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Cameron EG, Nahmou M, Toth AB, Heo L, Tanasa B, Dalal R, Yan W, Nallagatla P, Xia X, Hay S, Knasel C, Stiles TL, Douglas C, Atkins M, Sun C, Ashouri M, Bian M, Chang KC, Russano K, Shah S, Woodworth MB, Galvao J, Nair RV, Kapiloff MS, Goldberg JL. A molecular switch for neuroprotective astrocyte reactivity. Nature 2024; 626:574-582. [PMID: 38086421 DOI: 10.1038/s41586-023-06935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/05/2023] [Indexed: 01/27/2024]
Abstract
The intrinsic mechanisms that regulate neurotoxic versus neuroprotective astrocyte phenotypes and their effects on central nervous system degeneration and repair remain poorly understood. Here we show that injured white matter astrocytes differentiate into two distinct C3-positive and C3-negative reactive populations, previously simplified as neurotoxic (A1) and neuroprotective (A2)1,2, which can be further subdivided into unique subpopulations defined by proliferation and differential gene expression signatures. We find the balance of neurotoxic versus neuroprotective astrocytes is regulated by discrete pools of compartmented cyclic adenosine monophosphate derived from soluble adenylyl cyclase and show that proliferating neuroprotective astrocytes inhibit microglial activation and downstream neurotoxic astrocyte differentiation to promote retinal ganglion cell survival. Finally, we report a new, therapeutically tractable viral vector to specifically target optic nerve head astrocytes and show that raising nuclear or depleting cytoplasmic cyclic AMP in reactive astrocytes inhibits deleterious microglial or macrophage cell activation and promotes retinal ganglion cell survival after optic nerve injury. Thus, soluble adenylyl cyclase and compartmented, nuclear- and cytoplasmic-localized cyclic adenosine monophosphate in reactive astrocytes act as a molecular switch for neuroprotective astrocyte reactivity that can be targeted to inhibit microglial activation and neurotoxic astrocyte differentiation to therapeutic effect. These data expand on and define new reactive astrocyte subtypes and represent a step towards the development of gliotherapeutics for the treatment of glaucoma and other optic neuropathies.
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Affiliation(s)
- Evan G Cameron
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - Michael Nahmou
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anna B Toth
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lyong Heo
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA
| | - Bogdan Tanasa
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Roopa Dalal
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Wenjun Yan
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Pratima Nallagatla
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA
| | - Xin Xia
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sarah Hay
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Cara Knasel
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Melissa Atkins
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Catalina Sun
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Masoumeh Ashouri
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Minjuan Bian
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Kun-Che Chang
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Kristina Russano
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sahil Shah
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- University of California, San Diego, La Jolla, CA, USA
| | - Mollie B Woodworth
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Joana Galvao
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Ramesh V Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Palo Alto, CA, USA
| | - Michael S Kapiloff
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Medicine and Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jeffrey L Goldberg
- Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA.
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Woodworth MB, Greig LC, Goldberg JL. Intrinsic and Induced Neuronal Regeneration in the Mammalian Retina. Antioxid Redox Signal 2023; 39:1039-1052. [PMID: 37276181 PMCID: PMC10715439 DOI: 10.1089/ars.2023.0309] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/05/2023] [Accepted: 05/14/2023] [Indexed: 06/07/2023]
Abstract
Significance: Retinal neurons are vulnerable to disease and injury, which can result in neuronal death and degeneration leading to irreversible vision loss. The human retina does not regenerate to replace neurons lost to disease or injury. However, cells within the retina of other animals are capable of regenerating neurons, and homologous cells within the mammalian retina could potentially be prompted to do the same. Activating evolutionarily silenced intrinsic regenerative capacity of the mammalian retina could slow, or even reverse, vision loss, leading to an improved quality of life for millions of people. Recent Advances: During development, neurons in the retina are generated progressively by retinal progenitor cells, with distinct neuron types born over developmental time. Many genes function in this process to specify the identity of newly generated neuron types, and these appropriate states of gene expression inform recent regenerative work. When regeneration is initiated in other vertebrates, including birds and fish, specific signaling pathways control the efficiency of regeneration, and these conserved pathways are likely to be important in mammals as well. Critical Issues: Using insights from development and from other animals, limited regeneration from intrinsic cell types has been demonstrated in the mammalian retina, but it is able only to generate a subset of partially differentiated retinal neuron types. Future Directions: Future studies should aim at increasing the efficiency of regeneration, activating regeneration in a targeted fashion across the retina, and improving the ability to generate specific types of retinal neurons to replace those lost to disease or injury. Antioxid. Redox Signal. 39, 1039-1052.
