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Kang J, Gong J, Yang C, Lin X, Yan L, Gong Y, Xu H. Application of Human Stem Cell Derived Retinal Organoids in the Exploration of the Mechanisms of Early Retinal Development. Stem Cell Rev Rep 2023:10.1007/s12015-023-10553-x. [PMID: 37269529 DOI: 10.1007/s12015-023-10553-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2023] [Indexed: 06/05/2023]
Abstract
The intricate neural circuit of retina extracts salient features of the natural world and forms bioelectric impulse as the origin of vision. The early development of retina is a highly complex and coordinated process in morphogenesis and neurogenesis. Increasing evidence indicates that stem cells derived human retinal organoids (hROs) in vitro faithfully recapitulates the embryonic developmental process of human retina no matter in the transcriptome, cellular biology and histomorphology. The emergence of hROs greatly deepens on the understanding of early development of human retina. Here, we reviewed the events of early retinal development both in animal embryos and hROs studies, which mainly comprises the formation of optic vesicle and optic cup shape, differentiation of retinal ganglion cells (RGCs), photoreceptor cells (PRs) and its supportive retinal pigment epithelium cells (RPE). We also discussed the classic and frontier molecular pathways up to date to decipher the underlying mechanisms of early development of human retina and hROs. Finally, we summarized the application prospect, challenges and cutting-edge techniques of hROs for uncovering the principles and mechanisms of retinal development and related developmental disorder. hROs is a priori selection for studying human retinal development and function and may be a fundamental tool for unlocking the unknown insight into retinal development and disease.
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Affiliation(s)
- Jiahui Kang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China
| | - Jing Gong
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Cao Yang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China
| | - Xi Lin
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China
| | - Lijuan Yan
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China
| | - Yu Gong
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
- Department of Ophthalmology, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, China.
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, 400038, China.
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2
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Petridou E, Godinho L. Cellular and Molecular Determinants of Retinal Cell Fate. Annu Rev Vis Sci 2022; 8:79-99. [DOI: 10.1146/annurev-vision-100820-103154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The vertebrate retina is regarded as a simple part of the central nervous system (CNS) and thus amenable to investigations of the determinants of cell fate. Its five neuronal cell classes and one glial cell class all derive from a common pool of progenitors. Here we review how each cell class is generated. Retinal progenitors progress through different competence states, in each of which they generate only a small repertoire of cell classes. The intrinsic state of the progenitor is determined by the complement of transcription factors it expresses. Thus, although progenitors are multipotent, there is a bias in the types of fates they generate during any particular time window. Overlying these competence states are stochastic mechanisms that influence fate decisions. These mechanisms are determined by a weighted set of probabilities based on the abundance of a cell class in the retina. Deterministic mechanisms also operate, especially late in development, when preprogrammed progenitors solely generate specific fates.
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Affiliation(s)
- Eleni Petridou
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany;,
- Graduate School of Systemic Neurosciences (GSN), Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Leanne Godinho
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany;,
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3
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Shiau F, Ruzycki PA, Clark BS. A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq. Dev Biol 2021; 478:41-58. [PMID: 34146533 PMCID: PMC8386138 DOI: 10.1016/j.ydbio.2021.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
Recent advances in high throughput single-cell RNA sequencing (scRNA-seq) technology have enabled the simultaneous transcriptomic profiling of thousands of individual cells in a single experiment. To investigate the intrinsic process of retinal development, researchers have leveraged this technology to quantify gene expression in retinal cells across development, in multiple species, and from numerous important models of human disease. In this review, we summarize recent applications of scRNA-seq and discuss how these datasets have complemented and advanced our understanding of retinal progenitor cell competence, cell fate specification, and differentiation. Finally, we also highlight the outstanding questions in the field that advances in single-cell data generation and analysis will soon be able to answer.
