1
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Tresenrider A, Hooper M, Todd L, Kierney F, Blasdel N, Trapnell C, Reh TA. A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia. bioRxiv 2024:2023.09.26.559569. [PMID: 37808650 PMCID: PMC10557658 DOI: 10.1101/2023.09.26.559569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Retinal degeneration in mammals causes permanent loss of vision, due to an inability to regenerate naturally. Some non-mammalian vertebrates show robust regeneration, via Muller glia (MG). We have recently made significant progress in stimulating adult mouse MG to regenerate functional neurons by transgenic expression of the proneural transcription factor Ascl1. While these results showed that MG can serve as an endogenous source of neuronal replacement, the efficacy of this process is limited. With the goal of improving this in mammals, we designed a small molecule screen using sci-Plex, a method to multiplex up to thousands of single nucleus RNA-seq conditions into a single experiment. We used this technology to screen a library of 92 compounds, identified, and validated two that promote neurogenesis in vivo. Our results demonstrate that high-throughput single-cell molecular profiling can substantially improve the discovery process for molecules and pathways that can stimulate neural regeneration and further demonstrate the potential for this approach to restore vision in patients with retinal disease.
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Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Marcus Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Faith Kierney
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Nicolai Blasdel
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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2
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Pavlou M, Probst M, Blasdel N, Prieve AR, Reh TA. The impact of timing and injury mode on induced neurogenesis in the adult mammalian retina. Stem Cell Reports 2024; 19:239-253. [PMID: 38278154 PMCID: PMC10874861 DOI: 10.1016/j.stemcr.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024] Open
Abstract
Regeneration of neurons has important implications for human health, and the retina provides an accessible system to study the potential of replacing neurons following injury. In previous work, we generated transgenic mice in which neurogenic transcription factors were expressed in Müller glia (MG) and showed that they stimulated neurogenesis following inner retinal damage. It was unknown, however, whether the timing or mode of injury mattered in this process. Here, we explored these parameters on induced neurogenesis from MG and show that MG expressing Ascl1 will generate new bipolar neurons with similar efficiency irrespective of injury mode or timing. However, MG that express Ascl1-Atoh1 produce a new type of retinal ganglion-like cell after outer retinal damage, which is absent with inner retinal damage. Our data suggest that although cell fate is primarily dictated by neurogenic transcription factors, the inflammatory state of MG relative to injury can influence the outcome of induced neurogenesis.
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Affiliation(s)
- Marina Pavlou
- Department of Biological Structure, University of Washington, Seattle, WA, USA; Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Marlene Probst
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Nicolai Blasdel
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Aric R Prieve
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA; Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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3
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Wohlschlegel J, Finkbeiner C, Hoffer D, Kierney F, Prieve A, Murry AD, Haugan AK, Ortuño-Lizarán I, Rieke F, Golden SA, Reh TA. ASCL1 induces neurogenesis in human Müller glia. Stem Cell Reports 2023; 18:2400-2417. [PMID: 38039971 PMCID: PMC10724232 DOI: 10.1016/j.stemcr.2023.10.021] [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: 03/22/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023] Open
Abstract
In mammals, loss of retinal cells due to disease or trauma is an irreversible process that can lead to blindness. Interestingly, regeneration of retinal neurons is a well established process in some non-mammalian vertebrates and is driven by the Müller glia (MG), which are able to re-enter the cell cycle and reprogram into neurogenic progenitors upon retinal injury or disease. Progress has been made to restore this mechanism in mammals to promote retinal regeneration: MG can be stimulated to generate new neurons in vivo in the adult mouse retina after the over-expression of the pro-neural transcription factor Ascl1. In this study, we applied the same strategy to reprogram human MG derived from fetal retina and retinal organoids into neurons. Combining single cell RNA sequencing, single cell ATAC sequencing, immunofluorescence, and electrophysiology we demonstrate that human MG can be reprogrammed into neurogenic cells in vitro.
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Affiliation(s)
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Dawn Hoffer
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Faith Kierney
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Aric Prieve
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Alexandria D Murry
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Alexandra K Haugan
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | | | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Sam A Golden
- Department of Biological Structure, University of Washington, Seattle, WA, USA; Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA; Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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4
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Johnson TV, Baranov P, Di Polo A, Fortune B, Gokoffski KK, Goldberg JL, Guido W, Kolodkin AL, Mason CA, Ou Y, Reh TA, Ross AG, Samuels BC, Zack DJ. The Retinal Ganglion Cell Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration Consortium. Ophthalmol Sci 2023; 3:100390. [PMID: 38025164 PMCID: PMC10630665 DOI: 10.1016/j.xops.2023.100390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 12/01/2023]
Abstract
Purpose The Retinal Ganglion Cell (RGC) Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration (RReSTORe) consortium was founded in 2021 to help address the numerous scientific and clinical obstacles that impede development of vision-restorative treatments for patients with optic neuropathies. The goals of the RReSTORe consortium are: (1) to define and prioritize the most critical challenges and questions related to RGC regeneration; (2) to brainstorm innovative tools and experimental approaches to meet these challenges; and (3) to foster opportunities for collaborative scientific research among diverse investigators. Design and Participants The RReSTORe consortium currently includes > 220 members spanning all career stages worldwide and is directed by an organizing committee comprised of 15 leading scientists and physician-scientists of diverse backgrounds. Methods Herein, we describe the structure and organization of the RReSTORe consortium, its activities to date, and the perceived impact that the consortium has had on the field based on a survey of participants. Results In addition to helping propel the field of regenerative medicine as applied to optic neuropathies, the RReSTORe consortium serves as a framework for developing large collaborative groups aimed at tackling audacious goals that may be expanded beyond ophthalmology and vision science. Conclusions The development of innovative interventions capable of restoring vision for patients suffering from optic neuropathy would be transformative for the ophthalmology field, and may set the stage for functional restoration in other central nervous system disorders. By coordinating large-scale, international collaborations among scientists with diverse and complementary expertise, we are confident that the RReSTORe consortium will help to accelerate the field toward clinical translation. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Thomas V. Johnson
- Wilmer Eye Institute and Cellular & Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Petr Baranov
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Maryland
| | - Adriana Di Polo
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada, Neuroscience Division, Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Brad Fortune
- Discoveries in Sight Research Laboratories, Devers Eye Institute and Legacy Research Institute, Legacy Health, Portland, Oregon
| | | | - Jeffrey L. Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California
| | - William Guido
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky
| | - Alex L. Kolodkin
- Solomon H Snyder Department of Neuroscience and Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Carol A. Mason
- Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Department of Pathology & Cell Biology, and Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Yvonne Ou
- Department of Ophthalmology, University of California, San Francisco, California
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Ahmara G. Ross
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brian C. Samuels
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama
| | - Donald J. Zack
- Departments of Ophthalmology (Wilmer Eye Institute), Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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5
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Soucy JR, Todd L, Kriukov E, Phay M, Malechka VV, Rivera JD, Reh TA, Baranov P. Controlling donor and newborn neuron migration and maturation in the eye through microenvironment engineering. Proc Natl Acad Sci U S A 2023; 120:e2302089120. [PMID: 37931105 PMCID: PMC10655587 DOI: 10.1073/pnas.2302089120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/30/2023] [Indexed: 11/08/2023] Open
Abstract
Ongoing cell therapy trials have demonstrated the need for precision control of donor cell behavior within the recipient tissue. We present a methodology to guide stem cell-derived and endogenously regenerated neurons by engineering the microenvironment. Being an "approachable part of the brain," the eye provides a unique opportunity to study neuron fate and function within the central nervous system. Here, we focused on retinal ganglion cells (RGCs)-the neurons in the retina are irreversibly lost in glaucoma and other optic neuropathies but can potentially be replaced through transplantation or reprogramming. One of the significant barriers to successful RGC integration into the existing mature retinal circuitry is cell migration toward their natural position in the retina. Our in silico analysis of the single-cell transcriptome of the developing human retina identified six receptor-ligand candidates, which were tested in functional in vitro assays for their ability to guide human stem cell-derived RGCs. We used our lead molecule, SDF1, to engineer an artificial gradient in the retina, which led to a 2.7-fold increase in donor RGC migration into the ganglion cell layer (GCL) and a 3.3-fold increase in the displacement of newborn RGCs out of the inner nuclear layer. Only donor RGCs that migrated into the GCL were found to express mature RGC markers, indicating the importance of proper structure integration. Together, these results describe an "in silico-in vitro-in vivo" framework for identifying, selecting, and applying soluble ligands to control donor cell function after transplantation.
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Affiliation(s)
- Jonathan R. Soucy
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology, Harvard Medical School, Boston, MA02114
| | - Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA98195
| | - Emil Kriukov
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology, Harvard Medical School, Boston, MA02114
| | - Monichan Phay
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology, Harvard Medical School, Boston, MA02114
| | - Volha V. Malechka
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology, Harvard Medical School, Boston, MA02114
| | - John Dayron Rivera
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology, Harvard Medical School, Boston, MA02114
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA98195
| | - Petr Baranov
- The Schepens Eye Research Institute of Massachusetts Eye and Ear, Boston, MA02114
- Department of Ophthalmology, Harvard Medical School, Boston, MA02114
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6
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Pavlou M, Reh TA. Cell-Based Therapies: Strategies for Regeneration. Cold Spring Harb Perspect Med 2023; 13:a041306. [PMID: 36878647 PMCID: PMC10626262 DOI: 10.1101/cshperspect.a041306] [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: 03/08/2023]
Abstract
The neural retina of mammals, like most of the rest of the central nervous system, does not regenerate new neurons after they are lost through damage or disease. The ability of nonmammalian vertebrates, like fish and amphibians, is remarkable, and lessons learned over the last 20 years have revealed some of the mechanisms underlying this potential. This knowledge has recently been applied to mammals to develop methods that can stimulate regeneration in mice. In this review, we highlight the progress in this area, and propose a "wish list" of how the clinical implementation of regenerative strategies could be applicable to various human retinal diseases.
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Affiliation(s)
- Marina Pavlou
- Department of Biological Structure, University of Washington School of Medicine, Institute of Stem Cells and Regenerative Medicine, Seattle, Washington 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington School of Medicine, Institute of Stem Cells and Regenerative Medicine, Seattle, Washington 98195, USA
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7
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Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YHH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv 2023:2023.09.26.559521. [PMID: 37808736 PMCID: PMC10557686 DOI: 10.1101/2023.09.26.559521] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.
