1
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Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. scX: A user-friendly tool for scRNA-seq exploration. ArXiv 2024:arXiv:2311.00012v2. [PMID: 37961742 PMCID: PMC10635291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on the Shiny framework that streamlines the analysis, exploration, and visualization of single-cell experiments. With an interactive graphic interface, implemented as a web application, scX provides easy access to key scRNAseq analyses, including marker identification, gene expression profiling, and differential gene expression analysis. Additionally, scX seamlessly integrates with commonly used single-cell Seurat and Single-CellExperiment R objects, resulting in efficient processing and visualization of varied datasets. Overall, scX serves as a valuable and user-friendly tool for effortless exploration and sharing of single-cell data, simplifying some of the complexities inherent in scRNAseq analysis.
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Affiliation(s)
- Tomás Vega Waichman
- Integrative Systems Biology Lab, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
| | - M Luz Vercesi
- Integrative Systems Biology Lab, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
| | - Ariel A Berardino
- Integrative Systems Biology Lab, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1425 FQB, Argentina
| | - Maximiliano S Beckel
- Integrative Systems Biology Lab, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1425 FQB, Argentina
| | - Damiana Giacomini
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1425 FQB, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
| | - Natalí B Rasetto
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1425 FQB, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
| | - Magalí Herrero
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1425 FQB, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
| | - Daniela J Di Bella
- Dept. of Stem Cells and Regenerative Biology, Harvard University & Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola Arlotta
- Dept. of Stem Cells and Regenerative Biology, Harvard University & Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alejandro F Schinder
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1425 FQB, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
| | - Ariel Chernomoretz
- Integrative Systems Biology Lab, Leloir Institute, Buenos Aires, C1405 BWE, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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2
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Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. bioRxiv 2024:2023.11.03.565477. [PMID: 38260428 PMCID: PMC10802403 DOI: 10.1101/2023.11.03.565477] [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: 01/24/2024]
Abstract
The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressing Sox4 or Sox11 remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation.
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3
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Weninger A, Arlotta P. A family portrait of human brain cells. Science 2023; 382:168-169. [PMID: 37824657 DOI: 10.1126/science.adk4857] [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] [Indexed: 10/14/2023]
Abstract
A cell census provides information on the source of human brain specialization.
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Affiliation(s)
- Alyssa Weninger
- Department of Psychology and Neuroscience and Department of Nutrition, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Paola Arlotta
- 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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4
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Pigoni M, Uzquiano A, Paulsen B, Kedaigle AJ, Yang SM, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, Tucewicz A, Tropp SY, Tsafou K, Jin X, Barrett L, Chen F, Boyden ES, Regev A, Levin JZ, Arlotta P. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Hum Mol Genet 2023; 32:2773-2786. [PMID: 37384417 PMCID: PMC10481103 DOI: 10.1093/hmg/ddad107] [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: 03/31/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Abstract
De novo heterozygous loss-of-function mutations in phosphatase and tensin homolog (PTEN) are strongly associated with autism spectrum disorders; however, it is unclear how heterozygous mutations in this gene affect different cell types during human brain development and how these effects vary across individuals. Here, we used human cortical organoids from different donors to identify cell-type specific developmental events that are affected by heterozygous mutations in PTEN. We profiled individual organoids by single-cell RNA-seq, proteomics and spatial transcriptomics and revealed abnormalities in developmental timing in human outer radial glia progenitors and deep-layer cortical projection neurons, which varied with the donor genetic background. Calcium imaging in intact organoids showed that both accelerated and delayed neuronal development phenotypes resulted in similar abnormal activity of local circuits, irrespective of genetic background. The work reveals donor-dependent, cell-type specific developmental phenotypes of PTEN heterozygosity that later converge on disrupted neuronal activity.
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Affiliation(s)
- Martina Pigoni
- 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
| | - Ana Uzquiano
- 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
| | - Bruna Paulsen
- 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
| | - Amanda J Kedaigle
- 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
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sung Min Yang
- 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
| | - Panagiotis Symvoulidis
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvia Velasco
- 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
| | - Rafaela Sartore
- 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
| | - Kwanho Kim
- 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
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashley Tucewicz
- 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
| | - Sarah Yoshimi Tropp
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Lindy Barrett
- 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
| | - Fei Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Harvard-MIT Health Sciences & Technology Program (HST), Harvard Medical School, Boston, MA 02115, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA 02138, USA
- Department of Brain of Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- 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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5
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Arlotta P, Gage FH. Neural Organoids and the Quest to Understand and Treat Psychiatric Disease. Biol Psychiatry 2023; 93:588-589. [PMID: 36889858 DOI: 10.1016/j.biopsych.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/10/2023]
Affiliation(s)
- Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California.
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6
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Fossati V, Greco V, Arlotta P, Aiyar RS. Susan L. Solomon (1951-2022): Advocate, Innovator, Catalyst. Stem Cell Reports 2022; 17:2579-2581. [PMID: 36516737 PMCID: PMC9813825 DOI: 10.1016/j.stemcr.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, USA
| | - Valentina Greco
- Department of Genetics and Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Raeka S Aiyar
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, USA.
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7
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Arlotta P, Noggle S, Rossi D. Susan Solomon. Cell Stem Cell 2022; 29:1619-1620. [DOI: 10.1016/j.stem.2022.11.008] [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: 12/05/2022]
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8
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Cable J, Arlotta P, Parker KK, Hughes AJ, Goodwin K, Mummery CL, Kamm RD, Engle SJ, Tagle DA, Boj SF, Stanton AE, Morishita Y, Kemp ML, Norfleet DA, May EE, Lu A, Bashir R, Feinberg AW, Hull SM, Gonzalez AL, Blatchley MR, Montserrat Pulido N, Morizane R, McDevitt TC, Mishra D, Mulero-Russe A. Engineering multicellular living systems-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1518:183-195. [PMID: 36177947 PMCID: PMC9771928 DOI: 10.1111/nyas.14896] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The ability to engineer complex multicellular systems has enormous potential to inform our understanding of biological processes and disease and alter the drug development process. Engineering living systems to emulate natural processes or to incorporate new functions relies on a detailed understanding of the biochemical, mechanical, and other cues between cells and between cells and their environment that result in the coordinated action of multicellular systems. On April 3-6, 2022, experts in the field met at the Keystone symposium "Engineering Multicellular Living Systems" to discuss recent advances in understanding how cells cooperate within a multicellular system, as well as recent efforts to engineer systems like organ-on-a-chip models, biological robots, and organoids. Given the similarities and common themes, this meeting was held in conjunction with the symposium "Organoids as Tools for Fundamental Discovery and Translation".
