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Boivin B, Roet KCD, Huang X, Karhohs KW, Rohban MH, Sandoe J, Wiskow O, Maeda R, Grantham A, Dornon MK, Shao J, Frost D, Baker D, Eggan K, Carpenter AE, Woolf CJ. A multiparametric activity profiling platform for neuron disease phenotyping and drug screening. Mol Biol Cell 2022; 33:ar54. [PMID: 34910584 PMCID: PMC9265164 DOI: 10.1091/mbc.e21-10-0481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Patient stem cell-derived models enable imaging of complex disease phenotypes and the development of scalable drug discovery platforms. Current preclinical methods for assessing cellular activity do not, however, capture the full intricacies of disease-induced disturbances and instead typically focus on a single parameter, which impairs both the understanding of disease and the discovery of effective therapeutics. Here, we describe a cloud-based image processing and analysis platform that captures the intricate activity profile revealed by GCaMP fluorescence recordings of intracellular calcium changes and enables the discovery of molecules that correct 153 parameters that define the amyotrophic lateral sclerosis motor neuron disease phenotype. In a high-throughput screen, we identified compounds that revert the multiparametric disease profile to that found in healthy cells, a novel and robust measure of therapeutic potential quite distinct from unidimensional screening. This platform can guide the development of therapeutics that counteract the multifaceted pathological features of diseased cellular activity.
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Affiliation(s)
- Bruno Boivin
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Kasper C D Roet
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Xuan Huang
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Kyle W Karhohs
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA 02142
| | - Mohammad H Rohban
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA 02142
| | - Jack Sandoe
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Rie Maeda
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Alyssa Grantham
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Mary K Dornon
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Jenny Shao
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Devlin Frost
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115
| | - Dylan Baker
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138
| | - Anne E Carpenter
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA 02142
| | - Clifford J Woolf
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115.,Department of Neurobiology, Harvard Medical School, Boston, MA 02115
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2
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Huang X, Roet KCD, Zhang L, Brault A, Berg AP, Jefferson AB, Klug-McLeod J, Leach KL, Vincent F, Yang H, Coyle AJ, Jones LH, Frost D, Wiskow O, Chen K, Maeda R, Grantham A, Dornon MK, Klim JR, Siekmann MT, Zhao D, Lee S, Eggan K, Woolf CJ. Human amyotrophic lateral sclerosis excitability phenotype screen: Target discovery and validation. Cell Rep 2021; 35:109224. [PMID: 34107252 PMCID: PMC8209673 DOI: 10.1016/j.celrep.2021.109224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/14/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Drug development is hampered by poor target selection. Phenotypic screens using neurons differentiated from patient stem cells offer the possibility to validate known and discover novel disease targets in an unbiased fashion. To identify targets for managing hyperexcitability, a pathological feature of amyotrophic lateral sclerosis (ALS), we design a multi-step screening funnel using patient-derived motor neurons. High-content live cell imaging is used to evaluate neuronal excitability, and from a screen against a chemogenomic library of 2,899 target-annotated compounds, 67 reduce the hyperexcitability of ALS motor neurons carrying the SOD1(A4V) mutation, without cytotoxicity. Bioinformatic deconvolution identifies 13 targets that modulate motor neuron excitability, including two known ALS excitability modulators, AMPA receptors and Kv7.2/3 ion channels, constituting target validation. We also identify D2 dopamine receptors as modulators of ALS motor neuron excitability. This screen demonstrates the power of human disease cell-based phenotypic screens for identifying clinically relevant targets for neurological disorders. Motor neuron hyperexcitability is observed in both ALS patients and their iPSC-derived neurons. Combining a high-content live imaging excitability phenotypic assay, high-throughput screening against a cross-annotated chemogenomic library, and bioinformatic enrichment analysis, Huang et al. identify targets modulating the hyperexcitability of ALS patient-derived motor neurons in an unbiased manner.