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Affiliation(s)
- Mitchell R. Vollger
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kiara C. Eldred
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Elliott Swanson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | - Yong-Han H. Cheng
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Yizi Mao
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elizabeth E. Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Katherine M. Munson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | | | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kathleen A. Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | | | | | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Stephanie M. Sherman
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Amy L. Yuen
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | - Thomas A. Reh
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Peter H. Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Fuki M. Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gail P. Jarvik
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Yasemin Sancak
- University of Washington School of Medicine, Department of Pharmacology, Seattle, WA, USA
| | - Katrina M. Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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8
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Soucy JR, Aguzzi EA, Cho J, Gilhooley MJ, Keuthan C, Luo Z, Monavarfeshani A, Saleem MA, Wang XW, Wohlschlegel J, Baranov P, Di Polo A, Fortune B, Gokoffski KK, Goldberg JL, Guido W, Kolodkin AL, Mason CA, Ou Y, Reh TA, Ross AG, Samuels BC, Welsbie D, Zack DJ, Johnson TV. Retinal ganglion cell repopulation for vision restoration in optic neuropathy: a roadmap from the RReSTORe Consortium. Mol Neurodegener 2023; 18:64. [PMID: 37735444 PMCID: PMC10514988 DOI: 10.1186/s13024-023-00655-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Retinal ganglion cell (RGC) death in glaucoma and other optic neuropathies results in irreversible vision loss due to the mammalian central nervous system's limited regenerative capacity. RGC repopulation is a promising therapeutic approach to reverse vision loss from optic neuropathies if the newly introduced neurons can reestablish functional retinal and thalamic circuits. In theory, RGCs might be repopulated through the transplantation of stem cell-derived neurons or via the induction of endogenous transdifferentiation. The RGC Repopulation, Stem Cell Transplantation, and Optic Nerve Regeneration (RReSTORe) Consortium was established to address the challenges associated with the therapeutic repair of the visual pathway in optic neuropathy. In 2022, the RReSTORe Consortium initiated ongoing international collaborative discussions to advance the RGC repopulation field and has identified five critical areas of focus: (1) RGC development and differentiation, (2) Transplantation methods and models, (3) RGC survival, maturation, and host interactions, (4) Inner retinal wiring, and (5) Eye-to-brain connectivity. Here, we discuss the most pertinent questions and challenges that exist on the path to clinical translation and suggest experimental directions to propel this work going forward. Using these five subtopic discussion groups (SDGs) as a framework, we suggest multidisciplinary approaches to restore the diseased visual pathway by leveraging groundbreaking insights from developmental neuroscience, stem cell biology, molecular biology, optical imaging, animal models of optic neuropathy, immunology & immunotolerance, neuropathology & neuroprotection, materials science & biomedical engineering, and regenerative neuroscience. While significant hurdles remain, the RReSTORe Consortium's efforts provide a comprehensive roadmap for advancing the RGC repopulation field and hold potential for transformative progress in restoring vision in patients suffering from optic neuropathies.
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Affiliation(s)
- Jonathan R Soucy
- Department of Ophthalmology, Schepens Eye Research Institute of Mass. Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Erika A Aguzzi
- The Institute of Ophthalmology, University College London, London, England, UK
| | - Julie Cho
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael James Gilhooley
- The Institute of Ophthalmology, University College London, London, England, UK
- Moorfields Eye Hospital, London, England, UK
| | - Casey Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ziming Luo
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Meher A Saleem
- Bascom Palmer Eye Institute, University of Miami Health System, Miami, FL, USA
| | - Xue-Wei Wang
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Petr Baranov
- Department of Ophthalmology, Schepens Eye Research Institute of Mass. Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Adriana Di Polo
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada
- University of Montreal Hospital Research Centre, Montreal, QC, Canada
| | - Brad Fortune
- Discoveries in Sight Research Laboratories, Devers Eye Institute and Legacy Research Institute, Legacy Health, Portland, OR, USA
| | - Kimberly K Gokoffski
- Department of Ophthalmology, Roski Eye Institute, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - William Guido
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Alex L Kolodkin
- The Solomon H Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carol A Mason
- Departments of Pathology and Cell Biology, Neuroscience, and Ophthalmology, College of Physicians and Surgeons, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Yvonne Ou
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Ahmara G Ross
- Departments of Ophthalmology and Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian C Samuels
- Department of Ophthalmology and Visual Sciences, Callahan Eye Hospital, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Derek Welsbie
- Shiley Eye Institute and Viterbi Family Department of Ophthalmology, University of California, San Diego, CA, USA
| | - Donald J Zack
- Glaucoma Center of Excellence, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, 21287 MD, USA
- Departments of Neuroscience, Molecular Biology & Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas V Johnson
- Departments of Neuroscience, Molecular Biology & Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Cellular & Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, 21287 MD, USA.
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9
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Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity. Cell Rep Methods 2023; 3:100548. [PMID: 37671011 PMCID: PMC10475847 DOI: 10.1016/j.crmeth.2023.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/16/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023]
Abstract
With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA sequencing (RNA-seq) multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10× methods produce highly concordant cell-class compositions and then expand sci-Plex to analyze the cell-class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to 6 weeks later. Our data show sci-Plex's potential to dramatically scale up the analysis of treatment conditions on relevant human models.
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Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Kiara C. Eldred
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sophia Cuschieri
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dawn Hoffer
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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10
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Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity. bioRxiv 2023:2023.05.31.543087. [PMID: 37398481 PMCID: PMC10312535 DOI: 10.1101/2023.05.31.543087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell class compositions and then expand sci-Plex to analyze the cell class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to six weeks later. Our data show sci-Plex's potential to dramatically scale-up the analysis of treatment conditions on relevant human models.
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Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Kiara C. Eldred
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sophia Cuschieri
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dawn Hoffer
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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11
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Johnson TV, Calkins DJ, Fortune B, Goldberg JL, La Torre A, Lamba DA, Meyer JS, Reh TA, Wallace VA, Zack DJ, Baranov P. The importance of unambiguous cell origin determination in neuronal repopulation studies. iScience 2023; 26:106361. [PMID: 37009209 PMCID: PMC10060674 DOI: 10.1016/j.isci.2023.106361] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Neuronal repopulation achieved through transplantation or transdifferentiation from endogenous sources holds tremendous potential for restoring function in chronic neurodegenerative disease or acute injury. Key to the evaluation of neuronal engraftment is the definitive discrimination of new or donor neurons from preexisting cells within the host tissue. Recent work has identified mechanisms by which genetically encoded donor cell reporters can be transferred to host neurons through intercellular material transfer. In addition, labeling transplanted and endogenously transdifferentiated neurons through viral vector transduction can yield misexpression in host cells in some circumstances. These issues can confound the tracking and evaluation of repopulated neurons in regenerative experimental paradigms. Using the retina as an example, we discuss common reasons for artifactual labeling of endogenous host neurons with donor cell reporters and suggest strategies to prevent erroneous conclusions based on misidentification of cell origin.
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Affiliation(s)
- Thomas V. Johnson
- Glaucoma Center of Excellence, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Cellular & Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Corresponding author
| | - David J. Calkins
- The Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brad Fortune
- Discoveries in Sight Research Laboratories, Devers Eye Institute and Legacy Research Institute, Legacy Healthy, Portland, OR, USA
| | - Jeffrey L. Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anna La Torre
- Department of Cell Biology & Human Anatomy, University of California Davis, Davis, CA, USA
| | - Deepak A. Lamba
- Department of Ophthalmology and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Jason S. Meyer
- Departments of Medical & Molecular Genetics, Ophthalmology (Glick Eye Institute), Pharmacology & Toxicology, and Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Valerie A. Wallace
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Departments of Laboratory Medicine & Pathobiology, and Ophthalmology & Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Donald J. Zack
- Glaucoma Center of Excellence, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Departments of Neuroscience, Molecular Biology & Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Petr Baranov
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Corresponding author
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12
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Todd L, Jenkins W, Finkbeiner C, Hooper MJ, Donaldson PC, Pavlou M, Wohlschlegel J, Ingram N, Rieke F, Reh TA. Reprogramming Müller glia to regenerate ganglion-like cells in adult mouse retina with developmental transcription factors. Sci Adv 2022; 8:eabq7219. [PMID: 36417510 PMCID: PMC9683702 DOI: 10.1126/sciadv.abq7219] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/26/2022] [Indexed: 06/11/2023]
Abstract
Many neurodegenerative diseases cause degeneration of specific types of neurons. For example, glaucoma leads to death of retinal ganglion cells, leaving other neurons intact. Neurons are not regenerated in the adult mammalian central nervous system. However, in nonmammalian vertebrates, glial cells spontaneously reprogram into neural progenitors and replace neurons after injury. We have recently developed strategies to stimulate regeneration of functional neurons in the adult mouse retina by overexpressing the proneural factor Ascl1 in Müller glia. Here, we test additional transcription factors (TFs) for their ability to direct regeneration to particular types of retinal neurons. We engineered mice to express different combinations of TFs in Müller glia, including Ascl1, Pou4f2, Islet1, and Atoh1. Using immunohistochemistry, single-cell RNA sequencing, single-cell assay for transposase-accessible chromatin sequencing, and electrophysiology, we find that retinal ganglion-like cells can be regenerated in the damaged adult mouse retina in vivo with targeted overexpression of developmental retinal ganglion cell TFs.
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Affiliation(s)
- Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Wesley Jenkins
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marcus J. Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Phoebe C. Donaldson
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marina Pavlou
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Juliette Wohlschlegel
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Norianne Ingram
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 91895, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 91895, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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13
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Palazzo I, Todd LJ, Hoang TV, Reh TA, Blackshaw S, Fischer AJ. Cover Image, Volume 70, Issue 7. Glia 2022. [DOI: 10.1002/glia.24187] [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: 11/11/2022]
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14
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Palazzo I, Todd LJ, Hoang TV, Reh TA, Blackshaw S, Fischer AJ. NFkB-signaling promotes glial reactivity and suppresses Müller glia-mediated neuron regeneration in the mammalian retina. Glia 2022; 70:1380-1401. [PMID: 35388544 DOI: 10.1002/glia.24181] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/25/2022]
Abstract
Müller glia (MG) in mammalian retinas are incapable of regenerating neurons after damage, whereas the MG in lower vertebrates regenerate functional neurons. Identification of cell signaling pathways and gene regulatory networks that regulate MG-mediated regeneration is key to harnessing the regenerative potential of MG. Here, we study how NFkB-signaling influences glial responses to damage and reprogramming of MG into neurons in the rodent retina. We find activation of NFkB and dynamic expression of NFkB-associated genes in MG after damage, however damage-induced NFkB activation is inhibited by microglia ablation. Knockout of NFkB in MG suppressed the accumulation of immune cells after damage. Inhibition of NFkB following NMDA-damage significantly enhanced the reprogramming of Ascl1-overexpressing MG into neuron-like cells. scRNA-seq of retinal glia following inhibition of NFkB reveals coordination with signaling via TGFβ2 and suppression of NFI and Id transcription factors. Inhibition of Smad3 signal transducer or Id transcription factors increased numbers of neuron-like cells produced by Ascl1-overexpressing MG. We conclude that NFkB is a key signaling hub that is activated in MG after damage, mediates the accumulation of immune cells, and suppresses the neurogenic potential of MG.
