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Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Campbell LJ, Boyd P, Palazzo I, Nagashima M, Silva NJ, Hitchcock PF, Qian J, Hyde DR, Blackshaw S. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. Nat Commun 2023; 14:8477. [PMID: 38123561 PMCID: PMC10733277 DOI: 10.1038/s41467-023-44142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes through Müller glia (MG) reprogramming and asymmetric cell division that produces a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, do MG reprogram to a developmental retinal progenitor cell (RPC) state? Second, to what extent does regeneration recapitulate retinal development? And finally, does loss of different retinal cell subtypes induce unique MG regeneration responses? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. Here we show that injury induces MG to reprogram to a state similar to late-stage RPCs. However, there are major transcriptional differences between MGPCs and RPCs, as well as major transcriptional differences between activated MG and MGPCs when different retinal cell subtypes are damaged. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Maria Iribarne
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Dmitri Serjanov
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Yijie Zhai
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Thanh Hoang
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Leah J Campbell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Patrick Boyd
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Isabella Palazzo
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Mikiko Nagashima
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Nicholas J Silva
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Peter F Hitchcock
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| | - David R Hyde
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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Blackshaw S, Lyu P, Zhai Y, Qian J, Iribarne M, Serjanov D, Campbell L, Boyd P, Hyde D, Palazzo I, Hoang T, Nagashima M, Silva N, Hitchcock P. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. RESEARCH SQUARE 2023:rs.3.rs-3294233. [PMID: 37790324 PMCID: PMC10543505 DOI: 10.21203/rs.3.rs-3294233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
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Affiliation(s)
| | | | - Yijie Zhai
- Johns Hopkins University School of Medicine
| | - Jiang Qian
- Johns Hopkins University School of Medicine
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Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Campbell LJ, Boyd P, Palazzo I, Nagashima M, Silva NJ, HItchcock PF, Qian J, Hyde DR, Blackshaw S. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552451. [PMID: 37609307 PMCID: PMC10441373 DOI: 10.1101/2023.08.08.552451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
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