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Affiliation(s)
- Fion Shiau
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A Ruzycki
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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4
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West ER, Cepko CL. Development and diversification of bipolar interneurons in the mammalian retina. Dev Biol 2021; 481:30-42. [PMID: 34534525 DOI: 10.1016/j.ydbio.2021.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022]
Abstract
The bipolar interneurons of the mammalian retina have evolved as a diverse set of cells with distinct subtype characteristics, which reflect specialized contributions to visual circuitry. Fifteen subtypes of bipolar interneurons have been identified in the mouse retina, each with characteristic gene expression, morphology, and light responses. This review provides an overview of the developmental events that underlie the generation of the diverse bipolar cell class, summarizing the current knowledge of genetic programs that establish and maintain bipolar subtype fates, as well as the events that shape the final distribution of bipolar subtypes. With much left to be discovered, bipolar interneurons present an ideal model system for studying the interplay between cell-autonomous and non-cell-autonomous mechanisms that influence neuronal subtype development within the central nervous system.
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Affiliation(s)
- Emma R West
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Constance L Cepko
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Regulatory Mechanisms of Retinal Photoreceptors Development at Single Cell Resolution. Int J Mol Sci 2021; 22:ijms22168357. [PMID: 34445064 PMCID: PMC8395061 DOI: 10.3390/ijms22168357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/18/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Photoreceptors are critical components of the retina and play a role in the first step of the conversion of light to electric signals. With the discovery of the intrinsically photosensitive retinal ganglion cells, which regulate non-image-forming visual processes, our knowledge of the photosensitive cell family in the retina has deepened. Photoreceptor development is regulated by specific genes and proteins and involves a series of molecular processes including DNA transcription, post-transcriptional modification, protein translation, and post-translational modification. Single-cell sequencing is a promising technology for the study of photoreceptor development. This review presents an overview of the types of human photoreceptors, summarizes recent discoveries in the regulatory mechanisms underlying their development at single-cell resolution, and outlines the prospects in this field.
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6
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Chen X, Emerson MM. Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states. Sci Rep 2021; 11:14525. [PMID: 34267251 PMCID: PMC8282820 DOI: 10.1038/s41598-021-93692-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022] Open
Abstract
Notch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
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Affiliation(s)
- Xueqing Chen
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.
- Biochemistry PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
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7
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Wagstaff EL, Heredero Berzal A, Boon CJF, Quinn PMJ, ten Asbroek ALMA, Bergen AA. The Role of Small Molecules and Their Effect on the Molecular Mechanisms of Early Retinal Organoid Development. Int J Mol Sci 2021; 22:7081. [PMID: 34209272 PMCID: PMC8268497 DOI: 10.3390/ijms22137081] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 12/12/2022] Open
Abstract
Early in vivo embryonic retinal development is a well-documented and evolutionary conserved process. The specification towards eye development is temporally controlled by consecutive activation or inhibition of multiple key signaling pathways, such as the Wnt and hedgehog signaling pathways. Recently, with the use of retinal organoids, researchers aim to manipulate these pathways to achieve better human representative models for retinal development and disease. To achieve this, a plethora of different small molecules and signaling factors have been used at various time points and concentrations in retinal organoid differentiations, with varying success. Additions differ from protocol to protocol, but their usefulness or efficiency has not yet been systematically reviewed. Interestingly, many of these small molecules affect the same and/or multiple pathways, leading to reduced reproducibility and high variability between studies. In this review, we make an inventory of the key signaling pathways involved in early retinogenesis and their effect on the development of the early retina in vitro. Further, we provide a comprehensive overview of the small molecules and signaling factors that are added to retinal organoid differentiation protocols, documenting the molecular and functional effects of these additions. Lastly, we comparatively evaluate several of these factors using our established retinal organoid methodology.
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Affiliation(s)
- Ellie L. Wagstaff
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands;
| | - Andrea Heredero Berzal
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands; (A.H.B.); (C.J.F.B.)
| | - Camiel J. F. Boon
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands; (A.H.B.); (C.J.F.B.)