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Affiliation(s)
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kevin Kit Parker
- Wyss Institute for Biologically Inspired Engineering and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Alex J Hughes
- Department of Bioengineering, School of Engineering and Applied Science and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Christine L Mummery
- Department of Anatomy and Embryology and LUMC hiPSC Hotel, Leiden University Medical Center, Leiden, the Netherlands
| | - Roger D Kamm
- Department of Mechanical Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sandra J Engle
- Translational Biology, Biogen, Cambridge, Massachusetts, USA
| | - Danilo A Tagle
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Sylvia F Boj
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Alice E Stanton
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yoshihiro Morishita
- Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Melissa L Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Dennis A Norfleet
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Elebeoba E May
- Department of Biomedical Engineering and HEALTH Research Institute, University of Houston, Houston, Texas, USA
- Wisconsin Institute of Discovery and Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aric Lu
- Wyss Institute for Biologically Inspired Engineering and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
- Draper Laboratory, Biological Engineering Division, Cambridge, Massachusetts, USA
| | - Rashid Bashir
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois, USA
- Holonyak Micro & Nanotechnology Laboratory, Department of Electrical and Computer Engineering and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Adam W Feinberg
- Department of Biomedical Engineering and Department of Materials Science & Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Sarah M Hull
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - Anjelica L Gonzalez
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
| | - Michael R Blatchley
- BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, USA
| | | | - Ryuji Morizane
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Todd C McDevitt
- The Gladstone Institutes and Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Deepak Mishra
- Department of Biological Engineering, Synthetic Biology Center, Cambridge, Massachusetts, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Adriana Mulero-Russe
- Parker H. Petit Institute for Bioengineering and Bioscience and School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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9
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Hyun I, Scharf-Deering JC, Sullivan S, Aach JD, Arlotta P, Baum ML, Church GM, Goldenberg A, Greely HT, Khoshakhlagh P, Kohman RE, Lopes M, Lowenthal C, Lu A, Ng AHM, Pasca SP, Paulsen B, Pigoni M, Scott CT, Silbersweig DA, Skylar-Scott MA, Truog RD, Lunshof JE. How collaboration between bioethicists and neuroscientists can advance research. Nat Neurosci 2022; 25:1399-1401. [PMID: 36258039 DOI: 10.1038/s41593-022-01187-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Insoo Hyun
- Center for Bioethics, Harvard Medical School, Boston, MA, USA. .,Center for Life Sciences and Public Learning, Museum of Science, Boston, MA, USA.
| | - J C Scharf-Deering
- Department of Bioethics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sarah Sullivan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Matthew L Baum
- Brigham and Women's Hospital, Department of Psychiatry, Boston, MA, USA.,Harvard Medical School, Department of Psychiatry, Boston, MA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aaron Goldenberg
- Department of Bioethics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | | | - Richie E Kohman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland
| | - Melissa Lopes
- Office of the Vice Provost of Research, Harvard University, Cambridge, MA, USA
| | | | - Aric Lu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA.,Biological Engineering Division, Draper Laboratory, Cambridge, MA, USA
| | | | - Sergiu P Pasca
- Department of Psychiatry and Behavioral Sciences, , Stanford University, Stanford, CA, USA.,Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Bruna Paulsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Martina Pigoni
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - David A Silbersweig
- Department of Psychiatry and Institute for the Neurosciences, Brigham and Women's/Faulkner Hospitals, Boston, MA, USA
| | - Mark A Skylar-Scott
- Department of Bioengineering, Betty Irene Moore Children's Heart Center, Stanford University, Stanford, CA, USA.,Basic Science and Engineering Initiative, Children's Heart Center, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Robert D Truog
- Center for Bioethics, Harvard Medical School, Boston, MA, USA
| | - Jeantine E Lunshof
- Center for Bioethics, Harvard Medical School, Boston, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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10
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Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell 2022; 185:3770-3788.e27. [PMID: 36179669 PMCID: PMC9990683 DOI: 10.1016/j.cell.2022.09.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [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: 03/20/2021] [Revised: 03/25/2022] [Accepted: 09/01/2022] [Indexed: 01/26/2023]
Abstract
Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development.
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Affiliation(s)
- Ana Uzquiano
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda J Kedaigle
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martina Pigoni
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bruna Paulsen
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tyler Faits
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Surya Nagaraja
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Noelia Antón-Bolaños
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chiara Gerhardinger
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashley Tucewicz
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Jason Buenrostro
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvia Velasco
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell & 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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11
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Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Muotri AR, Park IH, Reiner O, Song H, Studer L, Temple S, Testa G, Treutlein B, Vaccarino FM. A nomenclature consensus for nervous system organoids and assembloids. Nature 2022; 609:907-910. [PMID: 36171373 PMCID: PMC10571504 DOI: 10.1038/s41586-022-05219-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [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: 01/27/2022] [Accepted: 07/10/2022] [Indexed: 12/20/2022]
Abstract
Self-organizing three-dimensional cellular models derived from human pluripotent stem cells or primary tissue have great potential to provide insights into how the human nervous system develops, what makes it unique and how disorders of the nervous system arise, progress and could be treated. Here, to facilitate progress and improve communication with the scientific community and the public, we clarify and provide a basic framework for the nomenclature of human multicellular models of nervous system development and disease, including organoids, assembloids and transplants.
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Affiliation(s)
- Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA.
| | - Paola Arlotta
- 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
| | - Helen S Bateup
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - J Gray Camp
- Roche Institute for Translational Bioengineering, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Arnold R Kriegstein
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | | | - Guo-Li Ming
- Department of Neuroscience, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alysson R Muotri
- Departments of Pediatrics and Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Stem Cell Program, Archealization Center, Center for Academic Research and Training in Anthropogeny, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Orly Reiner
- Weizmann Institute of Science, Rehovot, Israel
| | - Hongjun Song
- Department of Neuroscience, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | | | - Giuseppe Testa
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Human Technopole, Milan, Italy
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
- Yale Kavli Institute for Neuroscience, New Haven, CT, USA
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12
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Stogsdill JA, Kim K, Binan L, Farhi SL, Levin JZ, Arlotta P. Pyramidal neuron subtype diversity governs microglia states in the neocortex. Nature 2022; 608:750-756. [PMID: 35948630 PMCID: PMC10502800 DOI: 10.1038/s41586-022-05056-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [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: 09/29/2020] [Accepted: 06/30/2022] [Indexed: 12/14/2022]
Abstract
Microglia are specialized macrophages in the brain parenchyma that exist in multiple transcriptional states and reside within a wide range of neuronal environments1-4. However, how and where these states are generated remains poorly understood. Here, using the mouse somatosensory cortex, we demonstrate that microglia density and molecular state acquisition are determined by the local composition of pyramidal neuron classes. Using single-cell and spatial transcriptomic profiling, we unveil the molecular signatures and spatial distributions of diverse microglia populations and show that certain states are enriched in specific cortical layers, whereas others are broadly distributed throughout the cortex. Notably, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures the distribution of local, layer-enriched homeostatic microglia to match the new neuronal niche. Leveraging the transcriptional diversity of pyramidal neurons in the neocortex, we construct a ligand-receptor atlas describing interactions between individual pyramidal neuron subtypes and microglia states, revealing rules of neuron-microglia communication. Our findings uncover a fundamental role for neuronal diversity in instructing the acquisition of microglia states as a potential mechanism for fine-tuning neuroimmune interactions within the cortical local circuitry.