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Affiliation(s)
- Mollie B. Woodworth
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Luciano C. Greig
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Jeffrey L. Goldberg
- Department of Ophthalmology, Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Palo Alto, California, USA
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Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic analysis. bioRxiv 2023:2023.02.16.528875. [PMID: 36824714 PMCID: PMC9949094 DOI: 10.1101/2023.02.16.528875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Genetic mosaic analysis, in which mutant cells reside intermingled with wild-type cells, is a powerful experimental approach, but has not been widely used in mice because existing genome-based strategies require complicated and protracted breeding schemes. We have developed an alternative approach termed BEAM (for Binary Expression Aleatory Mosaic) that relies on sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following delivery of DNA constructs by transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. Any gene of interest can be mis-expressed or deleted in one population for comparison with intermingled control cells. We have extensively optimized and characterized this system both in vitro and in vivo , and demonstrate its power for investigating cell autonomy, identifying temporally or spatially aberrant phenotypes, revealing changes in cell proliferation or death, and controlling for procedural variability.
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Lodato MA, Rodin RE, Bohrson CL, Coulter ME, Barton AR, Kwon M, Sherman MA, Vitzthum CM, Luquette LJ, Yandava CN, Yang P, Chittenden TW, Hatem NE, Ryu SC, Woodworth MB, Park PJ, Walsh CA. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science 2018; 359:555-559. [PMID: 29217584 PMCID: PMC5831169 DOI: 10.1126/science.aao4426] [Citation(s) in RCA: 355] [Impact Index Per Article: 59.2] [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: 07/21/2017] [Accepted: 11/22/2017] [Indexed: 12/27/2022]
Abstract
It has long been hypothesized that aging and neurodegeneration are associated with somatic mutation in neurons; however, methodological hurdles have prevented testing this hypothesis directly. We used single-cell whole-genome sequencing to perform genome-wide somatic single-nucleotide variant (sSNV) identification on DNA from 161 single neurons from the prefrontal cortex and hippocampus of 15 normal individuals (aged 4 months to 82 years), as well as 9 individuals affected by early-onset neurodegeneration due to genetic disorders of DNA repair (Cockayne syndrome and xeroderma pigmentosum). sSNVs increased approximately linearly with age in both areas (with a higher rate in hippocampus) and were more abundant in neurodegenerative disease. The accumulation of somatic mutations with age-which we term genosenium-shows age-related, region-related, and disease-related molecular signatures and may be important in other human age-associated conditions.
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Affiliation(s)
- Michael A Lodato
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Neuroscience and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael E Coulter
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Neuroscience and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA
| | - Alison R Barton
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Minseok Kwon
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Carl M Vitzthum
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chandri N Yandava
- Computational Statistics and Bioinformatics Group, Advanced Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
| | - Pengwei Yang
- Computational Statistics and Bioinformatics Group, Advanced Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
| | - Thomas W Chittenden
- Computational Statistics and Bioinformatics Group, Advanced Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicole E Hatem
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven C Ryu
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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D'Gama AM, Woodworth MB, Hossain AA, Bizzotto S, Hatem NE, LaCoursiere CM, Najm I, Ying Z, Yang E, Barkovich AJ, Kwiatkowski DJ, Vinters HV, Madsen JR, Mathern GW, Blümcke I, Poduri A, Walsh CA. Somatic Mutations Activating the mTOR Pathway in Dorsal Telencephalic Progenitors Cause a Continuum of Cortical Dysplasias. Cell Rep 2017; 21:3754-3766. [PMID: 29281825 PMCID: PMC5752134 DOI: 10.1016/j.celrep.2017.11.106] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/02/2017] [Accepted: 11/29/2017] [Indexed: 01/16/2023] Open
Abstract
Focal cortical dysplasia (FCD) and hemimegalencephaly (HME) are epileptogenic neurodevelopmental malformations caused by mutations in mTOR pathway genes. Deep sequencing of these genes in FCD/HME brain tissue identified an etiology in 27 of 66 cases (41%). Radiographically indistinguishable lesions are caused by somatic activating mutations in AKT3, MTOR, and PIK3CA and germline loss-of-function mutations in DEPDC5, NPRL2, and TSC1/2, including TSC2 mutations in isolated HME demonstrating a "two-hit" model. Mutations in the same gene cause a disease continuum from FCD to HME to bilateral brain overgrowth, reflecting the progenitor cell and developmental time when the mutation occurred. Single-cell sequencing demonstrated mTOR activation in neurons in all lesions. Conditional Pik3ca activation in the mouse cortex showed that mTOR activation in excitatory neurons and glia, but not interneurons, is sufficient for abnormal cortical overgrowth. These data suggest that mTOR activation in dorsal telencephalic progenitors, in some cases specifically the excitatory neuron lineage, causes cortical dysplasia.