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Peter M. J. Quinn
- Jonas Children’s Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center—New York-Presbyterian Hospital, New York, NY 10032, USA;
| | | | - Arthur A. Bergen
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands;
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands; (A.H.B.); (C.J.F.B.)
- Netherlands Institute for Neuroscience (NIN-KNAW), 1105 BA Amsterdam, The Netherlands
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8
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Kaufman ML, Park KU, Goodson NB, Chew S, Bersie S, Jones KL, Lamba DA, Brzezinski JA. Transcriptional profiling of murine retinas undergoing semi-synchronous cone photoreceptor differentiation. Dev Biol 2019; 453:155-167. [PMID: 31163126 DOI: 10.1016/j.ydbio.2019.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Uncovering the gene regulatory networks that control cone photoreceptor formation has been hindered because cones only make up a few percent of the retina and form asynchronously during development. To overcome these limitations, we used a γ-secretase inhibitor, DAPT, to disrupt Notch signaling and force proliferating retinal progenitor cells to rapidly adopt neuronal identity. We treated mouse retinal explants at the peak of cone genesis with DAPT and examined tissues at several time-points by histology and bulk RNA-sequencing. We found that this treatment caused supernumerary cone formation in an overwhelmingly synchronized fashion. This analysis revealed several categorical patterns of gene expression changes over time relative to DMSO treated control explants. These were placed in the temporal context of the activation of Otx2, a transcription factor that is expressed at the onset of photoreceptor development and that is required for both rod and cone formation. One group of interest had genes, such as Mybl1, Ascl1, Neurog2, and Olig2, that became upregulated by DAPT treatment before Otx2. Two other groups showed upregulated gene expression shortly after Otx2, either transiently or permanently. This included genes such as Mybl1, Meis2, and Podxl. Our data provide a developmental timeline of the gene expression events that underlie the initial steps of cone genesis and maturation. Applying this strategy to human retinal organoid cultures was also sufficient to induce a massive increase in cone genesis. Taken together, our results provide a temporal framework that can be used to elucidate the gene regulatory logic controlling cone photoreceptor development.
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Affiliation(s)
- Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Noah B Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shereen Chew
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Stephanie Bersie
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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9
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Phillips MJ, Jiang P, Howden S, Barney P, Min J, York NW, Chu LF, Capowski EE, Cash A, Jain S, Barlow K, Tabassum T, Stewart R, Pattnaik BR, Thomson JA, Gamm DM. A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types. Stem Cells 2018; 36:313-324. [PMID: 29230913 PMCID: PMC5823737 DOI: 10.1002/stem.2755] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/31/2017] [Accepted: 11/29/2017] [Indexed: 11/07/2022]
Abstract
Cell type-specific investigations commonly use gene reporters or single-cell analytical techniques. However, reporter line development is arduous and generally limited to a single gene of interest, while single-cell RNA (scRNA)-sequencing (seq) frequently yields equivocal results that preclude definitive cell identification. To examine gene expression profiles of multiple retinal cell types derived from human pluripotent stem cells (hPSCs), we performed scRNA-seq on optic vesicle (OV)-like structures cultured under cGMP-compatible conditions. However, efforts to apply traditional scRNA-seq analytical methods based on unbiased algorithms were unrevealing. Therefore, we developed a simple, versatile, and universally applicable approach that generates gene expression data akin to those obtained from reporter lines. This method ranks single cells by expression level of a bait gene and searches the transcriptome for genes whose cell-to-cell rank order expression most closely matches that of the bait. Moreover, multiple bait genes can be combined to refine datasets. Using this approach, we provide further evidence for the authenticity of hPSC-derived retinal cell types. Stem Cells 2018;36:313-324.