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Affiliation(s)
- Jeffrey A Stogsdill
- 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
| | - Kwanho Kim
- 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
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Loïc Binan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Optical Profiling Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Optical Profiling Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola Arlotta
- 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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13
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Abstract
Axons form the long-range connections of biological neuronal networks, which are built through the developmental process of axon guidance. Here, we describe a protocol to precisely and non-invasively control axonal growth trajectories in live zebrafish embryos using focal light activation of a photoactivatable Rac1. We outline techniques for photostimulation, time-lapse imaging, and immunohistochemistry. These approaches enable engineering of long-range axonal circuitry or repair of defective circuits in living zebrafish, despite a milieu of competing endogenous signals and repulsive barriers. For complete details on the use and execution of this protocol, please refer to Harris et al. (2020).
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Affiliation(s)
- James M. Harris
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Andy Yu-Der Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paola Arlotta
- 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 02138, USA
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14
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Matho KS, Huilgol D, Galbavy W, He M, Kim G, An X, Lu J, Wu P, Di Bella DJ, Shetty AS, Palaniswamy R, Hatfield J, Raudales R, Narasimhan A, Gamache E, Levine JM, Tucciarone J, Szelenyi E, Harris JA, Mitra PP, Osten P, Arlotta P, Huang ZJ. Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature 2021; 598:182-187. [PMID: 34616069 PMCID: PMC8494647 DOI: 10.1038/s41586-021-03955-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [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: 04/23/2020] [Accepted: 08/25/2021] [Indexed: 11/09/2022]
Abstract
Diverse types of glutamatergic pyramidal neurons mediate the myriad processing streams and output channels of the cerebral cortex1,2, yet all derive from neural progenitors of the embryonic dorsal telencephalon3,4. Here we establish genetic strategies and tools for dissecting and fate-mapping subpopulations of pyramidal neurons on the basis of their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable the combinatorial targeting of major progenitor types and projection classes. Combinatorial strategies confer viral access to subsets of pyramidal neurons defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of subpopulations of pyramidal neurons that assemble cortical processing networks and output channels.
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Affiliation(s)
- Katherine S Matho
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Dhananjay Huilgol
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - William Galbavy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, USA
| | - Miao He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Gukhan Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Xu An
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Jiangteng Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Shanghai Jiaotong University Medical School, Shanghai, China
| | - Priscilla Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Ashwin S Shetty
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Joshua Hatfield
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Raudales
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, USA
| | - Arun Narasimhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Eric Gamache
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Jesse M Levine
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience and Medical Scientist Training Program, Stony Brook University, New York, NY, USA
| | - Jason Tucciarone
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience and Medical Scientist Training Program, Stony Brook University, New York, NY, USA
- Department of Psychiatry, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Eric Szelenyi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Julie A Harris
- Program in Neuroscience and Medical Scientist Training Program, Stony Brook University, New York, NY, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Paola Arlotta
- 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
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
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15
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Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. Author Correction: Molecular logic of cellular diversification in the mouse cerebral cortex. Nature 2021; 596:E11. [PMID: 34341543 DOI: 10.1038/s41586-021-03797-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniela J Di Bella
- 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
| | - Ehsan Habibi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert R Stickels
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriele Scalia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juliana Brown
- 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
| | - Payman Yadollahpour
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sung Min Yang
- 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
| | - Catherine Abbate
- 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
| | - Tommaso Biancalani
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Evan Z Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fei Chen
- 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
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
| | - Paola Arlotta
- 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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16
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Abstract
Scientists have been fascinated by the human brain for centuries, yet knowledge of the cellular and molecular events that build the human brain during embryogenesis and of how abnormalities in this process lead to neurological disease remains very superficial. In particular, the lack of experimental models for a process that largely occurs during human in utero development, and is therefore poorly accessible for study, has hindered progress in mechanistic understanding. Advances in stem cell-derived models of human organogenesis, in the form of three-dimensional organoid cultures, and transformative new analytic technologies have opened new experimental pathways for investigation of aspects of development, evolution, and pathology of the human brain. Here, we consider the biology of brain organoids, compared and contrasted with the endogenous human brain, and highlight experimental strategies to use organoids to pioneer new understanding of human brain pathology.
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Affiliation(s)
- Silvia Velasco
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bruna Paulsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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17
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Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. Molecular logic of cellular diversification in the mouse cerebral cortex. Nature 2021; 595:554-559. [PMID: 34163074 PMCID: PMC9006333 DOI: 10.1038/s41586-021-03670-5] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/24/2021] [Indexed: 02/06/2023]
Abstract
The mammalian cerebral cortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function1,2. However, the molecular logic that governs the establishment and organization of cortical cell types remains unknown, largely due to the large number of cell classes that undergo dynamic cell-state transitions over extended developmental timelines. Here we generate a comprehensive atlas of the developing mouse neocortex, using single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin using sequencing. We sampled the neocortex every day throughout embryonic corticogenesis and at early postnatal ages, and complemented the sequencing data with a spatial transcriptomics time course. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer their spatial organization and the gene regulatory programs that accompany their lineage bifurcation decisions and differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities that are linked to aberrant corticogenesis in mutant mice. The data provide a global picture of the regulatory mechanisms that govern cellular diversification in the neocortex.
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Affiliation(s)
- Daniela J. Di Bella
- 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
| | - Ehsan Habibi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Gabriele Scalia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Current address: Genentech, South San Francisco, CA, USA
| | - Juliana Brown
- 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
| | - Payman Yadollahpour
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sung Min Yang
- 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
| | - Catherine Abbate
- 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
| | - Tommasso Biancalani
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Current address: Genentech, South San Francisco, CA, USA
| | - Evan Z. Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fei Chen
- 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
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Current address: Genentech, South San Francisco, CA, USA,Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA,Correspondence should be addressed to and
| | - Paola Arlotta
- 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,Correspondence should be addressed to and
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18
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Yang SM, Michel K, Jokhi V, Nedivi E, Arlotta P. Neuron class-specific responses govern adaptive myelin remodeling in the neocortex. Science 2021; 370:370/6523/eabd2109. [PMID: 33335032 DOI: 10.1126/science.abd2109] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022]
Abstract
Myelin plasticity is critical for neurological function, including learning and memory. However, it is unknown whether this plasticity reflects uniform changes across all neuronal subtypes, or whether myelin dynamics vary between neuronal classes to enable fine-tuning of adaptive circuit responses. We performed in vivo two-photon imaging of myelin sheaths along single axons of excitatory callosal neurons and inhibitory parvalbumin-expressing interneurons in adult mouse visual cortex. We found that both neuron types show homeostatic myelin remodeling under normal vision. However, monocular deprivation results in adaptive myelin remodeling only in parvalbumin-expressing interneurons. An initial increase in elongation of myelin segments is followed by contraction of a separate cohort of segments. This data indicates that distinct classes of neurons individualize remodeling of their myelination profiles to diversify circuit tuning in response to sensory experience.
