—phenotypes that we subsequently observed in C9orf72 loss-of-function macrophages. Overall, our findings demonstrate that C9ORF72 and SMCR8 have interdependent functions in suppressing autoimmunity as well as negatively regulating lysosomal exocytosis—processes of potential importance to ALS.
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Affiliation(s)
- Yingying Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aaron Burberry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jin-Yuan Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jackson Sandoe
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Namrata D Udeshi
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tanya Svinkina
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Joanie Mok
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Maura Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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Vogt MA, Ehsaei Z, Knuckles P, Higginbottom A, Helmbrecht MS, Kunath T, Eggan K, Williams LA, Shaw PJ, Wurst W, Floss T, Huber AB, Taylor V. TDP-43 induces p53-mediated cell death of cortical progenitors and immature neurons. Sci Rep 2018; 8:8097. [PMID: 29802307 PMCID: PMC5970242 DOI: 10.1038/s41598-018-26397-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a key player in neurodegenerative diseases including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Accumulation of TDP-43 is associated with neuronal death in the brain. How increased and disease-causing mutant forms of TDP-43 induce cell death remains unclear. Here we addressed the role of TDP-43 during neural development and show that reduced TDP-43 causes defects in neural stem/progenitor cell proliferation but not cell death. However, overexpression of wild type and TDP-43A315T proteins induce p53-dependent apoptosis of neural stem/progenitors and human induced pluripotent cell (iPS)-derived immature cortical neurons. We show that TDP-43 induces expression of the proapoptotic BH3-only genes Bbc3 and Bax, and that p53 inhibition rescues TDP-43 induced cell death of embryonic mouse, and human cortical neurons, including those derived from TDP-43G298S ALS patient iPS cells. Hence, an increase in wild type and mutant TDP-43 induces p53-dependent cell death in neural progenitors developing neurons and this can be rescued. These findings may have important implications for accumulated or mutant TDP-43 induced neurodegenerative diseases.
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Affiliation(s)
- Miriam A Vogt
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland.,Ludwig-Maximilians University Munich, Feodor-Lynen-Strasse 17, 81377, München, Germany
| | - Zahra Ehsaei
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | | | - Tilo Kunath
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Kevin Eggan
- Harvard Stem Cell Institute, Harvard University, Howard Hughes Medical Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Luis A Williams
- Harvard Stem Cell Institute, Harvard University, Howard Hughes Medical Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385A Glossop Road, Sheffield, S10 2HQ, UK
| | - Wolfgang Wurst
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Thomas Floss
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Andrea B Huber
- Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.,ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland.
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41
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Hazelbaker DZ, Beccard A, Bara AM, Dabkowski N, Messana A, Mazzucato P, Lam D, Manning D, Eggan K, Barrett LE. A Scaled Framework for CRISPR Editing of Human Pluripotent Stem Cells to Study Psychiatric Disease. Stem Cell Reports 2018; 9:1315-1327. [PMID: 29020615 PMCID: PMC5639480 DOI: 10.1016/j.stemcr.2017.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Scaling of CRISPR-Cas9 technology in human pluripotent stem cells (hPSCs) represents an important step for modeling complex disease and developing drug screens in human cells. However, variables affecting the scaling efficiency of gene editing in hPSCs remain poorly understood. Here, we report a standardized CRISPR-Cas9 approach, with robust benchmarking at each step, to successfully target and genotype a set of psychiatric disease-implicated genes in hPSCs and provide a resource of edited hPSC lines for six of these genes. We found that transcriptional state and nucleosome positioning around targeted loci was not correlated with editing efficiency. However, editing frequencies varied between different hPSC lines and correlated with genomic stability, underscoring the need for careful cell line selection and unbiased assessments of genomic integrity. Together, our step-by-step quantification and in-depth analyses provide an experimental roadmap for scaling Cas9-mediated editing in hPSCs to study psychiatric disease, with broader applicability for other polygenic diseases.