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Affiliation(s)
- Isabella Palazzo
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Levi J Todd
- Department of Biological Structure, College of Medicine, University of Washington, Seattle, Washington, USA
| | - Thanh V Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas A Reh
- Department of Biological Structure, College of Medicine, University of Washington, Seattle, Washington, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andy J Fischer
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
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15
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Finkbeiner C, Ortuño-Lizarán I, Sridhar A, Hooper M, Petter S, Reh TA. Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition. Cell Rep 2022; 38:110294. [DOI: 10.1016/j.celrep.2021.110294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/04/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
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16
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Hamner MA, McDonough A, Gong DC, Todd LJ, Rojas G, Hodecker S, Ransom CB, Reh TA, Ransom BR, Weinstein JR. Microglial depletion abolishes ischemic preconditioning in white matter. Glia 2021; 70:661-674. [PMID: 34939240 DOI: 10.1002/glia.24132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/31/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/17/2023]
Abstract
Ischemic preconditioning (IPC) is a phenomenon whereby a brief, non-injurious ischemic exposure enhances tolerance to a subsequent ischemic challenge. The mechanism of IPC has mainly been studied in rodent stroke models where gray matter (GM) constitutes about 85% of the cerebrum. In humans, white matter (WM) is 50% of cerebral volume and is a critical component of stroke damage. We developed a novel CNS WM IPC model using the mouse optic nerve (MON) and identified the involved immune signaling pathways. Here we tested the hypothesis that microglia are necessary for WM IPC. Microglia were depleted by treatment with the colony stimulating factor 1 receptor (CSF1R) inhibitor PLX5622. MONs were exposed to transient ischemia in vivo, acutely isolated 72 h later, and subjected to oxygen-glucose deprivation (OGD) to simulate a severe ischemic injury (i.e., stroke). Functional and structural axonal recovery was assessed by recording compound action potentials (CAPs) and by microscopy using quantitative stereology. Microglia depletion eliminated IPC-mediated protection. In control mice, CAP recovery was improved in preconditioned MONs compared with non-preconditioned MONs, however, in PLX5622-treated mice, we observed no difference in CAP recovery between preconditioned and non-preconditioned MONs. Microgliadepletion also abolished IPC protective effects on axonal integrity and survival of mature (APC+ ) oligodendrocytes after OGD. IPC-mediated protection was independent of retinal injury suggesting it results from mechanistic processes intrinsic to ischemia-exposed WM. We conclude that preconditioned microglia are critical for IPC in WM. The "preconditioned microglia" phenotype might protect against other CNS pathologies and is a neurotherapeutic horizon worth exploring.
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Affiliation(s)
- Margaret A Hamner
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Ashley McDonough
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Davin C Gong
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Levi J Todd
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, Washington, USA
| | - German Rojas
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Sibylle Hodecker
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Christopher B Ransom
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Thomas A Reh
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Bruce R Ransom
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA.,Neuroscience Department, City University of Hong Kong, Kowloon, Hong Kong
| | - Jonathan R Weinstein
- Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, USA.,Department of Neurological Surgery, School of Medicine, University of Washington, Seattle, Washington, USA
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17
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Todd L, Hooper MJ, Haugan AK, Finkbeiner C, Jorstad N, Radulovich N, Wong CK, Donaldson PC, Jenkins W, Chen Q, Rieke F, Reh TA. Efficient stimulation of retinal regeneration from Müller glia in adult mice using combinations of proneural bHLH transcription factors. Cell Rep 2021; 37:109857. [PMID: 34686336 PMCID: PMC8691131 DOI: 10.1016/j.celrep.2021.109857] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 07/26/2021] [Revised: 09/02/2021] [Accepted: 09/28/2021] [Indexed: 12/27/2022] Open
Abstract
Regenerative neuroscience aims to stimulate endogenous repair in the nervous system to replace neurons lost from degenerative diseases. Recently, we reported that overexpressing the transcription factor Ascl1 in Müller glia (MG) is sufficient to stimulate MG to regenerate functional neurons in the adult mouse retina. However, this process is inefficient, and only a third of the Ascl1-expressing MG generate new neurons. Here, we test whether proneural transcription factors of the Atoh1/7 class can further promote the regenerative capacity of MG. We find that the combination of Ascl1:Atoh1 is remarkably efficient at stimulating neurogenesis, even in the absence of retinal injury. Using electrophysiology and single-cell RNA sequencing (scRNA-seq), we demonstrate that Ascl1:Atoh1 generates a diversity of retinal neuron types, with the majority expressing characteristics of retinal ganglion cells. Our results provide a proof of principle that combinations of developmental transcription factors can substantially improve glial reprogramming to neurons and expand the repertoire of regenerated cell fates.
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Affiliation(s)
- Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marcus J Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Alexandra K Haugan
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Nikolas Jorstad
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Radulovich
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Claire K Wong
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Phoebe C Donaldson
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Wesley Jenkins
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Qiang Chen
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 91895, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 91895, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.
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18
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Eldred KC, Reh TA. Human retinal model systems: Strengths, weaknesses, and future directions. Dev Biol 2021; 480:114-122. [PMID: 34529997 DOI: 10.1016/j.ydbio.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The retina is a complex neuronal structure that converts light energy into visual perception. Many specialized aspects of the primate retina, including a cone rich macula for high acuity vision, ocular size, and cell type diversity are not found in other animal models. In addition, the unique morphologies and distinct laminar positions of cell types found in the retina make this model system ideal for the study of neuronal cell fate specification. Many key early events of human retinal development are inaccessible to investigation as they occur during gestation. For these reasons, it has been necessary to develop retinal model systems to gain insight into human-specific retinal development and disease. Recent advances in culturing retinal tissue have generated new systems for retinal research and have moved us closer to generating effective regenerative therapies for vision loss. Here, we describe the strengths, weaknesses, and future directions for different human retinal model systems including dissociated primary tissue, explanted primary tissue, retinospheres, and stem cell-derived retinal organoids.
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Affiliation(s)
- Kiara C Eldred
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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19
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Kang S, Larbi D, Andrade M, Reardon S, Reh TA, Wohl SG. A Comparative Analysis of Reactive Müller Glia Gene Expression After Light Damage and microRNA-Depleted Müller Glia-Focus on microRNAs. Front Cell Dev Biol 2021; 8:620459. [PMID: 33614628 PMCID: PMC7891663 DOI: 10.3389/fcell.2020.620459] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Müller glia (MG) are the predominant glia in the neural retina and become reactive after injury or in disease. microRNAs (miRNAs) are translational repressors that regulate a variety of processes during development and are required for MG function. However, no data is available about the MG miRNAs in reactive gliosis. Therefore, in this study, we aimed to profile miRNAs and mRNAs in reactive MG 7 days after light damage. Light damage was performed for 8 h at 10,000 lux; this leads to rapid neuronal loss and strong MG reactivity. miRNAs were profiled using the Nanostring platform, gene expression analysis was conducted via microarray. We compared the light damage dataset with the dataset of Dicer deleted MG in order to find similarities and differences. We found: (1) The vast majority of MG miRNAs declined in reactive MG 7 days after light damage. (2) Only four miRNAs increased after light damage, which included miR-124. (3) The top 10 genes found upregulated in reactive MG after light damage include Gfap, Serpina3n, Ednrb and Cxcl10. (4) The miRNA decrease in reactive MG 7 days after injury resembles the profile of Dicer-depleted MG after one month. (5) The comparison of both mRNA expression datasets (light damage and Dicer-cKO) showed 1,502 genes were expressed under both conditions, with Maff , Egr2, Gadd45b, and Atf3 as top upregulated candidates. (6) The DIANA-TarBase v.8 miRNA:RNA interaction tool showed that three miRNAs were found to be present in all networks, i.e., after light damage, and in the combined data set; these were miR-125b-5p, let-7b and let-7c. Taken together, results show there is an overlap of gene regulatory events that occur in reactive MG after light damage (direct damage of neurons) and miRNA-depleted MG (Dicer-cKO), two very different paradigms. This suggests that MG miRNAs play an important role in a ubiquitous MG stress response and manipulating these miRNAs could be a first step to attenuate gliosis.
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Affiliation(s)
- Seoyoung Kang
- Department of Biological and Vision Sciences, College of Optometry, The State University of New York, New York, NY, United States
| | - Daniel Larbi
- Department of Biological and Vision Sciences, College of Optometry, The State University of New York, New York, NY, United States
| | - Monica Andrade
- Department of Biological and Vision Sciences, College of Optometry, The State University of New York, New York, NY, United States
| | - Sara Reardon
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, United States
| | - Thomas A. Reh
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, United States
| | - Stefanie G. Wohl
- Department of Biological and Vision Sciences, College of Optometry, The State University of New York, New York, NY, United States
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20
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Todd L, Finkbeiner C, Wong CK, Hooper MJ, Reh TA. Microglia Suppress Ascl1-Induced Retinal Regeneration in Mice. Cell Rep 2020; 33:108507. [PMID: 33326790 DOI: 10.1016/j.celrep.2020.108507] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022] Open
Abstract
The innate immune system plays key roles in tissue regeneration. For example, microglia promote neurogenesis in Müller glia in birds and fish after injury. Although mammalian retina does not normally regenerate, neurogenesis can be induced in mouse Müller glia by Ascl1, a proneural transcription factor. We show that in mice, microglia inhibit the Ascl1-mediated retinal regeneration, suggesting that the innate immune system limits the regenerative response to injury.
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Affiliation(s)
- Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Claire K Wong
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marcus J Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.
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21
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VandenBosch LS, Wohl SG, Wilken MS, Hooper M, Finkbeiner C, Cox K, Chipman L, Reh TA. Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potential. Sci Rep 2020; 10:13615. [PMID: 32788677 PMCID: PMC7423883 DOI: 10.1038/s41598-020-70334-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Diseases and damage to the retina lead to losses in retinal neurons and eventual visual impairment. Although the mammalian retina has no inherent regenerative capabilities, fish have robust regeneration from Müller glia (MG). Recently, we have shown that driving expression of Ascl1 in adult mouse MG stimulates neural regeneration. The regeneration observed in the mouse is limited in the variety of neurons that can be derived from MG; Ascl1-expressing MG primarily generate bipolar cells. To better understand the limits of MG-based regeneration in mouse retinas, we used ATAC- and RNA-seq to compare newborn progenitors, immature MG (P8-P12), and mature MG. Our analysis demonstrated developmental differences in gene expression and accessible chromatin between progenitors and MG, primarily in neurogenic genes. Overexpression of Ascl1 is more effective in reprogramming immature MG, than mature MG, consistent with a more progenitor-like epigenetic landscape in the former. We also used ASCL1 ChIPseq to compare the differences in ASCL1 binding in progenitors and reprogrammed MG. We find that bipolar-specific accessible regions are more frequently linked to bHLH motifs and ASCL1 binding. Overall, our analysis indicates a loss of neurogenic gene expression and motif accessibility during glial maturation that may prevent efficient reprogramming.