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Affiliation(s)
- Xuan Huang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Kasper C D Roet
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Liying Zhang
- Medicine Design, Pfizer, Cambridge, MA 02139, USA
| | - Amy Brault
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Allison P Berg
- Rare Disease Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Anne B Jefferson
- Pfizer Centers for Therapeutic Innovation (CTI), San Francisco, CA 94080, USA
| | | | - Karen L Leach
- Pfizer Centers for Therapeutic Innovation (CTI), Cambridge, MA 02139, USA
| | | | - Hongying Yang
- Pfizer Centers for Therapeutic Innovation (CTI), Cambridge, MA 02139, USA
| | - Anthony J Coyle
- Pfizer Centers for Therapeutic Innovation (CTI), Cambridge, MA 02139, USA
| | - Lyn H Jones
- Medicine Design, Pfizer, Cambridge, MA 02139, USA
| | - Devlin Frost
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Kuchuan Chen
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Rie Maeda
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Alyssa Grantham
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mary K Dornon
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Marco T Siekmann
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Dongyi Zhao
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Seungkyu Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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3
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Kiskinis E, Kralj JM, Zou P, Weinstein EN, Zhang H, Tsioras K, Wiskow O, Ortega JA, Eggan K, Cohen AE. All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. Stem Cell Reports 2018; 10:1991-2004. [PMID: 29779896 PMCID: PMC5993648 DOI: 10.1016/j.stemcr.2018.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 11/26/2022] Open
Abstract
Human induced pluripotent stem cell (iPSC)-derived neurons are an attractive substrate for modeling disease, yet the heterogeneity of these cultures presents a challenge for functional characterization by manual patch-clamp electrophysiology. Here, we describe an optimized all-optical electrophysiology, “Optopatch,” pipeline for high-throughput functional characterization of human iPSC-derived neuronal cultures. We demonstrate the method in a human iPSC-derived motor neuron (iPSC-MN) model of amyotrophic lateral sclerosis (ALS). In a comparison of iPSC-MNs with an ALS-causing mutation (SOD1 A4V) with their genome-corrected controls, the mutants showed elevated spike rates under weak or no stimulus and greater likelihood of entering depolarization block under strong optogenetic stimulus. We compared these results with numerical simulations of simple conductance-based neuronal models and with literature results in this and other iPSC-based models of ALS. Our data and simulations suggest that deficits in slowly activating potassium channels may underlie the changes in electrophysiology in the SOD1 A4V mutation. All-optical electrophysiology enables high-throughput assays in hiPSC-derived neurons Neurons derived from ALS patients fire differently from genome-corrected controls A deficit in the Kv7 potassium current can explain the difference in firing
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Affiliation(s)
- Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peng Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eli N Weinstein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Hongkang Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Konstantinos Tsioras
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Alberto Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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4
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Ray MK, Wiskow O, King MJ, Ismail N, Ergun A, Wang Y, Plys AJ, Davis CP, Kathrein K, Sadreyev R, Borowsky ML, Eggan K, Zon L, Galloway JL, Kingston RE. CAT7 and cat7l Long Non-coding RNAs Tune Polycomb Repressive Complex 1 Function during Human and Zebrafish Development. J Biol Chem 2016; 291:19558-72. [PMID: 27405765 DOI: 10.1074/jbc.m116.730853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Indexed: 11/06/2022] Open
Abstract
The essential functions of polycomb repressive complex 1 (PRC1) in development and gene silencing are thought to involve long non-coding RNAs (lncRNAs), but few specific lncRNAs that guide PRC1 activity are known. We screened for lncRNAs, which co-precipitate with PRC1 from chromatin and found candidates that impact polycomb group protein (PcG)-regulated gene expression in vivo A novel lncRNA from this screen, CAT7, regulates expression and polycomb group binding at the MNX1 locus during early neuronal differentiation. CAT7 contains a unique tandem repeat domain that shares high sequence similarity to a non-syntenic zebrafish analog, cat7l Defects caused by interference of cat7l RNA during zebrafish embryogenesis were rescued by human CAT7 RNA, enhanced by interference of a PRC1 component, and suppressed by interference of a known PRC1 target gene, demonstrating cat7l genetically interacts with a PRC1. We propose a model whereby PRC1 acts in concert with specific lncRNAs and that CAT7/cat7l represents convergent lncRNAs that independently evolved to tune PRC1 repression at individual loci.