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Affiliation(s)
- Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne M Bara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicole Dabkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Angelica Messana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrizia Mazzucato
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daisy Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Danielle Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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42
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Kiskinis E, Kralj JM, Zou P, Weinstein EN, Zhang H, Tsioras K, Wiskow O, Ortega JA, Eggan K, Cohen AE. All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. Stem Cell Reports 2018; 10:1991-2004. [PMID: 29779896 PMCID: PMC5993648 DOI: 10.1016/j.stemcr.2018.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 11/26/2022] Open
Abstract
Human induced pluripotent stem cell (iPSC)-derived neurons are an attractive substrate for modeling disease, yet the heterogeneity of these cultures presents a challenge for functional characterization by manual patch-clamp electrophysiology. Here, we describe an optimized all-optical electrophysiology, “Optopatch,” pipeline for high-throughput functional characterization of human iPSC-derived neuronal cultures. We demonstrate the method in a human iPSC-derived motor neuron (iPSC-MN) model of amyotrophic lateral sclerosis (ALS). In a comparison of iPSC-MNs with an ALS-causing mutation (SOD1 A4V) with their genome-corrected controls, the mutants showed elevated spike rates under weak or no stimulus and greater likelihood of entering depolarization block under strong optogenetic stimulus. We compared these results with numerical simulations of simple conductance-based neuronal models and with literature results in this and other iPSC-based models of ALS. Our data and simulations suggest that deficits in slowly activating potassium channels may underlie the changes in electrophysiology in the SOD1 A4V mutation. All-optical electrophysiology enables high-throughput assays in hiPSC-derived neurons Neurons derived from ALS patients fire differently from genome-corrected controls A deficit in the Kv7 potassium current can explain the difference in firing
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Affiliation(s)
- Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peng Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eli N Weinstein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Hongkang Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Konstantinos Tsioras
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Alberto Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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43
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Andrews PW, Ben-David U, Benvenisty N, Coffey P, Eggan K, Knowles BB, Nagy A, Pera M, Reubinoff B, Rugg-Gunn PJ, Stacey GN. Assessing the Safety of Human Pluripotent Stem Cells and Their Derivatives for Clinical Applications. Stem Cell Reports 2018; 9:1-4. [PMID: 28700896 DOI: 10.1016/j.stemcr.2017.05.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 01/09/2023] Open
Abstract
Pluripotent stem cells may acquire genetic and epigenetic variants during culture following their derivation. At a conference organized by the International Stem Cell Initiative, and held at The Jackson Laboratory, Bar Harbor, Maine, October 2016, participants discussed how the appearance of such variants can be monitored and minimized and, crucially, how their significance for the safety of therapeutic applications of these cells can be assessed. A strong recommendation from the meeting was that an international advisory group should be set up to review the genetic and epigenetic changes observed in human pluripotent stem cell lines and establish a framework for evaluating the risks that they may pose for clinical use.
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Affiliation(s)
- Peter W Andrews
- Department of Biomedical Science, Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK.
| | | | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Peter Coffey
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Neuroscience Research Institute, University of California, Santa Barbara, CA 93117, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Barbara B Knowles
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Siriraj Center of Excellence for Stem Cell Research, Mahidol University, Bangkok 10700, Thailand
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada; Monash University, ARMI, Melbourne, Victoria 3800, Australia
| | - Martin Pera
- Stem Cells Australia, Melbourne Brain Centre, The University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Anatomy and Neurosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Florey Neuroscience & Mental Health Institute, Melbourne, VIC 3052, Australia; Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
| | - Benjamin Reubinoff
- Department of Obstetrics and Gynecology, Hadassah Human Embryonic Stem Cells Research Center, The Goldyne-Savad Institute of Gene Therapy, Hadassah-Hebrew University Hospital, Jerusalem 91120, Israel
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Glyn N Stacey
- UK Stem Cell Bank, Advanced Therapies Division, NIBSC-MHRA, London EN6 3QG, UK
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44
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Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Abecasis G, Arguello PA, Blangero J, Boehnke M, Daly MJ, Eggan K, Geschwind DH, Glahn DC, Goldstein DB, Gur RE, Handsaker RE, McCarroll SA, Ophoff RA, Palotie A, Pato CN, Sabatti C, State MW, Willsey AJ, Hyman SE, Addington AM, Lehner T, Freimer NB. Publisher Correction: Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci 2018; 21:1017. [PMID: 29549319 DOI: 10.1038/s41593-018-0102-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the consortium authorship and corresponding authors were not presented correctly. In the PDF and print versions, the Whole Genome Sequencing for Psychiatric Disorders (WGSPD) consortium was missing from the author list at the beginning of the paper, where it should have appeared as the seventh author; it was present in the author list at the end of the paper, but the footnote directing readers to the Supplementary Note for a list of members was missing. In the HTML version, the consortium was listed as the last author instead of as the seventh, and the line directing readers to the Supplementary Note for a list of members appeared at the end of the paper under Author Information but not in association with the consortium name itself. Also, this line stated that both member names and affiliations could be found in the Supplementary Note; in fact, only names are given. In all versions of the paper, the corresponding author symbols were attached to A. Jeremy Willsey, Steven E. Hyman, Anjene M. Addington and Thomas Lehner; they should have been attached, respectively, to Steven E. Hyman, Anjene M. Addington, Thomas Lehner and Nelson B. Freimer. As a result of this shift, the respective contact links in the HTML version did not lead to the indicated individuals. The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Donna M Werling
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Goncalo Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, Brownsville, TX, USA
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - Raquel E Gur
- Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roel A Ophoff
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carlos N Pato