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Affiliation(s)
- Sung Min Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Michel
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vahbiz Jokhi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elly Nedivi
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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19
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Jin X, Simmons SK, Guo A, Shetty AS, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin JZ, Regev A, Zhang F, Arlotta P. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science 2021; 370:370/6520/eaaz6063. [PMID: 33243861 DOI: 10.1126/science.aaz6063] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 05/24/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022]
Abstract
The number of disease risk genes and loci identified through human genetic studies far outstrips the capacity to systematically study their functions. We applied a scalable genetic screening approach, in vivo Perturb-Seq, to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay (ASD/ND) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing mouse brain in utero, followed by single-cell RNA-sequencing of perturbed cells in the postnatal brain. We identified cell type-specific and evolutionarily conserved gene modules from both neuronal and glial cell classes. Recurrent gene modules and cell types are affected across this cohort of perturbations, representing key cellular effects across sets of ASD/ND risk genes. In vivo Perturb-Seq allows us to investigate how diverse mutations affect cell types and states in the developing organism.
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Affiliation(s)
- Xin Jin
- Society of Fellows, Harvard University, Cambridge, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,McGovern Institute of Brain Science, Department of Brain and Cognitive Science, Department of Biological Engineering, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Sean K Simmons
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Guo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashwin S Shetty
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle Ko
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA
| | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahbiz Jokhi
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA
| | - Elise Robinson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Paul Oyler
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA
| | - Nathan Curry
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA
| | - Giulio Deangeli
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA
| | - Simona Lodato
- Department of Biomedical Sciences and Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Clinical and Research Center, Humanitas University, Milan, Italy
| | - Joshua Z Levin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute of Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,McGovern Institute of Brain Science, Department of Brain and Cognitive Science, Department of Biological Engineering, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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20
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Zonouzi M, Berger D, Jokhi V, Kedaigle A, Lichtman J, Arlotta P. Individual Oligodendrocytes Show Bias for Inhibitory Axons in the Neocortex. Cell Rep 2020; 27:2799-2808.e3. [PMID: 31167127 DOI: 10.1016/j.celrep.2019.05.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 01/18/2019] [Revised: 04/03/2019] [Accepted: 05/02/2019] [Indexed: 12/24/2022] Open
Abstract
Reciprocal communication between neurons and oligodendrocytes is essential for the generation and localization of myelin, a critical feature of the CNS. In the neocortex, individual oligodendrocytes can myelinate multiple axons; however, the neuronal origin of the myelinated axons has remained undefined and, while largely assumed to be from excitatory pyramidal neurons, it also includes inhibitory interneurons. This raises the question of whether individual oligodendrocytes display bias for the class of neurons that they myelinate. Here, we find that different classes of cortical interneurons show distinct patterns of myelin distribution starting from the onset of myelination, suggesting that oligodendrocytes can recognize the class identity of individual types of interneurons that they target. Notably, we show that some oligodendrocytes disproportionately myelinate the axons of inhibitory interneurons, whereas others primarily target excitatory axons or show no bias. These results point toward very specific interactions between oligodendrocytes and neurons and raise the interesting question of why myelination is differentially directed toward different neuron types.
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Affiliation(s)
- Marzieh Zonouzi
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Daniel Berger
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Vahbiz Jokhi
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Amanda Kedaigle
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeff Lichtman
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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21
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Harris JM, Wang AYD, Boulanger-Weill J, Santoriello C, Foianini S, Lichtman JW, Zon LI, Arlotta P. Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects. Dev Cell 2020; 53:577-588.e7. [PMID: 32516597 PMCID: PMC7375170 DOI: 10.1016/j.devcel.2020.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 04/25/2019] [Revised: 03/12/2020] [Accepted: 05/11/2020] [Indexed: 01/12/2023]
Abstract
Axons connect neurons together, establishing the wiring architecture of neuronal networks. Axonal connectivity is largely built during embryonic development through highly constrained processes of axon guidance, which have been extensively studied. However, the inability to control axon guidance, and thus neuronal network architecture, has limited investigation of how axonal connections influence subsequent development and function of neuronal networks. Here, we use zebrafish motor neurons expressing a photoactivatable Rac1 to co-opt endogenous growth cone guidance machinery to precisely and non-invasively direct axon growth using light. Axons can be guided over large distances, within complex environments of living organisms, overriding competing endogenous signals and redirecting axons across potent repulsive barriers to construct novel circuitry. Notably, genetic axon guidance defects can be rescued, restoring functional connectivity. These data demonstrate that intrinsic growth cone guidance machinery can be co-opted to non-invasively build new connectivity, allowing investigation of neural network dynamics in intact living organisms.
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Affiliation(s)
- James M. Harris
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Andy Yu-Der Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Current Address: Tufts University School of Medicine, Boston, MA 02115, USA
| | - Jonathan Boulanger-Weill
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
| | - Stephan Foianini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Leonard I. Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA.,Lead contact. Correspondence:
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22
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Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic Acids Res 2020; 48:e4. [PMID: 31728515 PMCID: PMC7145626 DOI: 10.1093/nar/gkz968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/23/2019] [Revised: 09/09/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Thousands of frozen, archived tissue samples from the human central nervous system (CNS) are currently available in brain banks. As recent developments in RNA sequencing technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that an understanding of this diversity would greatly benefit from deeper transcriptional analyses. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples that have been stored long-term. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohistochemical isolation of nuclei of specific cell types from frozen human tissue, followed by bulk RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.