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Affiliation(s)
- Mridula K Ray
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Ole Wiskow
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138
| | - Matthew J King
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114
| | - Nidha Ismail
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114
| | - Ayla Ergun
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02114
| | - Yanqun Wang
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Aaron J Plys
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Christopher P Davis
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Katie Kathrein
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Boston, Massachusetts, 02115, and
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02114
| | - Mark L Borowsky
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02138, The Howard Hughes Medical Institute, Cambridge, MA 02138
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Boston, Massachusetts, 02115, and
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02114,
| | - Robert E Kingston
- From the Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114,
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5
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Falk A, Koch P, Kesavan J, Takashima Y, Ladewig J, Alexander M, Wiskow O, Tailor J, Trotter M, Pollard S, Smith A, Brüstle O. Capture of neuroepithelial-like stem cells from pluripotent stem cells provides a versatile system for in vitro production of human neurons. PLoS One 2012; 7:e29597. [PMID: 22272239 PMCID: PMC3260177 DOI: 10.1371/journal.pone.0029597] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 11/30/2011] [Indexed: 01/17/2023] Open
Abstract
Human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC) provide new prospects for studying human neurodevelopment and modeling neurological disease. In particular, iPSC-derived neural cells permit a direct comparison of disease-relevant molecular pathways in neurons and glia derived from patients and healthy individuals. A prerequisite for such comparative studies are robust protocols that efficiently yield standardized populations of neural cell types. Here we show that long-term self-renewing neuroepithelial-like stem cells (lt-NES cells) derived from 3 hESC and 6 iPSC lines in two independent laboratories exhibit consistent characteristics including i) continuous expandability in the presence of FGF2 and EGF; ii) stable neuronal and glial differentiation competence; iii) characteristic transcription factor profile; iv) hindbrain specification amenable to regional patterning; v) capacity to generate functionally mature human neurons. We further show that lt-NES cells are developmentally distinct from fetal tissue-derived radial glia-like stem cells. We propose that lt-NES cells provide an interesting tool for studying human neurodevelopment and may serve as a standard system to facilitate comparative analyses of hESC and hiPSC-derived neural cells from control and diseased genetic backgrounds.
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Affiliation(s)
- Anna Falk
- Department of Biochemistry, Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, United Kingdom
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn and Hertie Foundation, Bonn, Germany
| | - Jaideep Kesavan
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn and Hertie Foundation, Bonn, Germany
| | - Yasuhiro Takashima
- Department of Biochemistry, Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, United Kingdom
| | - Julia Ladewig
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn and Hertie Foundation, Bonn, Germany
| | - Michael Alexander
- Institute of Human Genetics, LIFE & BRAIN Center, University of Bonn, Bonn, Germany
| | - Ole Wiskow
- Department of Biochemistry, Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, United Kingdom
| | - Jignesh Tailor
- Department of Biochemistry, Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Trotter
- Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Steven Pollard
- Department of Biochemistry, Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, United Kingdom
| | - Austin Smith
- Department of Biochemistry, Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, United Kingdom
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn and Hertie Foundation, Bonn, Germany
- * E-mail:
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Gómez-López S, Wiskow O, Favaro R, Nicolis SK, Price DJ, Pollard SM, Smith A. Sox2 and Pax6 maintain the proliferative and developmental potential of gliogenic neural stem cells In vitro. Glia 2011; 59:1588-99. [PMID: 21766338 DOI: 10.1002/glia.21201] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 05/25/2011] [Indexed: 02/02/2023]
Abstract
Radial-glia-like neural stem (NS) cells may be derived from neural tissues or via differentiation of pluripotent embryonic stem (ES) cells. However, the mechanisms controlling NS cell propagation and differentiation are not yet fully understood. Here we investigated the roles of Sox2 and Pax6, transcription factors widely expressed in central nervous system (CNS) progenitors, in mouse NS cells. Conditional deletion of either Sox2 or Pax6 in forebrain-derived NS cells reduced their clonogenicity in a gene dosage-dependent manner. Cells heterozygous for either gene displayed moderate proliferative defects, which may relate to human pathologies attributed to SOX2 or PAX6 deficiencies. In the complete absence of Sox2, cells exited the cell cycle with concomitant downregulation of neural progenitor markers Nestin and Blbp. This occurred despite expression of the close relative Sox3. Ablation of Pax6 also caused major proliferative defects. However, a subpopulation of cells was able to expand continuously without Pax6. These Pax6-null cells retained progenitor markers but had altered morphology. They exhibited compromised differentiation into astrocytes and oligodendrocytes, highlighting that the role of Pax6 extends beyond neurogenic competence. Overall these findings indicate that Sox2 and Pax6 are both critical for self-renewal of differentiation-competent radial glia-like NS cells.
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Affiliation(s)
- Sandra Gómez-López
- Wellcome Trust Centre for Stem Cell Research and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
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