- Department of Psychiatry, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chiara Sabatti
- Department of Health Research and Policy, Division of Biostatistics, Stanford University, Stanford, CA, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Steven E Hyman
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | | | - Thomas Lehner
- National Institute of Mental Health, Bethesda, MD, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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45
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Burberry A, Suzuki N, Wang JY, Moccia R, Mordes DA, Stewart MH, Suzuki-Uematsu S, Ghosh S, Singh A, Merkle FT, Koszka K, Li QZ, Zon L, Rossi DJ, Trowbridge JJ, Notarangelo LD, Eggan K. Loss-of-function mutations in the C9ORF72 mouse ortholog cause fatal autoimmune disease. Sci Transl Med 2017; 8:347ra93. [PMID: 27412785 DOI: 10.1126/scitranslmed.aaf6038] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/21/2016] [Indexed: 12/14/2022]
Abstract
C9ORF72 mutations are found in a significant fraction of patients suffering from amyotrophic lateral sclerosis and frontotemporal dementia, yet the function of the C9ORF72 gene product remains poorly understood. We show that mice harboring loss-of-function mutations in the ortholog of C9ORF72 develop splenomegaly, neutrophilia, thrombocytopenia, increased expression of inflammatory cytokines, and severe autoimmunity, ultimately leading to a high mortality rate. Transplantation of mutant mouse bone marrow into wild-type recipients was sufficient to recapitulate the phenotypes observed in the mutant animals, including autoimmunity and premature mortality. Reciprocally, transplantation of wild-type mouse bone marrow into mutant mice improved their phenotype. We conclude that C9ORF72 serves an important function within the hematopoietic system to restrict inflammation and the development of autoimmunity.
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Affiliation(s)
- Aaron Burberry
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Naoki Suzuki
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jin-Yuan Wang
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rob Moccia
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel A Mordes
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Morag H Stewart
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Satomi Suzuki-Uematsu
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sulagna Ghosh
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ajay Singh
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Florian T Merkle
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn Koszka
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Quan-Zhen Li
- Departments of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Leonard Zon
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Harvard Medical School, Boston, MA 02115, USA
| | - Derrick J Rossi
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA. Harvard Medical School, Boston, MA 02115, USA
| | | | - Luigi D Notarangelo
- Harvard Medical School, Boston, MA 02115, USA. Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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46
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Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Abecasis G, Arguello PA, Blangero J, Boehnke M, Daly MJ, Eggan K, Geschwind DH, Glahn DC, Goldstein DB, Gur RE, Handsaker RE, McCarroll SA, Ophoff RA, Palotie A, Pato CN, Sabatti C, State MW, Willsey AJ, Hyman SE, Addington AM, Lehner T, Freimer NB. Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci 2017; 20:1661-1668. [PMID: 29184211 PMCID: PMC7785336 DOI: 10.1038/s41593-017-0017-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As technology advances, whole genome sequencing (WGS) is likely to supersede other genotyping technologies. The rate of this change depends on its relative cost and utility. Variants identified uniquely through WGS may reveal novel biological pathways underlying complex disorders and provide high-resolution insight into when, where, and in which cell type these pathways are affected. Alternatively, cheaper and less computationally intensive approaches may yield equivalent insights. Understanding the role of rare variants in the noncoding gene-regulating genome, through pilot WGS projects, will be critical to determine which of these two extremes best represents reality. With large cohorts, well-defined risk loci, and a compelling need to understand the underlying biology, psychiatric disorders have a role to play in this preliminary WGS assessment. The WGSPD consortium will integrate data for 18,000 individuals with psychiatric disorders, beginning with autism spectrum disorder, schizophrenia, bipolar disorder, and major depressive disorder, along with over 150,000 controls.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Donna M Werling
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Goncalo Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, Brownsville, TX, USA
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - Raquel E Gur
- Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roel A Ophoff
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carlos N Pato
- Department of Psychiatry, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chiara Sabatti
- Department of Health Research and Policy, Division of Biostatistics, Stanford University, Stanford, CA, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Steven E Hyman
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Anjene M Addington
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| | - Thomas Lehner
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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47
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Kawada J, Kaneda S, Kirihara T, Maroof A, Levi T, Eggan K, Fujii T, Ikeuchi Y. Generation of a Motor Nerve Organoid with Human Stem Cell-Derived Neurons. Stem Cell Reports 2017; 9:1441-1449. [PMID: 29107592 PMCID: PMC5831012 DOI: 10.1016/j.stemcr.2017.09.021] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022] Open
Abstract
During development, axons spontaneously assemble into a fascicle to form nerves and tracts in the nervous system as they extend within a spatially constrained path. However, understanding of the axonal fascicle has been hampered by lack of an in vitro model system. Here, we report generation of a nerve organoid composed of a robust fascicle of axons extended from a spheroid of human stem cell-derived motor neurons within our custom-designed microdevice. The device is equipped with a narrow channel providing a microenvironment that facilitates the growing axons to spontaneously assemble into a unidirectional fascicle. The fascicle was specifically made with axons. We found that it was electrically active and elastic and could serve as a model to evaluate degeneration of axons in vitro. This nerve organoid model should facilitate future studies on the development of the axonal fascicle and drug screening for diseases affecting axon fascicles. Axons spontaneously assembled into a unidirectional fascicle within a microchannel The axon fascicles were electrically active and elastic The axon fascicle can model degeneration of axons in vitro
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Affiliation(s)
- Jiro Kawada
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Shohei Kaneda
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Takaaki Kirihara
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Asif Maroof
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothée Levi
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Teruo Fujii
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan.