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Affiliation(s)
- Ryoji Amamoto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nathan C Curry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sonia Khurana
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Constance L Cepko
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Paola Arlotta
- 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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23
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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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24
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Velasco S, Kedaigle AJ, Simmons SK, Nash A, Rocha M, Quadrato G, Paulsen B, Nguyen L, Adiconis X, Regev A, Levin JZ, Arlotta P. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature 2019; 570:523-527. [PMID: 31168097 PMCID: PMC6906116 DOI: 10.1038/s41586-019-1289-x] [Citation(s) in RCA: 507] [Impact Index Per Article: 101.4] [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: 10/29/2018] [Accepted: 05/14/2019] [Indexed: 01/08/2023]
Abstract
Experimental models of the human brain are needed for basic understanding of its development and disease1. Human brain organoids hold unprecedented promise for this purpose; however, they are plagued by high organoid-to-organoid variability2,3. This has raised doubts as to whether developmental processes of the human brain can occur outside the context of embryogenesis with a degree of reproducibility that is comparable to the endogenous tissue. Here we show that an organoid model of the dorsal forebrain can reliably generate a rich diversity of cell types appropriate for the human cerebral cortex. We performed single-cell RNA-sequencing analysis of 166,242 cells isolated from 21 individual organoids, finding that 95% of the organoids generate a virtually indistinguishable compendium of cell types, following similar developmental trajectories and with a degree of organoid-to-organoid variability comparable to that of individual endogenous brains. Furthermore, organoids derived from different stem cell lines show consistent reproducibility in the cell types produced. The data demonstrate that reproducible development of the complex cellular diversity of the central nervous system does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments.
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Affiliation(s)
- Silvia Velasco
- 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 J Kedaigle
- 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
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Allison Nash
- 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
| | - Marina Rocha
- 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
| | - Giorgia Quadrato
- 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
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Bruna Paulsen
- 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
| | - Lan Nguyen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola Arlotta
- 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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25
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Abstract
Our ability to study the developing human brain has recently been dramatically advanced by the development of human 'brain organoids', three-dimensional culture systems that recapitulate selected aspects of human brain development in reductionist, yet complex, tissues in vitro. Here I discuss the promises and challenges this new model system presents.
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Affiliation(s)
- Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University
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26
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Quadrato G, Arlotta P. Present and future of modeling human brain development in 3D organoids. Curr Opin Cell Biol 2017; 49:47-52. [PMID: 29227864 DOI: 10.1016/j.ceb.2017.11.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/26/2017] [Indexed: 12/13/2022]
Abstract
Three-dimensional (3D) brain organoids derived from human pluripotent stem cells hold great potential to investigate complex human genetic states and to model aspects of human brain development and pathology. However, the field of brain organoids is still in its infancy, and their use has been limited by their variability and their inability to differentiate into 3D structures with reproducible anatomical organization. Here, starting from a review of basic principles of in vitro 'brain organogenesis', we discuss which aspects of human brain development and disease can be faithfully modeled with current brain organoid protocols, and discuss improvements that would allow them to become reliable tools to investigate complex features of human brain development and disease.
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Affiliation(s)
- Giorgia Quadrato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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27
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Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Min Yang S, Berger DR, Maria N, Scholvin J, Goldman M, Kinney JP, Boyden ES, Lichtman JW, Williams ZM, McCarroll SA, Arlotta P. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 2017; 545:48-53. [PMID: 28445462 DOI: 10.1038/nature22047] [Citation(s) in RCA: 735] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/07/2017] [Indexed: 12/18/2022]
Abstract
In vitro models of the developing brain such as three-dimensional brain organoids offer an unprecedented opportunity to study aspects of human brain development and disease. However, the cells generated within organoids and the extent to which they recapitulate the regional complexity, cellular diversity and circuit functionality of the brain remain undefined. Here we analyse gene expression in over 80,000 individual cells isolated from 31 human brain organoids. We find that organoids can generate a broad diversity of cells, which are related to endogenous classes, including cells from the cerebral cortex and the retina. Organoids could be developed over extended periods (more than 9 months), allowing for the establishment of relatively mature features, including the formation of dendritic spines and spontaneously active neuronal networks. Finally, neuronal activity within organoids could be controlled using light stimulation of photosensitive cells, which may offer a way to probe the functionality of human neuronal circuits using physiological sensory stimuli.
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Affiliation(s)
- Giorgia Quadrato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Tuan Nguyen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Evan Z Macosko
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John L Sherwood
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Sung Min Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Daniel R Berger
- Department of Cellular and Molecular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Natalie Maria
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jorg Scholvin
- Departments of Biological Engineering and Brain and Cognitive Sciences, MIT Media Lab and McGovern Institute, MIT, Cambridge, Massachusetts 02139, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Edward S Boyden
- Departments of Biological Engineering and Brain and Cognitive Sciences, MIT Media Lab and McGovern Institute, MIT, Cambridge, Massachusetts 02139, USA
| | - Jeff W Lichtman
- Department of Cellular and Molecular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ziv M Williams
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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28
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Arlotta P, Vanderhaeghen P. Editorial overview: Developmental neuroscience 2017. Curr Opin Neurobiol 2017; 42:A1-A4. [PMID: 28117212 DOI: 10.1016/j.conb.2017.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Paola Arlotta
- Harvard University, Department of Stem Cell and Regenerative Biology, Sherman Fairchild 358C, 7 Divinity Avenue, Cambridge, MA 02138, United States.
| | - Pierre Vanderhaeghen
- Université Libre de Bruxelles (ULB), Institute for Interdisciplinary Research (IRIBHM), ULB Institute of Neuroscience (UNI), WELBIO, Université Libre de Bruxelles, 808 Route de Lennik, B-1070 Brussels, Belgium.
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29
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Abstract
Homeosis is classically defined as the transformation of one body part into something that resembles another body part. We propose here to broaden the concept of homeosis to the many neuronal cell identity transformations that have been uncovered over the past few years upon removal of specific regulatory factors in organisms from Caenorhabditis elegans to Drosophila, zebrafish, and mice. The concept of homeosis provides a framework for the evolution of cell type diversity in the brain.