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Affiliation(s)
| | - Peng Jiang
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Sara Howden
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | | | | | | | - Li-Fang Chu
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | | | | | | | | | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Bikash R Pattnaik
- McPherson Eye Research Institute
- Department of Pediatrics
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - David M Gamm
- Waisman Center
- McPherson Eye Research Institute
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Abstract
Photoreceptors are highly specialized primary sensory neurons that sense light and initiate vision. This critical role is well demonstrated by the fact that visual impairment accompanies photoreceptor loss or dysfunction in many human diseases. With the remarkable advances in stem cell research, one therapeutic approach is to use stem cells to generate photoreceptors and then engraft them into diseased eyes. Knowledge of the molecular mechanisms that control photoreceptor genesis during normal development can greatly aid in the production of photoreceptor cells for this approach. This article will discuss advances in our understanding of the molecular mechanisms that regulate photoreceptor fate determination during development. Recent lineage studies have shown that there are distinct retinal progenitor cells (RPCs) that produce specific combinations of daughter cell types, including photoreceptors and other types of retinal cells. Gene regulatory networks, in which transcription factors interact via cis-regulatory DNA elements, have been discovered that operate within distinct RPCs, and/or newly postmitotic cells, to direct the choice of photoreceptor fate.
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Affiliation(s)
- Sui Wang
- Department of Genetics and Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States 2Howard Hughes Medical Institute, Boston, Massachusetts, United States
| | - Constance L Cepko
- Department of Genetics and Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States 2Howard Hughes Medical Institute, Boston, Massachusetts, United States
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11
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Aldiri I, Ajioka I, Xu B, Zhang J, Chen X, Benavente C, Finkelstein D, Johnson D, Akiyama J, Pennacchio LA, Dyer MA. Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma. Development 2016; 142:4092-106. [PMID: 26628093 PMCID: PMC4712833 DOI: 10.1242/dev.124800] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Retinal development requires precise temporal and spatial coordination of cell cycle exit, cell fate specification, cell migration and differentiation. When this process is disrupted, retinoblastoma, a developmental tumor of the retina, can form. Epigenetic modulators are central to precisely coordinating developmental events, and many epigenetic processes have been implicated in cancer. Studying epigenetic mechanisms in development is challenging because they often regulate multiple cellular processes; therefore, elucidating the primary molecular mechanisms involved can be difficult. Here we explore the role of Brg1 (Smarca4) in retinal development and retinoblastoma in mice using molecular and cellular approaches. Brg1 was found to regulate retinal size by controlling cell cycle length, cell cycle exit and cell survival during development. Brg1 was not required for cell fate specification but was required for photoreceptor differentiation and cell adhesion/polarity programs that contribute to proper retinal lamination during development. The combination of defective cell differentiation and lamination led to retinal degeneration in Brg1-deficient retinae. Despite the hypocellularity, premature cell cycle exit, increased cell death and extended cell cycle length, retinal progenitor cells persisted in Brg1-deficient retinae, making them more susceptible to retinoblastoma. ChIP-Seq analysis suggests that Brg1 might regulate gene expression through multiple mechanisms. Summary: The SWI/SNF protein Brg1 controls cell cycle length, cell cycle exit and cell survival, and is required for cell differentiation and retinal lamination, in the developing mouse retina.
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Affiliation(s)
- Issam Aldiri
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Itsuki Ajioka
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiakun Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Claudia Benavente
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dianna Johnson
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jennifer Akiyama
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94701, USA Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Len A Pennacchio
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94701, USA Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN 38163, USA Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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12
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Abstract
Photoreceptors have been the most intensively studied retinal cell type. Early lineage studies showed that photoreceptors are produced by retinal progenitor cells (RPCs) that produce only photoreceptor cells and by RPCs that produce both photoreceptor cells and other retinal cell types. More recent lineage studies have shown that there are intrinsic, molecular differences among these RPCs and that these molecular differences operate in gene regulatory networks (GRNs) that lead to the choice of the rod versus the cone fate. In addition, there are GRNs that lead to the choice of a photoreceptor fate and that of another retinal cell type. An example of such a GRN is one that drives the binary fate choice between a rod photoreceptor and bipolar cell. This GRN has many elements, including both feedforward and feedback regulatory loops, highlighting the complexity of such networks. This and other examples of retinal cell fate determination are reviewed here, focusing on the events that direct the choice of rod and cone photoreceptor fate.