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48
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Salick MR, Wells MF, Eggan K, Kaykas A. Modelling Zika Virus Infection of the Developing Human Brain In Vitro Using Stem Cell Derived Cerebral Organoids. J Vis Exp 2017. [PMID: 28994790 PMCID: PMC5752258 DOI: 10.3791/56404] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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] [Indexed: 01/30/2023] Open
Abstract
The recent emergence of Zika virus (ZIKV) in susceptible populations has led to an abrupt increase in microcephaly and other neurodevelopmental conditions in newborn infants. While mosquitos are the main route of viral transmission, it has also been shown to spread via sexual contact and vertical mother-to-fetus transmission. In this latter case of transmission, due to the unique viral tropism of ZIKV, the virus is believed to predominantly target the neural progenitor cells (NPCs) of the developing brain. Here a method for modeling ZIKV infection, and the resulting microcephaly, that occur when human cerebral organoids are exposed to live ZIKV is described. The organoids display high levels of virus within their neural progenitor population, and exhibit severe cell death and microcephaly over time. This three-dimensional cerebral organoid model allows researchers to conduct species-matched experiments to observe and potentially intervene with ZIKV infection of the developing human brain. The model provides improved relevance over standard two-dimensional methods, and contains human-specific cellular architecture and protein expression that are not possible in animal models.
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Affiliation(s)
- Max R Salick
- Department of Neuroscience, Novartis Institutes for BioMedical Research
| | - Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University
| | - Ajamete Kaykas
- Department of Neuroscience, Novartis Institutes for BioMedical Research;
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49
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Resetkova N, Groff A, Sakkas D, Penzias A, Rinn J, Eggan K. A deep dive into the human blastocyst: gene based sex differences in human embryos and the assessment of aneuploidy by transcriptome analysis - progress and limitations. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.460] [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: 10/18/2022]
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50
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Tripathi P, Rodriguez-Muela N, Klim JR, de Boer AS, Agrawal S, Sandoe J, Lopes CS, Ogliari KS, Williams LA, Shear M, Rubin LL, Eggan K, Zhou Q. Reactive Astrocytes Promote ALS-like Degeneration and Intracellular Protein Aggregation in Human Motor Neurons by Disrupting Autophagy through TGF-β1. Stem Cell Reports 2017; 9:667-680. [PMID: 28712846 PMCID: PMC5549875 DOI: 10.1016/j.stemcr.2017.06.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal and rapidly progressing motor neuron disease. Astrocytic factors are known to contribute to motor neuron degeneration and death in ALS. However, the role of astrocyte in promoting motor neuron protein aggregation, a disease hallmark of ALS, remains largely unclear. Here, using culture models of human motor neurons and primary astrocytes of different genotypes (wild-type or SOD1 mutant) and reactive states (non-reactive or reactive), we show that reactive astrocytes, regardless of their genotypes, reduce motor neuron health and lead to moderate neuronal loss. After prolonged co-cultures of up to 2 months, motor neurons show increased axonal and cytoplasmic protein inclusions characteristic of ALS. Reactive astrocytes induce protein aggregation in part by releasing transforming growth factor β1 (TGF-β1), which disrupts motor neuron autophagy through the mTOR pathway. These results reveal the important contribution of reactive astrocytes in promoting aspects of ALS pathology independent of genetic influences. Reactive astrocytes induce ALS-like protein aggregation in human motor neurons Reactive astrocytes have increased secretion of TGF-β1 TGF-β1 induces axonal and cytoplasmic protein aggregation in hMNs TGF-β1 activates PI3K/AKT/mTOR pathway and impairs autophagy in hMNs
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Affiliation(s)
- Pratibha Tripathi
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Natalia Rodriguez-Muela
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - A Sophie de Boer
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Sahil Agrawal
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Jackson Sandoe
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Claudia S Lopes
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Karolyn Sassi Ogliari
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Luis A Williams
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Matthew Shear
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Qiao Zhou
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
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