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Affiliation(s)
- Leah S VandenBosch
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Stefanie G Wohl
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA.,Department of Biological and Vision Sciences, College of Optometry, The State University of New York, New York, NY, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marcus Hooper
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA
| | - Kristen Cox
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA
| | - Laura Chipman
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA, 98195, USA. .,Institute for Stem Cells and Regenerative Medicine, University of Washington, Box 358056, Seattle, WA, 98109, USA.
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22
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Thompson DA, Iannaccone A, Ali RR, Arshavsky VY, Audo I, Bainbridge JWB, Besirli CG, Birch DG, Branham KE, Cideciyan AV, Daiger SP, Dalkara D, Duncan JL, Fahim AT, Flannery JG, Gattegna R, Heckenlively JR, Heon E, Jayasundera KT, Khan NW, Klassen H, Leroy BP, Molday RS, Musch DC, Pennesi ME, Petersen-Jones SM, Pierce EA, Rao RC, Reh TA, Sahel JA, Sharon D, Sieving PA, Strettoi E, Yang P, Zacks DN. Advancing Clinical Trials for Inherited Retinal Diseases: Recommendations from the Second Monaciano Symposium. Transl Vis Sci Technol 2020; 9:2. [PMID: 32832209 PMCID: PMC7414644 DOI: 10.1167/tvst.9.7.2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/12/2020] [Indexed: 12/18/2022] Open
Abstract
Major advances in the study of inherited retinal diseases (IRDs) have placed efforts to develop treatments for these blinding conditions at the forefront of the emerging field of precision medicine. As a result, the growth of clinical trials for IRDs has increased rapidly over the past decade and is expected to further accelerate as more therapeutic possibilities emerge and qualified participants are identified. Although guided by established principles, these specialized trials, requiring analysis of novel outcome measures and endpoints in small patient populations, present multiple challenges relative to study design and ethical considerations. This position paper reviews recent accomplishments and existing challenges in clinical trials for IRDs and presents a set of recommendations aimed at rapidly advancing future progress. The goal is to stimulate discussions among researchers, funding agencies, industry, and policy makers that will further the design, conduct, and analysis of clinical trials needed to accelerate the approval of effective treatments for IRDs, while promoting advocacy and ensuring patient safety.
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Affiliation(s)
- Debra A Thompson
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alessandro Iannaccone
- Department of Ophthalmology, Duke Eye Center, Duke University Medical Center, Durham, NC, USA
| | - Robin R Ali
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA.,Institute of Ophthalmology, University College London, London, UK
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke Eye Center, Duke University Medical Center, Durham, NC, USA
| | - Isabelle Audo
- Sorbonne Université, Institut de la Vision, INSERM, CNRS, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France
| | | | - Cagri G Besirli
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Artur V Cideciyan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven P Daiger
- Human Genetics Center, School of Public Health, University of Texas Health Science Center Houston, Houston, TX, USA
| | - Deniz Dalkara
- Sorbonne Université, Institut de la Vision, INSERM, CNRS, Paris, France
| | - Jacque L Duncan
- Department of Ophthalmology, University of California-San Francisco, San Francisco, CA, USA
| | - Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California-Berkeley, Berkeley, CA, USA
| | | | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Henry Klassen
- Gavin Herbert Eye Institute, Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA
| | - Bart P Leroy
- Department of Ophthalmology and Center Medical Genetics, Ghent University Hospital and University, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert S Molday
- Department of Biochemistry/Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C Musch
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science Center, Portland, OR, USA
| | - Simon M Petersen-Jones
- Small Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Rajesh C Rao
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Jose A Sahel
- Sorbonne Université, Institut de la Vision, INSERM, CNRS, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Rothschild, Paris, France.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul A Sieving
- Department of Ophthalmology and Center for Ocular Regenerative Therapy, University of California-Davis School of Medicine, Sacramento, CA, USA.,National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Enrica Strettoi
- Institute of Neuroscience, National Research Council (CNR), Pisa, Italy
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science Center, Portland, OR, USA
| | - David N Zacks
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
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23
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Jorstad NL, Wilken MS, Todd L, Finkbeiner C, Nakamura P, Radulovich N, Hooper MJ, Chitsazan A, Wilkerson BA, Rieke F, Reh TA. STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina. Cell Rep 2020; 30:2195-2208.e5. [PMID: 32075759 PMCID: PMC7148114 DOI: 10.1016/j.celrep.2020.01.075] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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: 07/03/2019] [Revised: 12/09/2019] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Müller glia (MG) serve as sources for retinal regeneration in non-mammalian vertebrates. We find that this process can be induced in mouse MG, after injury, by transgenic expression of the proneural transcription factor Ascl1 and the HDAC inhibitor TSA. However, new neurons are generated only from a subset of MG. Identifying factors that limit Ascl1-mediated MG reprogramming could make this process more efficient. In this study, we test whether injury-induced STAT activation hampers the ability of Ascl1 to reprogram MG into retinal neurons. Single-cell RNA-seq shows that progenitor-like cells derived from Ascl1-expressing MG have a higher level of STAT signaling than do those cells that become neurons. Ascl1-ChIPseq and ATAC-seq show that STAT potentially directs Ascl1 to developmentally inappropriate targets. Using a STAT inhibitor, in combination with our previously described reprogramming paradigm, we found a large increase in the ability of MG to generate neurons.
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Affiliation(s)
- Nikolas L Jorstad
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA; Department of Pathology, Molecular Medicine and Mechanisms of Disease Program, University of Washington, Seattle, WA 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Connor Finkbeiner
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Paul Nakamura
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Radulovich
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Marcus J Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Alex Chitsazan
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Brent A Wilkerson
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.
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24
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Wohl SG, Hooper MJ, Reh TA. MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Müller glia in mice. Development 2019; 146:dev179556. [PMID: 31383796 PMCID: PMC6765125 DOI: 10.1242/dev.179556] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022]
Abstract
Müller glial cells (MG) generate retinal progenitor (RPC)-like cells after injury in non-mammalian species, although this does not occur in the mammalian retina. Studies have profiled gene expression in these cells to define genes that may be relevant to their differences in neurogenic potential. However, less is known about differences in micro-RNA (miRNA) expression. In this study, we compared miRNAs from RPCs and MG to identify miRNAs more highly expressed in RPCs, and others more highly expressed in MG. To determine whether these miRNAs are relevant to the difference in neurogenic potential between these two cell types, we tested them in dissociated cultures of MG using either mimics or antagomiRs to increase or reduce expression, respectively. Among the miRNAs tested, miR-25 and miR-124 overexpression, or let-7 antagonism, induced Ascl1 expression and conversion of ∼40% of mature MG into a neuronal/RPC phenotype. Our results suggest that the differences in miRNA expression between MG and RPCs contribute to their difference in neurogenic potential, and that manipulations in miRNAs provide a new tool with which to reprogram MG for retinal regeneration.
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Affiliation(s)
- Stefanie G Wohl
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, WA 98195, USA
- Department of Biological and Vision Sciences, The State University of New York, College of Optometry, New York, NY 10036, USA
| | - Marcus J Hooper
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, WA 98195, USA
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25
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Abstract
The small RNA regulatory molecules called microRNAs (miRNAs) play key roles in the development of most organisms. The expression of many different miRNAs has been described in the developing and mature vertebrate retina. The ability of miRNAs to regulate a diversity of messenger RNA targets allows them to have effects on many different developmental processes, but the functions of only a few miRNAs have been documented to date. Developmental transitions between cell states appear to be particularly sensitive to miRNA loss of function, as evidenced by specific miRNA knockdowns or from global perturbations in miRNA levels (e.g., Dicer deletion). However, we are still in only the very early stages of understanding the range of cellular functions miRNAs control during development.
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Affiliation(s)
- Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA;
| | - Robert Hindges
- Centre for Developmental Neurobiology, MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, United Kingdom;
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26
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Zhang C, Yu WQ, Hoshino A, Huang J, Rieke F, Reh TA, Wong ROL. Development of ON and OFF cholinergic amacrine cells in the human fetal retina. J Comp Neurol 2018; 527:174-186. [PMID: 29405294 DOI: 10.1002/cne.24405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/13/2022]
Abstract
Choline acetyltransferase (ChAT) expressing retinal amacrine cells are present across vertebrates. These interneurons play important roles in the development of retinal projections to the brain and in motion detection, specifically in generating direction-selective responses to moving stimuli. ChAT amacrine cells typically comprise two spatially segregated populations that form circuits in the 'ON' or 'OFF' synaptic layers of the inner retina. This stereotypic arrangement is also found across the adult human retina, with the notable exception that ChAT expression is evident in the ON but not OFF layer of the fovea, a region specialized for high-acuity vision. We thus investigated whether the human fovea exhibits a developmental path for ON and OFF ChAT cells that is retinal location-specific. Our analysis shows that at each retinal location, human ON and OFF ChAT cells differentiate, form their separate synaptic layers, and establish non-random mosaics at about the same time. However, unlike in the adult fovea, ChAT immunostaining is initially robust in both ON and OFF populations, up until at least mid-gestation. ChAT expression in the OFF layer in the fovea is therefore significantly reduced after mid-gestation. OFF ChAT cells in the human fovea and in the retinal periphery thus follow distinct maturational paths.
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Affiliation(s)
- Chi Zhang
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Wan-Qing Yu
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Akina Hoshino
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Jing Huang
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Rachel O L Wong
- Department of Biological Structure, University of Washington, Seattle, Washington
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27
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Hoshino A, Ratnapriya R, Brooks MJ, Chaitankar V, Wilken MS, Zhang C, Starostik MR, Gieser L, La Torre A, Nishio M, Bates O, Walton A, Bermingham-McDonogh O, Glass IA, Wong ROL, Swaroop A, Reh TA. Molecular Anatomy of the Developing Human Retina. Dev Cell 2017; 43:763-779.e4. [PMID: 29233477 DOI: 10.1016/j.devcel.2017.10.029] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/15/2017] [Accepted: 10/26/2017] [Indexed: 02/07/2023]
Abstract
Clinical and genetic heterogeneity associated with retinal diseases makes stem-cell-based therapies an attractive strategy for personalized medicine. However, we have limited understanding of the timing of key events in the developing human retina, and in particular the factors critical for generating the unique architecture of the fovea and surrounding macula. Here we define three key epochs in the transcriptome dynamics of human retina from fetal day (D) 52 to 136. Coincident histological analyses confirmed the cellular basis of transcriptional changes and highlighted the dramatic acceleration of development in the fovea compared with peripheral retina. Human and mouse retinal transcriptomes show remarkable similarity in developmental stages, although morphogenesis was greatly expanded in humans. Integration of DNA accessibility data allowed us to reconstruct transcriptional networks controlling photoreceptor differentiation. Our studies provide insights into human retinal development and serve as a resource for molecular staging of human stem-cell-derived retinal organoids.