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Affiliation(s)
- Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Oliver Hobert
- Department of Biology and Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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30
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Affiliation(s)
- Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
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31
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Amamoto R, Huerta VGL, Takahashi E, Dai G, Grant AK, Fu Z, Arlotta P. Adult axolotls can regenerate original neuronal diversity in response to brain injury. eLife 2016; 5. [PMID: 27156560 PMCID: PMC4861602 DOI: 10.7554/elife.13998] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 12/21/2015] [Accepted: 04/07/2016] [Indexed: 12/11/2022] Open
Abstract
The axolotl can regenerate multiple organs, including the brain. It remains, however, unclear whether neuronal diversity, intricate tissue architecture, and axonal connectivity can be regenerated; yet, this is critical for recovery of function and a central aim of cell replacement strategies in the mammalian central nervous system. Here, we demonstrate that, upon mechanical injury to the adult pallium, axolotls can regenerate several of the populations of neurons present before injury. Notably, regenerated neurons acquire functional electrophysiological traits and respond appropriately to afferent inputs. Despite the ability to regenerate specific, molecularly-defined neuronal subtypes, we also uncovered previously unappreciated limitations by showing that newborn neurons organize within altered tissue architecture and fail to re-establish the long-distance axonal tracts and circuit physiology present before injury. The data provide a direct demonstration that diverse, electrophysiologically functional neurons can be regenerated in axolotls, but challenge prior assumptions of functional brain repair in regenerative species. DOI:http://dx.doi.org/10.7554/eLife.13998.001 Humans and other mammals have a very limited ability to regenerate new neurons in the brain to replace those that have been injured or damaged. In striking contrast, some animals like fish and salamanders are capable of filling in injured brain regions with new neurons. This is a complex task, as the brain is composed of many different types of neurons that are connected to each other in a highly organized manner across both short and long distances. The extent to which even the most regenerative species can build new brain regions was not known. Understanding any limitations will help to set realistic expectations for the success of potential treatments that aim to replace neurons in mammals. Amamoto et al. found that the brain of the axolotl, a species of salamander, could selectively regenerate the specific types of neurons that were damaged. This finding suggests that the brain is able to somehow sense which types of neurons are injured. The new neurons were able to mature into functional neurons, but they were limited in their ability to reconnect to their original, distant target neurons. More research is now needed to investigate how the axolotl brain recognizes which types of neurons have been damaged. It will also be important to understand which cells respond to the injury to give rise to the new neurons that fill the injury site, and to uncover the molecules that are important for governing this regenerative process. DOI:http://dx.doi.org/10.7554/eLife.13998.002
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Affiliation(s)
- Ryoji Amamoto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | | | - Emi Takahashi
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, United States
| | - Guangping Dai
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, United States
| | - Aaron K Grant
- Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, United States
| | - Zhanyan Fu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
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32
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Abstract
Achieving gender equality in science will require devising and implementing strategies to overcome the political, administrative, financial, and cultural challenges that exist in the current environment. In this forum, we propose an initial shortlist of recommendations to promote gender equality in science and stimulate future efforts to level the field.
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Affiliation(s)
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, SE1 9RT, UK
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33
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Tomassy GS, Dershowitz LB, Arlotta P. Diversity Matters: A Revised Guide to Myelination. Trends Cell Biol 2015; 26:135-147. [PMID: 26442841 DOI: 10.1016/j.tcb.2015.09.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [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: 06/30/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 11/28/2022]
Abstract
The evolutionary success of the vertebrate nervous system is largely due to a unique structural feature--the myelin sheath, a fatty envelope that surrounds the axons of neurons. By increasing the speed by which electrical signals travel along axons, myelin facilitates neuronal communication between distant regions of the nervous system. We review the cellular and molecular mechanisms that regulate the development of myelin as well as its homeostasis in adulthood. We discuss how finely tuned neuron-oligodendrocyte interactions are central to myelin formation during development and in the adult, and how these interactions can have profound implications for the plasticity of the adult brain. We also speculate how the functional diversity of both neurons and oligodendrocytes may impact on the myelination process in both health and disease.
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Affiliation(s)
- Giulio Srubek Tomassy
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lori Bowe Dershowitz
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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34
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Abstract
The neocortex is the part of the brain responsible for execution of higher-order brain functions, including cognition, sensory perception, and sophisticated motor control. During evolution, the neocortex has developed an unparalleled neuronal diversity, which still remains partly unclassified and unmapped at the functional level. Here, we broadly review the structural blueprint of the neocortex and discuss the current classification of its neuronal diversity. We then cover the principles and mechanisms that build neuronal diversity during cortical development and consider the impact of neuronal class-specific identity in shaping cortical connectivity and function.
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Affiliation(s)
- Simona Lodato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138; ,
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138; ,
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35
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Abstract
The neocortex is the part of the brain responsible for execution of higher-order brain functions, including cognition, sensory perception, and sophisticated motor control. During evolution, the neocortex has developed an unparalleled neuronal diversity, which still remains partly unclassified and unmapped at the functional level. Here, we broadly review the structural blueprint of the neocortex and discuss the current classification of its neuronal diversity. We then cover the principles and mechanisms that build neuronal diversity during cortical development and consider the impact of neuronal class-specific identity in shaping cortical connectivity and function.
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Affiliation(s)
- Simona Lodato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138; ,
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138; ,
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36
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Harris J, Tomassy GS, Arlotta P. Building blocks of the cerebral cortex: from development to the dish. Wiley Interdiscip Rev Dev Biol 2015; 4:529-44. [PMID: 25926310 DOI: 10.1002/wdev.192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 12/19/2022]
Abstract
Since Ramon y Cajal's examination of the cellular makeup of the cerebral cortex, it has been appreciated that this tissue exhibits some of the greatest degrees of cellular heterogeneity in the entire nervous system. This intricate structure emerges during a well-choreographed developmental process. Here, we review current classifications of the cellular constituents of the cerebral cortex and examine how these building blocks are forged during development. We also look at how basic developmental features underlying cortex formation in vivo have been applied to protocols aimed at generating cortical tissue in vitro.
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Affiliation(s)
- James Harris
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Giulio Srubek Tomassy
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
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37
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Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron 2015; 85:275-288. [PMID: 25556833 PMCID: PMC4430475 DOI: 10.1016/j.neuron.2014.12.024] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [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] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
Neuronal development requires a complex choreography of transcriptional decisions to obtain specific cellular identities. Realizing the ultimate goal of identifying genome-wide signatures that define and drive specific neuronal fates has been hampered by enormous complexity in both time and space during development. Here, we have paired high-throughput purification of pyramidal neuron subclasses with deep profiling of spatiotemporal transcriptional dynamics during corticogenesis to resolve lineage choice decisions. We identified numerous features ranging from spatial and temporal usage of alternative mRNA isoforms and promoters to a host of mRNA genes modulated during fate specification. Notably, we uncovered numerous long noncoding RNAs with restricted temporal and cell-type-specific expression. To facilitate future exploration, we provide an interactive online database to enable multidimensional data mining and dissemination. This multifaceted study generates a powerful resource and informs understanding of the transcriptional regulation underlying pyramidal neuron diversity in the neocortex. VIDEO ABSTRACT
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Affiliation(s)
- Bradley J. Molyneaux
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - Loyal A. Goff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Andrea C. Brettler
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - Siniša Hrvatin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
| | - John L. Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, United States
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, United States
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38
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Lodato S, Shetty AS, Arlotta P. Cerebral cortex assembly: generating and reprogramming projection neuron diversity. Trends Neurosci 2014; 38:117-25. [PMID: 25529141 DOI: 10.1016/j.tins.2014.11.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
The mammalian cerebral cortex is responsible for the highest levels of associative, cognitive and motor functions. In the central nervous system (CNS) the cortex stands as a prime example of extreme neuronal diversity, broadly classified into excitatory projection neurons (PNs) and inhibitory interneurons (INs). We review here recent progress made in understanding the strategies and mechanisms that shape PN diversity during embryogenesis, and discuss how PN classes may be maintained, postnatally, for the life of the organism. In addition, we consider the intriguing possibility that PNs may be amenable to directed reprogramming of their class-specific features to allow enhanced cortical plasticity in the adult.