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Affiliation(s)
- Constance L Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115;
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13
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Mansergh FC, Carrigan M, Hokamp K, Farrar GJ. Gene expression changes during retinal development and rod specification. Mol Vis 2015; 21:61-87. [PMID: 25678762 PMCID: PMC4301594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/16/2015] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) typically results from individual mutations in any one of >70 genes that cause rod photoreceptor cells to degenerate prematurely, eventually resulting in blindness. Gene therapies targeting individual RP genes have shown efficacy at clinical trial; however, these therapies require the surviving photoreceptor cells to be viable and functional, and may be economically feasible for only the more commonly mutated genes. An alternative potential treatment strategy, particularly for late stage disease, may involve stem cell transplants into the photoreceptor layer of the retina. Rod progenitors from postnatal mouse retinas can be transplanted and can form photoreceptors in recipient adult retinas; optimal numbers of transplantable cells are obtained from postnatal day 3-5 (P3-5) retinas. These cells can also be expanded in culture; however, this results in the loss of photoreceptor potential. Gene expression differences between postnatal retinas, cultured retinal progenitor cells (RPCs), and rod photoreceptor precursors were investigated to identify gene expression patterns involved in the specification of rod photoreceptors. METHODS Microarrays were used to investigate differences in gene expression between cultured RPCs that have lost photoreceptor potential, P1 retinas, and fresh P5 retinas that contain significant numbers of transplantable photoreceptors. Additionally, fluorescence-activated cell sorting (FACS) sorted Rho-eGFP-expressing rod photoreceptor precursors were compared with Rho-eGFP-negative cells from the same P5 retinas. Differential expression was confirmed with quantitative polymerase chain reaction (q-PCR). RESULTS Analysis of the microarray data sets, including the use of t-distributed stochastic neighbor embedding (t-SNE) to identify expression pattern neighbors of key photoreceptor specific genes, resulted in the identification of 636 genes differentially regulated during rod specification. Forty-four of these genes when mutated have previously been found to cause retinal disease. Although gene function in other tissues may be known, the retinal function of approximately 61% of the gene list is as yet undetermined. Many of these genes' promoters contain binding sites for the key photoreceptor transcription factors Crx and Nr2e3; moreover, the genomic clustering of differentially regulated genes appears to be non-random. CONCLUSIONS This study aids in understanding gene expression differences between rod photoreceptor progenitors versus cultured RPCs that have lost photoreceptor potential. The results provide insights into rod photoreceptor development and should expedite the development of cell-based treatments for RP. Furthermore, the data set includes a large number of retinopathy genes; less-well-characterized genes within this data set are a resource for those seeking to identify novel retinopathy genes in patients with RP (GEO accession: GSE59201).
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Affiliation(s)
- Fiona C Mansergh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew Carrigan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - G Jane Farrar
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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14
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Chiu IM, Barrett LB, Williams EK, Strochlic DE, Lee S, Weyer AD, Lou S, Bryman GS, Roberson DP, Ghasemlou N, Piccoli C, Ahat E, Wang V, Cobos EJ, Stucky CL, Ma Q, Liberles SD, Woolf CJ. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity. eLife 2014; 3. [PMID: 25525749 PMCID: PMC4383053 DOI: 10.7554/elife.04660] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/18/2014] [Indexed: 12/17/2022] Open
Abstract
The somatosensory nervous system is critical for the organism's ability to respond to
mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally
and anatomically diverse but their molecular profiles are not well-defined. Here, we
used transcriptional profiling to analyze the detailed molecular signatures of dorsal
root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4
labeling to purify three major non-overlapping classes of neurons: 1)
IB4+SNS-Cre/TdTomato+, 2)
IB4−SNS-Cre/TdTomato+, and 3)
Parv-Cre/TdTomato+ cells, encompassing the majority of
nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed
distinct expression patterns of ion channels, transcription factors, and GPCRs.
Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the
three populations demonstrated further diversity, with unbiased clustering analysis
identifying six distinct subgroups. These data significantly increase our knowledge
of the molecular identities of known DRG populations and uncover potentially novel
subsets, revealing the complexity and diversity of those neurons underlying
somatosensation. DOI:http://dx.doi.org/10.7554/eLife.04660.001 In the nervous system, a network of specialized neurons—known as the
somatosensory system—carries information about sensations including touch,
muscle position, temperature and pain. Distinct sets of somatosensory neurons are
thought to carry information about the different types of sensations. In young
animals, the precise switching on, or ‘expression’, of genes controls
the formation of the network of neurons. However, it is not known exactly which genes
are expressed in what types of neurons, where, or when. Here, Chiu et al. used a technique called flow cytometry using different fluorescent
markers to isolate a group of cells called Dorsal Root Ganglion (DRG) neurons in
mice. These neurons have long thread-like fibers that extend from the spinal cord to
the skin, muscles and joints all over the body. These fibers carry sensory
information to the spinal cord, where it can be relayed to the brain and processed.
The experiments compared three distinct types of DRG neuron and found that they
differed in their ability to send information to other cells. Chiu et al. analyzed the expression of all the genes in the three types of DRG
neurons. Each type of neuron had distinct groups of genes that were being expressed.
Also, several genes that are known to be important for sensation were expressed at
different levels in the different types of cells. Next, large numbers of single cells
were analyzed to find out the finer details about the three types of neuron. These
findings made it possible to further divide the DRG neurons into six distinct subsets
that matched previously known groups of somatosensory neurons, and also identified
new ones. Chiu et al.'s findings reveal the complexity and diversity of the neurons involved in
carrying information about sensations towards the brain. This is an important step in
classifying the nervous system, and uncovers many genes previously not linked to
sensation. The next challenges lie in understanding how the expression of these genes
in each type of neuron relates to their unique roles. DOI:http://dx.doi.org/10.7554/eLife.04660.002
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Affiliation(s)
- Isaac M Chiu
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Lee B Barrett
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Erika K Williams
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - David E Strochlic
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Seungkyu Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Andy D Weyer
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, United States
| | - Shan Lou
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Gregory S Bryman
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - David P Roberson
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Nader Ghasemlou
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Cara Piccoli
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Ezgi Ahat
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Victor Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Enrique J Cobos
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Cheryl L Stucky
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, United States
| | - Qiufu Ma
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Stephen D Liberles
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
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15
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A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina. Dev Cell 2014; 30:513-27. [PMID: 25155555 PMCID: PMC4304698 DOI: 10.1016/j.devcel.2014.07.018] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/16/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
Gene regulatory networks (GRNs) regulate critical events during development. In complex tissues, such as the mammalian central nervous system (CNS), networks likely provide the complex regulatory interactions needed to direct the specification of the many CNS cell types. Here, we dissect a GRN that regulates a binary fate decision between two siblings in the murine retina, the rod photoreceptor and bipolar interneuron. The GRN centers on Blimp1, one of the transcription factors (TFs) that regulates the rod versus bipolar cell fate decision. We identified a cis-regulatory module (CRM), B108, that mimics Blimp1 expression. Deletion of genomic B108 by CRISPR/Cas9 in vivo using electroporation abolished the function of Blimp1. Otx2 and RORβ were found to regulate Blimp1 expression via B108, and Blimp1 and Otx2 were shown to form a negative feedback loop that regulates the level of Otx2, which regulates the production of the correct ratio of rods and bipolar cells.