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Affiliation(s)
- Akina Hoshino
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew J Brooks
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijender Chaitankar
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA
| | - Chi Zhang
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA
| | - Margaret R Starostik
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linn Gieser
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna La Torre
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA; Department of Cell Biology and Human Anatomy, University of California Davis, Davis, CA 95616, USA
| | - Mario Nishio
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA
| | - Olivia Bates
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA
| | - Ashley Walton
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Ian A Glass
- Department of Pediatrics and Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Rachel O L Wong
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98105, USA.
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28
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Wohl SG, Jorstad NL, Levine EM, Reh TA. Müller glial microRNAs are required for the maintenance of glial homeostasis and retinal architecture. Nat Commun 2017; 8:1603. [PMID: 29150673 PMCID: PMC5693933 DOI: 10.1038/s41467-017-01624-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/02/2017] [Indexed: 01/21/2023] Open
Abstract
To better understand the roles of microRNAs in glial function, we used a conditional deletion of Dicer1 (Dicer-CKOMG) in retinal Müller glia (MG). Dicer1 deletion from the MG leads to an abnormal migration of the cells as early as 1 month after the deletion. By 6 months after Dicer1 deletion, the MG form large aggregations and severely disrupt normal retinal architecture and function. The most highly upregulated gene in the Dicer-CKOMG MG is the proteoglycan Brevican (Bcan) and overexpression of Bcan results in similar aggregations of the MG in wild-type retina. One potential microRNA that regulates Bcan is miR-9, and overexpression of miR-9 can partly rescue the effects of Dicer1 deletion on the MG phenotype. We also find that MG from retinitis pigmentosa patients display an increase in Brevican immunoreactivity at sites of MG aggregation, linking the retinal remodeling that occurs in chronic disease with microRNAs.
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Affiliation(s)
- Stefanie G Wohl
- Department of Biological Structure, University of Washington, Health Sciences Center, Box 357420, 1959 Pacific Street NE, Seattle, WA, 98195, USA
| | - Nikolas L Jorstad
- Department of Biological Structure, University of Washington, Health Sciences Center, Box 357420, 1959 Pacific Street NE, Seattle, WA, 98195, USA
| | - Edward M Levine
- Department of Ophthalmology and Visual Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Health Sciences Center, Box 357420, 1959 Pacific Street NE, Seattle, WA, 98195, USA.
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29
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Nakamura PA, Shimchuk AA, Tang S, Wang Z, DeGolier K, Ding S, Reh TA. Small molecule Photoregulin3 prevents retinal degeneration in the RhoP23H mouse model of retinitis pigmentosa. eLife 2017; 6. [PMID: 29148976 PMCID: PMC5693111 DOI: 10.7554/elife.30577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/24/2017] [Indexed: 12/25/2022] Open
Abstract
Regulation of rod gene expression has emerged as a potential therapeutic strategy to treat retinal degenerative diseases like retinitis pigmentosa (RP). We previously reported on a small molecule modulator of the rod transcription factor Nr2e3, Photoregulin1 (PR1), that regulates the expression of photoreceptor-specific genes. Although PR1 slows the progression of retinal degeneration in models of RP in vitro, in vivo analyses were not possible with PR1. We now report a structurally unrelated compound, Photoregulin3 (PR3) that also inhibits rod photoreceptor gene expression, potentially though Nr2e3 modulation. To determine the effectiveness of PR3 as a potential therapy for RP, we treated RhoP23H mice with PR3 and assessed retinal structure and function. PR3-treated RhoP23H mice showed significant structural and functional photoreceptor rescue compared with vehicle-treated littermate control mice. These results provide further support that pharmacological modulation of rod gene expression provides a potential strategy for the treatment of RP. There are several diseases that cause people to lose their eyesight and become blind. One of these diseases, called retinitis pigmentosa, kills cells at the back of the eye known as rod cells. At first, it affects vision in low light and peripheral vision, but later it affects vision during the daytime as well. There are no effective treatments for patients with retinitis pigmentosa. Yet previous genetic studies have shown that disrupting the activity of genes in rod cells can slow the progression of the disease and preserve vision in mice. As for all genes, proteins called transcription factors regulate the activity of rod cell genes. Nakamura et al. now report the discovery of a small drug-like molecule, that they name Photoregulin3, which alters the activity of a transcription factor that regulates rod genes. In follow-up experiments, mice with a mutation that replicates many of the features of retinitis pigmentosa were given Photoregulin3 to see if it could slow the progression of the disease. Indeed, Photoregulin3 could stop many of the rod cells from degenerating in the treated mice. At the end of the experiment, the mice treated with this small molecule had about twice as many rods as the control mice. The treated mice also responded better to flashes of light. Nakamura et al. hope that the findings will one day benefit patients with retinitis pigmentosa. But first more research needs to be done before testing Photoregulin3 in humans. For example, the drug-like molecule needs to be made more potent, and if possible adapted to work when given orally, meaning patients could take it as a pill.
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Affiliation(s)
- Paul A Nakamura
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, United States
| | - Andy A Shimchuk
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, United States
| | - Shibing Tang
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, University of California, San Francisco, San Francisco, United States
| | - Zhizhi Wang
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, United States
| | - Kole DeGolier
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, United States
| | - Sheng Ding
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, University of California, San Francisco, San Francisco, United States
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, United States
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30
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Jorstad NL, Wilken MS, Grimes WN, Wohl SG, VandenBosch LS, Yoshimatsu T, Wong RO, Rieke F, Reh TA. Stimulation of functional neuronal regeneration from Müller glia in adult mice. Nature 2017; 548:103-107. [PMID: 28746305 PMCID: PMC5991837 DOI: 10.1038/nature23283] [Citation(s) in RCA: 304] [Impact Index Per Article: 43.4] [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: 01/31/2017] [Accepted: 06/13/2017] [Indexed: 12/18/2022]
Abstract
Many retinal diseases lead to the loss of retinal neurons and cause visual impairment. The adult mammalian retina has little capacity for regeneration. By contrast, teleost fish functionally regenerate their retina following injury, and Müller glia (MG) are the source of regenerated neurons. The proneural transcription factor Ascl1 is upregulated in MG after retinal damage in zebrafish and is necessary for regeneration. Although Ascl1 is not expressed in mammalian MG after injury, forced expression of Ascl1 in mouse MG induces a neurogenic state in vitro and in vivo after NMDA (N-methyl-d-aspartate) damage in young mice. However, by postnatal day 16, mouse MG lose neurogenic capacity, despite Ascl1 overexpression. Loss of neurogenic capacity in mature MG is accompanied by reduced chromatin accessibility, suggesting that epigenetic factors limit regeneration. Here we show that MG-specific overexpression of Ascl1, together with a histone deacetylase inhibitor, enables adult mice to generate neurons from MG after retinal injury. The MG-derived neurons express markers of inner retinal neurons, synapse with host retinal neurons, and respond to light. Using an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), we show that the histone deacetylase inhibitor promotes accessibility at key gene loci in the MG, and allows more effective reprogramming. Our results thus provide a new approach for the treatment of blinding retinal diseases.
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Affiliation(s)
- Nikolas L Jorstad
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
- Department of Pathology, Molecular Medicine and Mechanisms of Disease Program, University of Washington, Seattle, Washington 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - William N Grimes
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Stefanie G Wohl
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Leah S VandenBosch
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Takeshi Yoshimatsu
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Rachel O Wong
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
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31
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Nakamura PA, Tang S, Shimchuk AA, Ding S, Reh TA. Potential of Small Molecule-Mediated Reprogramming of Rod Photoreceptors to Treat Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2017; 57:6407-6415. [PMID: 27893103 PMCID: PMC5134355 DOI: 10.1167/iovs.16-20177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 11/24/2022] Open
Abstract
Purpose Mutations in rod photoreceptor genes can cause retinitis pigmentosa (RP). Rod gene expression is regulated by the nuclear hormone receptor, Nr2e3. Genetic deletion of Nr2e3 reprograms rods into cells that resemble cone photoreceptors, and might therefore prevent their death from some forms of RP. There are no identified ligands for Nr2e3; however, reverse agonists might mimic the genetic rescue effect and may be therapeutically useful for the treatment of RP. Methods We screened for small molecule modulators of Nr2e3 using primary retinal cell cultures and characterized the most potent, which we have named photoregulin1 (PR1), in vitro and in vivo. We also tested the ability of PR1 to slow the progression of photoreceptor degeneration in two common mouse models of autosomal dominant RP, the RhoP23H and the Pde6brd1 mutations. Results In developing retina, PR1 causes a decrease in rod gene expression and an increase in S opsin+ cones. Photoregulin1 continues to inhibit rod gene expression in adult mice. When applied to two mouse models of RP, PR1 slows the degeneration of photoreceptors. Conclusions Chemical compounds identified as modulators of Nr2e3 activity may be useful for the treatment of RP through their effects on expression of disease-causing mutant genes.
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Affiliation(s)
- Paul A Nakamura
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, Washington, United States
| | - Shibing Tang
- University of California-San Francisco, UCSF School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco California, United States
| | - Andy A Shimchuk
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, Washington, United States
| | - Sheng Ding
- University of California-San Francisco, UCSF School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco California, United States
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, School of Medicine, Seattle, Washington, United States
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Abstract
The recent advances in cell-based therapies for the repair of the pigmented epithelium is providing additional impetus for the translation of photoreceptor transplantation to eventual clinical trials. The prospects for transplantation of photoreceptors as a potential therapy for the treatment of photoreceptor degeneration will depend on successfully addressing many critical issues in preclinical studies. Although most of the studies that have carried out transplants of photoreceptors have primarily used normal mice, there have been recent reports that have also shown some success following transplantation to mouse models of retinitis pigmentosa. However, while these results are promising, there are several key issues that require further investigation in order to better understand the optimum timing for transplantation, given the extensive remodeling of the retina that occurs in late stage disease.