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Affiliation(s)
- Simona Lodato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Ashwin S Shetty
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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39
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Arlotta P, Berninger B. Brains in metamorphosis: reprogramming cell identity within the central nervous system. Curr Opin Neurobiol 2014; 27:208-14. [PMID: 24800935 DOI: 10.1016/j.conb.2014.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 02/07/2014] [Revised: 04/04/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023]
Abstract
During embryonic development, uncommitted pluripotent cells undergo progressive epigenetic changes that lock them into a final differentiated state. Can mammalian cells change identity within the living organism? Direct lineage reprogramming of cells has attracted attention as a means to achieve organ regeneration. However, it is unclear whether cells in the CNS are endowed with the plasticity to reprogram. Neurons in particular are considered among the most immutable cell types, able to retain their class-specific traits for the lifespan of the organism. Here we focus on two experimental paradigms, glia-to-neuron and neuron-to-neuron conversion, to consider how lineage reprogramming has challenged the notion of CNS immutability, paving the way for the application of reprogramming strategies to reshape neurons and circuits in vivo.
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Affiliation(s)
- Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, USA.
| | - Benedikt Berninger
- Research group "Adult Neurogenesis and Cellular Reprogramming", Institute of Physiological Chemistry, and Focus Program Translational Neuroscience, University Medical Center, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 19, Mainz, Germany; Department of Physiological Genomics, Institute of Physiology, Ludwig Maximilians University Munich, Schillerstrasse 46, D-80336 Munich, Germany.
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40
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Tomassy GS, Berger DR, Chen HH, Kasthuri N, Hayworth KJ, Vercelli A, Seung HS, Lichtman JW, Arlotta P. Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex. Science 2014; 344:319-24. [PMID: 24744380 PMCID: PMC4122120 DOI: 10.1126/science.1249766] [Citation(s) in RCA: 346] [Impact Index Per Article: 34.6] [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: 11/02/2022]
Abstract
Myelin is a defining feature of the vertebrate nervous system. Variability in the thickness of the myelin envelope is a structural feature affecting the conduction of neuronal signals. Conversely, the distribution of myelinated tracts along the length of axons has been assumed to be uniform. Here, we traced high-throughput electron microscopy reconstructions of single axons of pyramidal neurons in the mouse neocortex and built high-resolution maps of myelination. We find that individual neurons have distinct longitudinal distribution of myelin. Neurons in the superficial layers displayed the most diversified profiles, including a new pattern where myelinated segments are interspersed with long, unmyelinated tracts. Our data indicate that the profile of longitudinal distribution of myelin is an integral feature of neuronal identity and may have evolved as a strategy to modulate long-distance communication in the neocortex.
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Affiliation(s)
- Giulio Srubek Tomassy
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge MA 02138
| | - Daniel R. Berger
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA 02139
| | - Hsu-Hsin Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge MA 02138
| | - Narayanan Kasthuri
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138
| | - Kenneth J. Hayworth
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138
| | - Alessandro Vercelli
- Neuroscience Institute Cavalieri Ottolenghi, Neuroscience Institute of Turin, Corso M. d’Azeglio 52, Turin, Italy10126
| | - H. Sebastian Seung
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA 02139
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge MA 02138
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41
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Abstract
In 2012, John Gurdon and Shinya Yamanaka shared the Nobel Prize for the demonstration that the identity of differentiated cells is not irreversibly determined but can be changed back to a pluripotent state under appropriate instructive signals. The principle that differentiated cells can revert to an embryonic state and even be converted directly from one cell type into another not only turns fundamental principles of development on their heads but also has profound implications for regenerative medicine. Replacement of diseased tissue with newly reprogrammed cells and modeling of human disease are concrete opportunities. Here, we focus on the central nervous system to consider whether and how reprogramming of cell identity may affect regeneration and modeling of a system historically considered immutable and hardwired.
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Affiliation(s)
- Ryoji Amamoto
- Department of Stem Cell and Regenerative Biology, Sherman Fairchild Building, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
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42
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Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife 2013; 2:e01749. [PMID: 24381249 PMCID: PMC3874104 DOI: 10.7554/elife.01749] [Citation(s) in RCA: 534] [Impact Index Per Article: 48.5] [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] [Indexed: 12/31/2022] Open
Abstract
Many studies are uncovering functional roles for long noncoding RNAs (lncRNAs), yet few have been tested for in vivo relevance through genetic ablation in animal models. To investigate the functional relevance of lncRNAs in various physiological conditions, we have developed a collection of 18 lncRNA knockout strains in which the locus is maintained transcriptionally active. Initial characterization revealed peri- and postnatal lethal phenotypes in three mutant strains (Fendrr, Peril, and Mdgt), the latter two exhibiting incomplete penetrance and growth defects in survivors. We also report growth defects for two additional mutant strains (linc–Brn1b and linc–Pint). Further analysis revealed defects in lung, gastrointestinal tract, and heart in Fendrr−/− neonates, whereas linc–Brn1b−/− mutants displayed distinct abnormalities in the generation of upper layer II–IV neurons in the neocortex. This study demonstrates that lncRNAs play critical roles in vivo and provides a framework and impetus for future larger-scale functional investigation into the roles of lncRNA molecules. DOI:http://dx.doi.org/10.7554/eLife.01749.001 The mammalian genome is comprised of DNA sequences that contain the templates for proteins, and other DNA sequences that do not code for proteins. The coding DNA sequences are transcribed to make messenger RNA molecules, which are then translated to make proteins. Researchers have known for many years that some of the noncoding DNA sequences are also transcribed to make other types of RNA molecules, such as transfer and ribosomal RNA. However, the true breadth and diversity of the roles played by these other RNA molecules have only recently begun to be fully appreciated. Mammalian genomes contain thousands of noncoding DNA sequences that are transcribed. Recent in vitro studies suggest that the resulting long noncoding RNA molecules can act as regulators of transcription, translation, and cell cycle. In vitro studies also suggest that these long noncoding RNA molecules may play a role in mammalian development and disease. Yet few in vivo studies have been performed to support or confirm such hypotheses. Now Sauvageau et al. have developed several lines of knockout mice to investigate a subset of noncoding RNA molecules known as long intergenic noncoding RNAs (lincRNAs). These experiments reveal that lincRNAs have a strong influence on the overall viability of mice, and also on a number of developmental processes, including the development of lungs and the cerebral cortex. Given that the vast majority of the human genome is transcribed, the mouse models developed by Sauvageau et al. represent an important step in determining the physiological relevance, on a genetic level, of the noncoding portion of the genome in vivo. DOI:http://dx.doi.org/10.7554/eLife.01749.002
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Affiliation(s)
- Martin Sauvageau
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
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43
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Abstract
During embryonic development, cells in an uncommitted pluripotent state undergo progressive epigenetic changes that lock them into a final restrictive differentiated state. However, recent advances have shown that not only is it possible for a fully differentiated cell to revert back to a pluripotent state, a process called nuclear reprogramming, but also that differentiated cells can be directly converted from one class into another without generating progenitor intermediates, a process known as direct lineage conversion. In this review, we discuss recent progress made in direct lineage reprogramming of differentiated cells into neurons and discuss some of the therapeutic implications of the findings.