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16
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Dixit R, Tachibana N, Touahri Y, Zinyk D, Logan C, Schuurmans C. Gene expression is dynamically regulated in retinal progenitor cells prior to and during overt cellular differentiation. Gene Expr Patterns 2013; 14:42-54. [PMID: 24148613 DOI: 10.1016/j.gep.2013.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 12/27/2022]
Abstract
The retina is comprised of one glial and six neuronal populations that are generated from a multipotent pool of retinal progenitor cells (RPCs) during development. To give rise to these different cell types, RPCs undergo temporal identity transitions, displaying distinct gene expression profiles at different stages of differentiation. Little, however, is known about temporal differences in RPC identities prior to the onset of overt cellular differentiation, during the period when a retinal identity is gradually acquired. Here we examined the sequential onset of expression of regional markers (i.e., homeodomain transcription factors) and cell fate determinants (i.e., basic-helix-loop-helix transcription factors and neurogenic genes) in RPCs from the earliest appearance of a morphologically-distinct retina. By performing a comparative analysis of the expression of a panel of 27 homeodomain, basic-helix-loop-helix and Notch pathway genes between embryonic day (E) 8.75 and postnatal day (P) 9, we identified six distinct RPC molecular profiles. At E8.75, the earliest stage assayed, murine RPCs expressed five homeodomain genes and a single neurogenic gene (Pax6, Six3, Six6, Rx, Otx2, Hes1). This early gene expression profile was remarkably similar to that of 'early' RPCs in the amphibian ciliary marginal zone (CMZ), where RPCs are compartmentalised according to developmental stage, and homologs of Pax6, Six3 and Rx are expressed in the 'early' stem cell zone. As development proceeds, expression of additional homeodomain, bHLH and neurogenic genes was gradually initiated in murine RPCs, allowing distinct genetic profiles to also be defined at E9.5, E10.5, E12.5, E15.5 and P0. In addition, RPCs in the postnatal ciliary margin, where retinal stem cells are retained throughout life, displayed a unique molecular signature, expressing all of the early-onset genes as well as several late-onset markers, indicative of a 'mixed' temporal identity. Taken together, the identification of temporal differences in gene expression in mammalian RPCs during pre-neurogenic developmental stages leads to new insights into how regional identities are progressively acquired during development, while comparisons at later stages highlight the dynamic nature of gene expression in temporally distinct RPC pools.
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Affiliation(s)
- Rajiv Dixit
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
| | - Nobuhiko Tachibana
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Yacine Touahri
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Dawn Zinyk
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Cairine Logan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Carol Schuurmans
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
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17
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Mizeracka K, DeMaso CR, Cepko CL. Notch1 is required in newly postmitotic cells to inhibit the rod photoreceptor fate. Development 2013; 140:3188-97. [PMID: 23824579 DOI: 10.1242/dev.090696] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Several models of cell fate determination can be invoked to explain how single retinal progenitor cells (RPCs) produce different cell types in a terminal division. To gain insight into this process, the effects of the removal of a cell fate regulator, Notch1, were studied in newly postmitotic cells using a conditional allele of Notch1 (N1-CKO) in mice. Almost all newly postmitotic N1-CKO cells became rod photoreceptors, whereas wild-type (WT) cells achieved a variety of fates. Single cell profiling of wild-type and N1-CKO retinal cells transitioning from progenitor to differentiated states revealed differential expression of inhibitor of DNA binding factors Id1 and Id3, as well as Notch-regulated ankyrin repeat protein (Nrarp). Misexpression of Id1 and Id3 was found to be sufficient to drive production of Müller glial cells and/or RPCs. Moreover, Id1 and Id3 were shown to partially rescue the production of bipolar and Müller glial cells in the absence of Notch1 in mitotic and newly postmitotic cells. Misexpression of Nrarp, a downstream target gene and inhibitor of the Notch signaling pathway, resulted in the overproduction of rod photoreceptors at the expense of Müller glial cells. These data demonstrate that cell fate decisions can be made in newly postmitotic retinal cells, and reveal some of the regulators downstream of Notch1 that influence the choice of rod and non-rod fates. Taken together, our results begin to address how different signals downstream from a common pathway lead to different fate outcomes.
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