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Chao JR, Lamba DA, Klesert TR, Torre AL, Hoshino A, Taylor RJ, Jayabalu A, Engel AL, Khuu TH, Wang RK, Neitz M, Neitz J, Reh TA. Transplantation of Human Embryonic Stem Cell-Derived Retinal Cells into the Subretinal Space of a Non-Human Primate. Transl Vis Sci Technol 2017; 6:4. [PMID: 28516002 PMCID: PMC5433804 DOI: 10.1167/tvst.6.3.4] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [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: 08/19/2016] [Accepted: 03/21/2017] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Previous studies have demonstrated the ability of retinal cells derived from human embryonic stem cells (hESCs) to survive, integrate into the host retina, and mediate light responses in murine mouse models. Our aim is to determine whether these cells can also survive and integrate into the retina of a nonhuman primate, Saimiri sciureus, following transplantation into the subretinal space. METHODS hESCs were differentiated toward retinal neuronal fates using our previously published technique and cultured for 60 to 70 days. Differentiated cells were further treated with 20 μM N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) for a period of 5 days immediately prior to subretinal transplantation. Differentiated cells were labeled with a lentivirus expressing GFP. One million cells (10,000 cells/μL) were injected into the submacular space into a squirrel monkey eye, using an ab externo technique. RESULTS RetCam imaging demonstrated the presence and survival of human donor cells 3 months after transplantation in the S. sciureus eye. Injected cells consolidated in the temporal macula. GFP+ axonal projections were observed to emanate from the central consolidation of cells at 1 month, with some projecting into the optic nerve by 3 months after transplantation. CONCLUSIONS Human ES cell-derived retinal neurons injected into the submacular space of a squirrel monkey survive at least 3 months postinjection without immunosuppression. Some donor cells appeared to integrate into the host inner retina, and numerous donor axonal projections were noted throughout, with some projecting into the optic nerve. TRANSLATIONAL RELEVANCE These data illustrate the feasibility of hESC-derived retinal cell replacement in the nonhuman primate eye.
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Affiliation(s)
- Jennifer R Chao
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Deepak A Lamba
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.,Buck Institute for Research on Aging, Novato, CA, USA
| | - Todd R Klesert
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.,Vitreoretinal Associates of Washington, Seattle, WA, USA
| | - Anna La Torre
- Department of Biological Structure, University of Washington, Seattle, WA, USA.,Department of Cell Biology and Human Anatomy, University of California, Davis, CA, USA
| | - Akina Hoshino
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Russell J Taylor
- Department of Biological Structure, University of Washington, Seattle, WA, USA.,University of Wisconsin, Madison, WI, USA
| | - Anu Jayabalu
- Department of Biological Structure, University of Washington, Seattle, WA, USA.,Universal Cells, Inc., Seattle, WA, USA
| | - Abbi L Engel
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Thomas H Khuu
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Ruikang K Wang
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.,Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Jay Neitz
- Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA
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Abstract
Retinal regeneration from resident Müller glia cells is robust in teleost fish, but is severely limited in birds and mammals. After neurotoxic injury, chick Müller glia can proliferate, and activate neurogenic genes, but they display limited capacity to differentiate into neurons. Developmental signaling molecules enhance this process. Regeneration of retinal neurons in rodents is even more limited. However, studies show evidence of proliferation and neurogenic gene expression after injury, with stronger effects in rats than mice, and differences between mouse strains. Mitogenic growth factors and Wnt signaling potentiate the proliferative response, while misexpression of the proneural transcription factor, Ascl1, reprograms to generate neurons from Müller glial in vitro, and stimulates neuronal regeneration in young mice, in vivo.
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Affiliation(s)
- Matthew S Wilken
- Department of Biological Structure, Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, United States
| | - Thomas A Reh
- Department of Biological Structure, Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, United States.
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Abstract
Photoreceptors--the light-sensitive cells in the vertebrate retina--have been extremely well-characterized with regards to their biochemistry, cell biology and physiology. They therefore provide an excellent model for exploring the factors and mechanisms that drive neural progenitors into a differentiated cell fate in the nervous system. As a result, great progress in understanding the transcriptional network that controls photoreceptor specification and differentiation has been made over the last 20 years. This progress has also enabled the production of photoreceptors from pluripotent stem cells, thereby aiding the development of regenerative medical approaches to eye disease. In this Review, we outline the signaling and transcription factors that drive vertebrate photoreceptor development and discuss how these function together in gene regulatory networks to control photoreceptor cell fate specification.
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Affiliation(s)
- Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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La Torre A, Hoshino A, Cavanaugh C, Ware CB, Reh TA. The GIPC1-Akt1 Pathway Is Required for the Specification of the Eye Field in Mouse Embryonic Stem Cells. Stem Cells 2015; 33:2674-85. [PMID: 26013465 DOI: 10.1002/stem.2062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 04/22/2015] [Indexed: 12/20/2022]
Abstract
During early patterning of the neural plate, a single region of the embryonic forebrain, the eye field, becomes competent for eye development. The hallmark of eye field specification is the expression of the eye field transcription factors (EFTFs). Experiments in fish, amphibians, birds, and mammals have demonstrated largely conserved roles for the EFTFs. Although some of the key signaling events that direct the synchronized expression of these factors to the eye field have been elucidated in fish and frogs, it has been more difficult to study these mechanisms in mammalian embryos. In this study, we have used two different methods for directed differentiation of mouse embryonic stem cells (mESCs) to generate eye field cells and retina in vitro to test for a role of the PDZ domain-containing protein GIPC1 in the specification of the mammalian eye primordia. We find that the overexpression of a dominant-negative form of GIPC1 (dnGIPC1), as well as the downregulation of endogenous GIPC1, is sufficient to inhibit the development of eye field cells from mESCs. GIPC1 interacts directly with IGFR and participates in Akt1 activation, and pharmacological inhibition of Akt1 phosphorylation mimics the dnGIPC1 phenotype. Our data, together with previous studies in Xenopus, support the hypothesis that the GIPC1-PI3K-Akt1 pathway plays a key role in eye field specification in vertebrates.
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Affiliation(s)
- Anna La Torre
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, Washington, USA.,Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, California, USA
| | - Akina Hoshino
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Christopher Cavanaugh
- Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Carol B Ware
- Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
| | - Thomas A Reh
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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37
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Zhang J, Taylor RJ, La Torre A, Wilken MS, Cox KE, Reh TA, Vetter ML. Ezh2 maintains retinal progenitor proliferation, transcriptional integrity, and the timing of late differentiation. Dev Biol 2015; 403:128-38. [PMID: 25989023 DOI: 10.1016/j.ydbio.2015.05.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [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: 02/14/2015] [Revised: 05/09/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
Abstract
Epigenetic regulation, including histone modification, is a critical component of gene regulation, although precisely how this contributes to the development of complex tissues such as the neural retina is still being explored. We show that during retinal development in mouse, there are dynamic patterns of expression of the polycomb repressive complex 2 (PRC2) catalytic subunit EZH2 in retinal progenitors and some differentiated cells, as well as dynamic changes in the histone modification H3K27me3. Using conditional knockout of Ezh2 using either Pax6-αCre or Six3-Cre, we find selective reduction in postnatal retinal progenitor proliferation, disruption of retinal lamination, and enhanced differentiation of several late born cell types in the early postnatal retina, including photoreceptors and Müller glia, which are ultimately increased in number and become reactive. RNA-seq identifies many non-retinal genes upregulated with loss of Ezh2, including multiple Hox genes and the cell cycle regulator Cdkn2a, which are established targets of EZH2-mediated repression. ChIP analysis confirms loss of the H3K27me3 modification at these loci. Similar gene upregulation is observed in retinal explants treated with an EZH2 chemical inhibitor. There is considerable overlap with EZH2-regulated genes reported in non-neural tissues, suggesting that EZH2 can regulate similar genes in multiple lineages. Our findings reveal a conserved role for EZH2 in constraining the expression of potent developmental regulators to maintain lineage integrity and retinal progenitor proliferation, as well as regulating the timing of late differentiation.
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Affiliation(s)
- Jianmin Zhang
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
| | - Russell J Taylor
- Department of Biological Structure, University of Washington, Seattle, WA, United States
| | - Anna La Torre
- Department of Biological Structure, University of Washington, Seattle, WA, United States
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, WA, United States; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States
| | - Kristen E Cox
- Department of Biological Structure, University of Washington, Seattle, WA, United States
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, United States
| | - Monica L Vetter
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States.
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38
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Affiliation(s)
- Volker Hartenstein
- Department of Biology, University of California, Los Angeles, California, USA
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39
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Ueki Y, Wilken MS, Cox KE, Chipman LB, Bermingham-McDonogh O, Reh TA. A transient wave of BMP signaling in the retina is necessary for Müller glial differentiation. Development 2015; 142:533-43. [PMID: 25605781 PMCID: PMC4302996 DOI: 10.1242/dev.118745] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The primary glial cells in the retina, the Müller glia, differentiate from retinal progenitors in the first postnatal week. CNTF/LIF/STAT3 signaling has been shown to promote their differentiation; however, another key glial differentiation signal, BMP, has not been examined during this period of Müller glial differentiation. In the course of our analysis of the BMP signaling pathway, we observed a transient wave of Smad1/5/8 signaling in the inner nuclear layer at the end of the first postnatal week, from postnatal day (P) 5 to P9, after the end of neurogenesis. To determine the function of this transient wave, we blocked BMP signaling during this period in vitro or in vivo, using either a BMP receptor antagonist or noggin (Nog). Either treatment leads to a reduction in expression of the Müller glia-specific genes Rlbp1 and Glul, and the failure of many of the Müller glia to repress the bipolar/photoreceptor gene Otx2. These changes in normal Müller glial differentiation result in permanent disruption of the retina, including defects in the outer limiting membrane, rosette formation and a reduction in functional acuity. Our results thus show that Müller glia require a transient BMP signal at the end of neurogenesis to fully repress the neural gene expression program and to promote glial gene expression. Summary: BMP signalling is transiently activated in the postnatal mouse retina to terminate the neurogenic program and promote the expression of glial-specific genes.
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Affiliation(s)
- Yumi Ueki
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Kristen E Cox
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Laura B Chipman
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | | | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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40
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Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS, Bender MA, Stamatoyannopoulos J, Reh TA. DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenetics Chromatin 2015; 8:8. [PMID: 25972927 PMCID: PMC4429822 DOI: 10.1186/1756-8935-8-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 12/29/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied this approach to the mouse CNS, including developing and mature neural retina, whole brain, and two well-characterized brain regions, the cerebellum and the cerebral cortex. RESULTS For the various regions and developmental stages of the CNS that we analyzed, there were approximately the same number of DHSs; however, there were many DHSs unique to each CNS region and developmental stage. Many of the DHSs are likely to mark enhancers that are specific to the specific CNS region and developmental stage. We validated the DNase I mapping approach for identification of CNS enhancers using the existing VISTA Browser database and with in vivo and in vitro electroporation of the retina. Analysis of transcription factor consensus sites within the DHSs shows distinct region-specific profiles of transcriptional regulators particular to each region. Clustering developmentally dynamic DHSs in the retina revealed enrichment of developmental stage-specific transcriptional regulators. Additionally, we found reporter gene activity in the retina driven from several previously uncharacterized regulatory elements surrounding the neurodevelopmental gene Otx2. Identification of DHSs shared between mouse and human showed region-specific differences in the evolution of cis-regulatory elements. CONCLUSIONS Overall, our results demonstrate the potential of genome-wide DNase I mapping to cis-regulatory questions regarding the regional diversity within the CNS. These data represent an extensive catalogue of potential cis-regulatory elements within the CNS that display region and temporal specificity, as well as a set of DHSs common to CNS tissues. Further examination of evolutionary conservation of DHSs between CNS regions and different species may reveal important cis-regulatory elements in the evolution of the mammalian CNS.