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44
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Abstract
Although myelination largely occurs during early postnatal life, myelinating oligodendrocytes are still generated in the adult brain. Myelin turnover in the adult is necessary for proper neuronal function and is gravely compromised in myelin disorders. The lineage relationship between adult neural stem cells and adult-born oligodendrocytes has been clarified, highlighting molecular pathways that could potentially be targeted to favour de novo myelination in pathological situations.
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45
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Abstract
Cortical and striatal interneurons are both generated within the ventral telencephalon, but their migratory journey takes them to very different destinations. Two articles in this issue (van den Berge et al., 2013; McKinsey et al., 2013) add an important molecular component to our understanding of how, during development, interneurons reach the cerebral cortex.
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Affiliation(s)
- Giulio S Tomassy
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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46
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Lodato S, Rouaux C, Arlotta P. ISDN2012_0263: Molecular development of projection neuron types and building of local microcircuitry in the cerebral cortex. Int J Dev Neurosci 2012. [DOI: 10.1016/j.ijdevneu.2012.10.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Simona Lodato
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeMAUnited States
| | - Caroline Rouaux
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeMAUnited States
| | - Paola Arlotta
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeMAUnited States
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47
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Abstract
Recent discoveries in nuclear reprogramming have challenged the dogma that the identity of terminally differentiated cells cannot be changed. The identification of molecular mechanisms that reprogram differentiated cells to a new identity carries profound implications for regenerative medicine across organ systems. The central nervous system (CNS) has historically been considered to be largely immutable. However, recent studies indicate that even the adult CNS is imparted with the potential to change under the appropriate stimuli. Here, we review current knowledge regarding the capability of distinct cells within the CNS to reprogram their identity and consider the role of developmental signals in directing these cell fate decisions. Finally, we discuss the progress and current challenges of using developmental signals to precisely direct the generation of individual neuronal subtypes in the postnatal CNS and in the dish.
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Affiliation(s)
- Caroline Rouaux
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
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48
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Abstract
The adult brain was thought to be a slowly decaying organ, a sophisticated but flawed machine condemned to inevitable decline. Today we know that the brain is more plastic than previously assumed, as most prominently demonstrated by the constitutive birth of new neurons that occurs in selected regions of the adult brain, even in humans. However, the overall modest capacity for endogenous repair of the central nervous system (CNS) has sparked interest in understanding the barriers to neuronal regeneration and in developing novel approaches to enable neuronal and circuit repair for therapeutic benefit in neurodegenerative disorders and traumatic injuries. Scientists recently assembled in Baeza, a picturesque town in the south of Spain, to discuss aspects of CNS regeneration. The picture that emerged shows how an integrated view of developmental and adult neurogenesis may inform the manipulation of neural progenitors, differentiated cells, and pluripotent stem cells for therapeutic benefit and foster new understanding of the inner limits of brain plasticity.
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Affiliation(s)
- Guillermina López-Bendito
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), San Joan d'Alacant, 03550, Spain.
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49
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Sohur US, Arlotta P, Macklis JD. Developmental Controls are Re-Expressed during Induction of Neurogenesis in the Neocortex of Young Adult Mice. Front Neurosci 2012; 6:12. [PMID: 22347158 PMCID: PMC3272649 DOI: 10.3389/fnins.2012.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 08/04/2011] [Accepted: 01/18/2012] [Indexed: 11/13/2022] Open
Abstract
Whether induction of low-level neurogenesis in normally non-neurogenic regions of the adult brain mimics aspects of developmental neurogenesis is currently unknown. Previously, we and others identified that biophysically induced, neuron subtype-specific apoptosis in mouse neocortex results in induction of neurogenesis of limited numbers of subtype-appropriate projection neurons with axonal projections to either thalamus or spinal cord, depending on the neuron subtype activated to undergo targeted apoptosis. Here, we test the hypothesis that developmental genes from embryonic corticogenesis are re-activated, and that some of these genes might underlie induction of low-level adult neocortical neurogenesis. We directly investigated this hypothesis via microarray analysis of microdissected regions of young adult mouse neocortex undergoing biophysically activated targeted apoptosis of neocortical callosal projection neurons. We compared the microarray results identifying differentially expressed genes with public databases of embryonic developmental genes. We find that, following activation of subtype-specific neuronal apoptosis, three distinct sets of normal developmental genes are selectively re-expressed in neocortical regions of induced neurogenesis in young adult mice: (1) genes expressed by subsets of progenitors and immature neurons in the developing ventricular and/or subventricular zones; (2) genes normally expressed by developmental radial glial progenitors; and (3) genes involved in synaptogenesis. Together with previous results, the data indicate that at least some developmental molecular controls over embryonic neurogenesis can be re-activated in the setting of induction of neurogenesis in the young adult neocortex, and suggest that some of these activate and initiate adult neuronal differentiation from endogenous progenitor populations. Understanding molecular mechanisms contributing to induced adult neurogenesis might enable directed CNS repair.
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Affiliation(s)
- U Shivraj Sohur
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University Cambridge, MA, USA
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50
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Lodato S, Rouaux C, Quast KB, Jantrachotechatchawan C, Studer M, Hensch TK, Arlotta P. Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex. Neuron 2011; 69:763-79. [PMID: 21338885 DOI: 10.1016/j.neuron.2011.01.015] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2010] [Indexed: 01/08/2023]
Abstract
In the mammalian cerebral cortex, the developmental events governing the integration of excitatory projection neurons and inhibitory interneurons into balanced local circuitry are poorly understood. We report that different subtypes of projection neurons uniquely and differentially determine the laminar distribution of cortical interneurons. We find that in Fezf2⁻/⁻ cortex, the exclusive absence of subcerebral projection neurons and their replacement by callosal projection neurons cause distinctly abnormal lamination of interneurons and altered GABAergic inhibition. In addition, experimental generation of either corticofugal neurons or callosal neurons below the cortex is sufficient to recruit cortical interneurons to these ectopic locations. Strikingly, the identity of the projection neurons generated, rather than strictly their birthdate, determines the specific types of interneurons recruited. These data demonstrate that in the neocortex individual populations of projection neurons cell-extrinsically control the laminar fate of interneurons and the assembly of local inhibitory circuitry.
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Affiliation(s)
- Simona Lodato
- Center for Regenerative Medicine and Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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