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Affiliation(s)
- Alissa M D'Gama
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Amer A Hossain
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Nicole E Hatem
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Imad Najm
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zhong Ying
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
| | - A James Barkovich
- Departments of Radiology and Diagnostic Imaging, Neurology, Pediatrics, and Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Harry V Vinters
- Departments of Pathology and Laboratory Medicine (Neuropathology) and Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph R Madsen
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, USA
| | - Gary W Mathern
- Departments of Neurosurgery and Psychiatry and Biobehavioral Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ingmar Blümcke
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Neuropathology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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6
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Greig LC, Woodworth MB, Greppi C, Macklis JD. Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex. Neuron 2017; 90:261-77. [PMID: 27100196 DOI: 10.1016/j.neuron.2016.03.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [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: 11/08/2013] [Revised: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 12/19/2022]
Abstract
While transcriptional controls over the size and relative position of cortical areas have been identified, less is known about regulators that direct acquisition of area-specific characteristics. Here, we report that the transcription factor Ctip1 functions in primary sensory areas to repress motor and activate sensory programs of gene expression, enabling establishment of sharp molecular boundaries defining functional areas. In Ctip1 mutants, abnormal gene expression leads to aberrantly motorized corticocortical and corticofugal output connectivity. Ctip1 critically regulates differentiation of layer IV neurons, and selective loss of Ctip1 in cortex deprives thalamocortical axons of their receptive "sensory field" in layer IV, which normally provides a tangentially and radially defined compartment of dedicated synaptic territory. Therefore, although thalamocortical axons invade appropriate cortical regions, they are unable to organize into properly configured sensory maps. Together, these data identify Ctip1 as a critical control over sensory area development.
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Affiliation(s)
- Luciano C Greig
- Department of Stem Cell and Regenerative Biology, Center for Brain Science and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Mollie B Woodworth
- Department of Stem Cell and Regenerative Biology, Center for Brain Science and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Chloé Greppi
- Department of Stem Cell and Regenerative Biology, Center for Brain Science and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology, Center for Brain Science and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02215, USA.
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7
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Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 2015; 350:94-98. [PMID: 26430121 DOI: 10.1126/science.aab1785] [Citation(s) in RCA: 372] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neurons live for decades in a postmitotic state, their genomes susceptible to DNA damage. Here we survey the landscape of somatic single-nucleotide variants (SNVs) in the human brain. We identified thousands of somatic SNVs by single-cell sequencing of 36 neurons from the cerebral cortex of three normal individuals. Unlike germline and cancer SNVs, which are often caused by errors in DNA replication, neuronal mutations appear to reflect damage during active transcription. Somatic mutations create nested lineage trees, allowing them to be dated relative to developmental landmarks and revealing a polyclonal architecture of the human cerebral cortex. Thus, somatic mutations in the brain represent a durable and ongoing record of neuronal life history, from development through postmitotic function.
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Affiliation(s)
- Michael A Lodato
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Semin Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gilad D Evrony
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bhaven K Mehta
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amir Karger
- Research Computing, Harvard Medical School, Boston, MA, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Thomas W Chittenden
- Research Computing, Harvard Medical School, Boston, MA, USA.,Complex Biological Systems Alliance, North Andover, MA, USA
| | - Alissa M D'Gama
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xuyu Cai
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
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8
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Greig LC, Woodworth MB, Galazo MJ, Padmanabhan H, Macklis JD. Molecular logic of neocortical projection neuron specification, development and diversity. Nat Rev Neurosci 2013; 14:755-69. [PMID: 24105342 DOI: 10.1038/nrn3586] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The sophisticated circuitry of the neocortex is assembled from a diverse repertoire of neuronal subtypes generated during development under precise molecular regulation. In recent years, several key controls over the specification and differentiation of neocortical projection neurons have been identified. This work provides substantial insight into the 'molecular logic' underlying cortical development and increasingly supports a model in which individual progenitor-stage and postmitotic regulators are embedded within highly interconnected networks that gate sequential developmental decisions. Here, we provide an integrative account of the molecular controls that direct the progressive development and delineation of subtype and area identity of neocortical projection neurons.
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Affiliation(s)
- Mollie B Woodworth
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Luciano Custo Greig
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Harvard Medical School, Boston, MA 02115, USA
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