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Affiliation(s)
- Matthew S Wilken
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA ; Molecular and Cellular Biology Program, University of Washington, MCB Program Office, T-466 Health Sciences Building, Box 357275, Seattle, WA 98195 USA
| | - Joseph A Brzezinski
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA ; Department of Ophthalmology, University of Colorado School of Medicine, 1675 Aurora Court, Aurora, CO 80045 USA
| | - Anna La Torre
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA
| | - Kyle Siebenthall
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Robert Thurman
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Peter Sabo
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Richard S Sandstrom
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Theresa K Canfield
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - R Scott Hansen
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Michael A Bender
- Department of Pediatrics, University of Washington, 1959 NE Pacific St, Health Sciences Building, Seattle, WA Box 356320, 98195 USA ; Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA
| | - John Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA
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41
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Thompson DA, Ali RR, Banin E, Branham KE, Flannery JG, Gamm DM, Hauswirth WW, Heckenlively JR, Iannaccone A, Jayasundera KT, Khan NW, Molday RS, Pennesi ME, Reh TA, Weleber RG, Zacks DN. Advancing therapeutic strategies for inherited retinal degeneration: recommendations from the Monaciano Symposium. Invest Ophthalmol Vis Sci 2015; 56:918-31. [PMID: 25667399 DOI: 10.1167/iovs.14-16049] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although rare in the general population, retinal dystrophies occupy a central position in current efforts to develop innovative therapies for blinding diseases. This status derives, in part, from the unique biology, accessibility, and function of the retina, as well as from the synergy between molecular discoveries and transformative advances in functional assessment and retinal imaging. The combination of these factors has fueled remarkable progress in the field, while at the same time creating complex challenges for organizing collective efforts aimed at advancing translational research. The present position paper outlines recent progress in gene therapy and cell therapy for this group of disorders, and presents a set of recommendations for addressing the challenges remaining for the coming decade. It is hoped that the formulation of these recommendations will stimulate discussions among researchers, funding agencies, industry, and policy makers that will accelerate the development of safe and effective treatments for retinal dystrophies and related diseases.
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Affiliation(s)
- Debra A Thompson
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Robin R Ali
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States Division of Molecular Therapy, University College London Institute of Ophthalmology, London, England, United Kingdom
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California-Berkeley, Berkeley, California, United States
| | - David M Gamm
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida College of Medicine, Gainesville, Florida, United States
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Alessandro Iannaccone
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark E Pennesi
- Casey Eye Institute and the Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, United States
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington, United States
| | - Richard G Weleber
- Casey Eye Institute and the Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, United States Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States
| | - David N Zacks
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
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42
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Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B. A comparative encyclopedia of DNA elements in the mouse genome. Nature 2015; 515:355-64. [PMID: 25409824 PMCID: PMC4266106 DOI: 10.1038/nature13992] [Citation(s) in RCA: 1135] [Impact Index Per Article: 126.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 10/24/2014] [Indexed: 12/11/2022]
Abstract
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.
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Affiliation(s)
- Feng Yue
- 1] Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA
| | - Yong Cheng
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Alessandra Breschi
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Weisheng Wu
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tyrone Ryba
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Carrie Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Benjamin D Pope
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Yin Shen
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Dmitri D Pervouchine
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Sarah Djebali
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Anthony Kirilusha
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Georgi K Marinov
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Brian A Williams
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Henry Amrhein
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Katherine Fisher-Aylor
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Igor Antoshechkin
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Gilberto DeSalvo
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Lei-Hoon See
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Meagan Fastuca
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Chris Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Alex Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Pablo Prieto
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Julien Lagarde
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Giovanni Bussotti
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Andrea Tanzer
- 1] Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain. [2] Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17/3/303, A-1090 Vienna, Austria
| | - Olgert Denas
- Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
| | - Kanwei Li
- Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
| | - M A Bender
- 1] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA. [2] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Miaohua Zhang
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Rachel Byron
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Mark T Groudine
- 1] Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. [2] Department of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA
| | - David McCleary
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Long Pham
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Samantha Kuan
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Lee Edsall
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Yi-Chieh Wu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Matthew D Rasmussen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Mukul S Bansal
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Manolis Kellis
- 1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Cheryl A Keller
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Christapher S Morrissey
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tejaswini Mishra
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Deepti Jain
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nergiz Dogan
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert S Harris
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip Cayting
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Trupti Kawli
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Alan P Boyle
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Shin Lin
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Yiing Lin
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Camden Jansen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Melissa S Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Drew T Erickson
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Vanessa M Kirkup
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Beatriz Lacerda de Sousa
- Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
| | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Pignatelli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jin Lian
- Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA
| | - Tamer Kahveci
- Computer &Information Sciences &Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Dongwon Lee
- McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA
| | - Miguel Ramalho Santos
- Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
| | - Javier Herrero
- 1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Cedric Notredame
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Audra Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Anthony Shafer
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alex P Reynolds
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R Scott Hansen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Marella De Bruijn
- MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Alexander Rudensky
- HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
| | - Steven Josefowicz
- HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
| | - Robert Samstein
- HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stuart H Orkin
- Dana Farber Cancer Institute, Harvard Medical School, Cambridge, Massachusetts 02138, USA
| | - Dana Levasseur
- University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA
| | - Thalia Papayannopoulou
- Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Kai-Hsin Chang
- University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA
| | - Arthur Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Srikanta Gosh
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Christine Disteche
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Piper Treuting
- Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Yanli Wang
- Bioinformatics and Genomics program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gerd A Blobel
- 1] Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. [2] Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Peter J Good
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Rebecca F Lowdon
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Leslie B Adams
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Xiao-Qiao Zhou
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Michael J Pazin
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Elise A Feingold
- NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA
| | - Barbara Wold
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - James Taylor
- Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA
| | - Sherman M Weissman
- Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA
| | - Roderic Guigo
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - David M Gilbert
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael A Beer
- McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
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43
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Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA. Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature 2015; 515:365-70. [PMID: 25409825 PMCID: PMC4405208 DOI: 10.1038/nature13972] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 10/15/2014] [Indexed: 12/27/2022]
Abstract
The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here we show that mouse TF footprints conjointly encode a regulatory lexicon that is ∼95% similar with that derived from human TF footprints. However, only ∼20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Furthermore, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results indicate that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry, enabling and potentiating cis-regulatory plasticity. Mouse genomic footprinting reveals conservation of transcription factor (TF) recognition repertoires and trans-regulatory circuitry despite massive turnover of DNA elements that contact TFs in vivo. Having generated genomic DNase I footprinting data of the mouse genome across 25 cell and tissue types, these authors use these data to quantify cis-versus-trans regulatory contributions to mammalian regulatory evolution. They describe more than 600 motifs that collectively are over 95% similar to that recognized in vivo by human transcription factors (TFs). Despite substantial turnover of the cis-regulatory landscape around each TF gene, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Conservation between mouse and human TF regulatory networks is particularly similar at the highest organization level. The work was performed as part of the mouse ENCODE project.
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Affiliation(s)
- Andrew B Stergachis
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Alex P Reynolds
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Miaohua Zhang
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Rachel Byron
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Sandra Stelhing-Sun
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R Scott Hansen
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Audra K Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Piper M Treuting
- Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Rajinder Kaul
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Mark Groudine
- 1] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA [2] Division of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA
| | - M A Bender
- 1] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA [2] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Elhanan Borenstein
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98102, USA [3] Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - John A Stamatoyannopoulos
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Department of Medicine, University of Washington, Seattle, Washington 98195, USA
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44
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Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science 2014; 346:1007-12. [PMID: 25411453 PMCID: PMC4337786 DOI: 10.1126/science.1246426] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [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: 12/14/2022]
Abstract
To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.
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Affiliation(s)
- Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Miaohua Zhang
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - R Scott Hansen
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sandra Stehling-Sun
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rachel Byron
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Audra K Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew S Wilken
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Steven Josefowicz
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Howard Hughes Medical Institute
| | - Robert Samstein
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Howard Hughes Medical Institute
| | - Kai-Hsin Chang
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute
| | - Marella De Bruijn
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Arthur Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alexander Rudensky
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Howard Hughes Medical Institute
| | - Stuart H Orkin
- Howard Hughes Medical Institute. Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Thalia Papayannopoulou
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Piper M Treuting
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mark Groudine
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Radiation Oncology, University of Washington, Seattle, WA 98109, USA
| | - M A Bender
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Division of Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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45
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Mathieu J, Zhang Z, Nelson A, Lamba DA, Reh TA, Ware C, Ruohola-Baker H. Hypoxia induces re-entry of committed cells into pluripotency. Stem Cells 2014; 31:1737-48. [PMID: 23765801 DOI: 10.1002/stem.1446] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 04/19/2013] [Accepted: 05/02/2013] [Indexed: 12/26/2022]
Abstract
Adult stem cells reside in hypoxic niches, and embryonic stem cells (ESCs) are derived from a low oxygen environment. However, it is not clear whether hypoxia is critical for stem cell fate since for example human ESCs (hESCs) are able to self-renew in atmospheric oxygen concentrations as well. We now show that hypoxia can govern cell fate decisions since hypoxia alone can revert hESC- or iPSC-derived differentiated cells back to a stem cell-like state, as evidenced by re-activation of an Oct4-promoter reporter. Hypoxia-induced "de-differentiated" cells also mimic hESCs in their morphology, long-term self-renewal capacity, genome-wide mRNA and miRNA profiles, Oct4 promoter methylation state, cell surface markers TRA1-60 and SSEA4 expression, and capacity to form teratomas. These data demonstrate that hypoxia can influence cell fate decisions and could elucidate hypoxic niche function.
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Affiliation(s)
- Julie Mathieu
- Department of Biochemistry, University of Washington, Seattle, Washington, USA; Institute for Stem Cell and Regenerative Medicine University of Washington, Seattle, Washington, USA
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Affiliation(s)
- David R Hyde
- Department of Biological Sciences and Center for Zebrafish Research, 027 Galvin Life Science Building, University of Notre Dame, Notre Dame, IN 46556, United States.
| | - Thomas A Reh
- Department of Biological Structure, Neurobiology and Behavior Program, and the Institute for Stem Cells and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, United States
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Brzezinski JA, Uoon Park K, Reh TA. Blimp1 (Prdm1) prevents re-specification of photoreceptors into retinal bipolar cells by restricting competence. Dev Biol 2013; 384:194-204. [PMID: 24125957 DOI: 10.1016/j.ydbio.2013.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 12/14/2022]
Abstract
During retinal development, photoreceptors and bipolar cells express the transcription factor Otx2. Blimp1 is transiently expressed in Otx2+ cells. Blimp1 deletion results in excess bipolar cell formation at the expense of photoreceptors. In principle, Blimp1 could be expressed only in Otx2+ cells that are committed to photoreceptor fate. Alternatively, Blimp1 could be expressed broadly in Otx2+ cells and silenced to allow bipolar cell development. To distinguish between these alternatives, we followed the fate of Blimp1 expressing cells using Blimp1-Cre mice and Lox-Stop-Lox reporter strains. We observed that Blimp1+ cells gave rise to all photoreceptors, but also to one third of bipolar cells, consistent with the latter alternative: that Blimp1 inhibits bipolar competence in Otx2+ cells and must be silenced to allow bipolar cell generation. To further test this hypothesis, we looked for transitioning rod photoreceptors in Blimp1 conditional knock-out (CKO) mice carrying the NRL-GFP transgene, which specifically labels rods. Control animals lacked NRL-GFP+ bipolar cells. In contrast, about half of the precociously generated bipolar cells in Blimp1 CKO mice co-expressed GFP, suggesting that rods become re-specified as bipolar cells. Birthdating analyses in control and Blimp1 CKO mice showed that bipolar cells were birthdated as early as E13.5 in Blimp1 CKO mice, five days before this cell type was generated in the wild-type retina. Taken together, our data suggest that early Otx2+ cells upregulate photoreceptor and bipolar genes, existing in a bistable state. Blimp1 likely forms a cross-repressive network with pro-bipolar factors such that the winner of this interaction stabilizes the photoreceptor or bipolar state, respectively.
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Affiliation(s)
- Joseph A Brzezinski
- Department of Ophthalmology. University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Pollak J, Wilken MS, Ueki Y, Cox KE, Sullivan JM, Taylor RJ, Levine EM, Reh TA. ASCL1 reprograms mouse Muller glia into neurogenic retinal progenitors. Development 2013; 140:2619-31. [PMID: 23637330 PMCID: PMC3666387 DOI: 10.1242/dev.091355] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [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] [Accepted: 04/03/2013] [Indexed: 12/14/2022]
Abstract
Non-mammalian vertebrates have a robust ability to regenerate injured retinal neurons from Müller glia (MG) that activate the gene encoding the proneural factor Achaete-scute homolog 1 (Ascl1; also known as Mash1 in mammals) and de-differentiate into progenitor cells. By contrast, mammalian MG have a limited regenerative response and fail to upregulate Ascl1 after injury. To test whether ASCL1 could restore neurogenic potential to mammalian MG, we overexpressed ASCL1 in dissociated mouse MG cultures and intact retinal explants. ASCL1-infected MG upregulated retinal progenitor-specific genes and downregulated glial genes. Furthermore, ASCL1 remodeled the chromatin at its targets from a repressive to an active configuration. MG-derived progenitors differentiated into cells that exhibited neuronal morphologies, expressed retinal subtype-specific neuronal markers and displayed neuron-like physiological responses. These results indicate that a single transcription factor, ASCL1, can induce a neurogenic state in mature MG.
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Affiliation(s)
- Julia Pollak
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
- Neurobiology and Behavior Program, University of Washington, Seattle, WA 98195, USA
| | - Matthew S. Wilken
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Yumi Ueki
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Kristen E. Cox
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Jane M. Sullivan
- Neurobiology and Behavior Program, University of Washington, Seattle, WA 98195, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Russell J. Taylor
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Edward M. Levine
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
- Neurobiology and Behavior Program, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
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Ueki Y, Reh TA. EGF stimulates Müller glial proliferation via a BMP-dependent mechanism. Glia 2013; 61:778-89. [PMID: 23362023 DOI: 10.1002/glia.22472] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/02/2013] [Indexed: 01/19/2023]
Abstract
Müller glia, the major type of glia in the retina, are mitotically quiescent under normal conditions, though they can be stimulated to proliferate in some pathological states. Among these stimuli, EGF is known to be a potent mitogen for Müller glia. However, the signaling pathways required for EGF-mediated proliferation of Müller glia are not clearly understood. In this study, postnatal day 12 (P12) or adult trp53(-/-) mouse retinas were explanted and cultured in the presence of EGF to stimulate Müller glial proliferation. Treatment with signaling inhibitors showed that activation of both MEK/ERK1/2 and PI3K/AKT pathways is required for EGF-induced proliferation of Müller glia. Interestingly, BMP/Smad1/5/8 activation downstream of PI3K/AKT signaling was also necessary for robust Müller glial proliferation, though activation of BMP/Smad1/5/8 signaling alone failed to stimulate their proliferation. In dissociated Müller glial culture, treatment with EGF induced the upregulation of Bmp7, and this upregulation was blocked significantly by co-treatment with the BMP inhibitor dorsomorphin, suggesting that BMP/Smad1/5/8 activation is mediated at least in part by an autocrine mechanism in Müller glia. A better understanding of how BMP/Smad1/5/8 signaling is involved in glial proliferation may have important implications for proliferative disorders, as well as for retinal regeneration in mammalian retinas.
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Affiliation(s)
- Yumi Ueki
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
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Abràmoff M, Abrams GW, Agarwal A, Ai E, Aiello LM, Aiello LP, Albert DM, Aschbrenner MW, Ávila M, Aylward GW, Bedell M, Belfort R, Bennett J, Bergstrom C, Besirli CG, Bhende PS, Binder S, Bird AC, Blodi BA, Blumenkranz MS, Boldt HC, Bornfeld N, Bottoni F, Boulton ME, Bowne SJ, Brantley MA, Bressler NM, Bressler SB, Bringmann A, Brinton DA, Brown GC, Brown JC, Brunner S, Bush RA, Cao D, Capone A, Carruthers D, Cavallerano JD, Chakravarthy U, Chan CC, Chan W, Charles S, Charteris DG, Chen DF, Chen J, Chen Y, Cheung CYL, Chew EY, Chiang A, Chiang MF, Constable IJ, Coscas G, Cruess AF, Cunningham ET, Curcio CA, Daiger SP, Damato BE, Davis JL, Davis MD, Day S, De Potter P, de Smet MD, Denniston AK, Dhaliwal RS, Ding X, Do DV, Dou G, Dunn WA, Ehlers JP, Engelbert M, Faia LJ, Falsini B, Fawzi AA, Fekrat S, Feldon SE, Fernandes RAB, Ferreyra HA, Ferrington DA, Ferris FL, Finger PT, Fisher SK, Fishman GA, Fleckenstein M, Flynn HW, Fok AC, Foulds WS, Freeman WR, Freton A, Friedlander M, Frishman LJ, Fu AD, Garcia Filho CADA, Garcia-Valenzuela E, Gaudric A, Gayed M, Genead MA, Gerding H, Giani A, Goldberg MF, Gombos DS, Gopal L, Gordon C, Goto H, Gragoudas ES, Grant MB, Green WR, Gregg RG, Gregor Z, Gregori G, Gregory-Evans K, Grob S, Groenewald C, Grossniklaus HE, Grover S, Gullapalli VK, Gupta A, Guthoff RF, Hahn P, Haller JA, Harbour JW, Haritoglou C, Hartnett ME, Hawkins BS, He S, Herwig MC, Heussen FM, Hinton DR, Holz FG, Houston SK, Hui YN, Humayun MS, Ikuno Y, Isaac D, Ishibashi T, Jabs DA, Jaffe GJ, Jampol LM, Joffe L, Johnson M, Johnson MW, Johnson RN, Joussen AM, Julian K, Jumper JM, Kaiser PK, Kampik A, Katamay R, Kay CN, Keane PA, Kenney MC, Khaderi KR, Khodair MA, Kim IK, Kim TW, Kirchhof B, Klein BE, Klein R, Konstantinidis L, Kozak I, Kuppermann BD, Labriola LT, Lai TY, Lam DS, Lam LA, Landers MB, Lane AM, Lavik EB, Leary JF, Lee SY, Lee TC, Leung LSB, Lewis DA, Lewis GP, Leys A, Li X, Liakopoulos S, Lin CP, Lin P, Liu DT, London NJ, Lujan BJ, Luo Y, Lutty GA, MacLaren R, Madreperla S, Maguire AM, Mainster MA, Mansfield NC, Markoe AM, Marmor MF, Martin DF, Massey SC, McCall MA, McCannel TA, McCutchan JA, McDonald HR, Mehta MP, Meier P, Merbs S, Meredith TA, Meyer CH, Mieler WF, Miller JW, Mirza RG, Mitter SK, Mittra RA, Miyake Y, Montemagno C, Moshiri A, Mruthyunjaya P, Muccioli C, Mullins RF, Murata T, Murphree AL, Murphy RP, Murray PI, Murray TG, Nagpal M, Namperumalsamy P, Nanda SK, Nguyen QD, Nussenblatt RB, Oh KT, Ohji M, Ohno-Matsui K, Palanker D, Patel PS, Pavlick AC, Peereboom DM, Pennesi ME, Pepose JS, Perry JD, Puliafito CA, Quiram PA, Raman R, Ramchandran RS, Rao HV, Rao NA, Rao PK, Rathinam SR, Recchia FM, Redmond KJ, Reh TA, Reichenbach A, Ritch R, Rosenfeld PJ, Rubin GS, Ruiz-Garcia H, Ryan SJ, Sadda SR, Sadun AA, Sakamoto T, Sampath AP, Schachat AP, Schmitz-Valckenberg S, Schwartz SG, Scott AW, Sebag J, Seddon JM, Sen HN, Sepah YJ, Sharma S, Sharma T, Sheu SJ, Shields CL, Shields JA, Shinoda K, Shukla D, Sieving PA, Silva PA, Silveira C, Singh AD, Smith SB, Smith WM, Sobrin L, Sodhi A, Sohn EH, Soubrane G, Spielberg L, Srivastava SK, Stachs O, Staurenghi G, Sternberg P, Stone EM, Sugino IK, Sullivan LS, Sullivan P, Sun JK, Sunness JS, Tadayoni R, Tang S, Terasaki H, Thomas MA, Thompson JT, Thumann G, Toth CA, Trese MT, Tsai JH, Turell ME, Turner PL, Udar N, Ulrich JN, Van Gelder RN, van Meurs JC, Vasconcelos-Santos DV, Vavvas DG, Vemulakonda GA, Wang H, Wang Y, Weiland JD, Weleber RG, Wharam MD, Wickham L, Wiedemann P, Wiley HE, Wilkinson C, Wilson DJ, Wolfensberger TJ, Wong D, Wong IY, Wong TY, Wu DM, Yandiev Y, Yang CH, Yang CM, Yannuzzi LA, Yasuda M, Yeh PT, Yehoshua Z, Yiu G, Yoon YH, Yu HG, Yuan A, Zarbin MA, Zhang JJ, Zhang K, Zhao M, Zhou P. Contributors. Retina 2013. [DOI: 10.1016/b978-1-4557-0737-9.00159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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