1
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Patierno BM, Emerson MM. Enhanced Plasmid-Based Transcriptional Activation in Developing Mouse Photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597220. [PMID: 38895286 PMCID: PMC11185626 DOI: 10.1101/2024.06.06.597220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Rod photoreceptor formation in the postnatal mouse is a widely used model system for studying mammalian photoreceptor development. This experimental paradigm provides opportunities for both gain and loss-of-function studies which can be accomplished through in vivo plasmid delivery and electroporation. However, the cis-regulatory elements used to implement this approach have not been fully evaluated or optimized for the unique transcriptional environment of photoreceptors. Here we report that the use of a photoreceptor cis-regulatory element from the Crx gene in combination with broadly active promoter elements can increase the targeting of developing rod photoreceptors in the mouse. This can lead to greater reporter expression, as well as enhanced misexpression and loss-of-function phenotypes in these cells. This study also highlights the importance of identifying and testing relevant cis-regulatory elements when planning cell subtype specific experiments. The use of the specific hybrid elements in this study will provide a more efficacious gene delivery system to study mammalian photoreceptor formation.
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Affiliation(s)
- Brendon M. Patierno
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031
| | - Mark M. Emerson
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031
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2
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Andreazzoli M, Longoni B, Angeloni D, Demontis GC. Retinoid Synthesis Regulation by Retinal Cells in Health and Disease. Cells 2024; 13:871. [PMID: 38786093 PMCID: PMC11120330 DOI: 10.3390/cells13100871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Vision starts in retinal photoreceptors when specialized proteins (opsins) sense photons via their covalently bonded vitamin A derivative 11cis retinaldehyde (11cis-RAL). The reaction of non-enzymatic aldehydes with amino groups lacks specificity, and the reaction products may trigger cell damage. However, the reduced synthesis of 11cis-RAL results in photoreceptor demise and suggests the need for careful control over 11cis-RAL handling by retinal cells. This perspective focuses on retinoid(s) synthesis, their control in the adult retina, and their role during retina development. It also explores the potential importance of 9cis vitamin A derivatives in regulating retinoid synthesis and their impact on photoreceptor development and survival. Additionally, recent advancements suggesting the pivotal nature of retinoid synthesis regulation for cone cell viability are discussed.
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Affiliation(s)
| | - Biancamaria Longoni
- Department of Translational Medicine and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy
| | - Debora Angeloni
- The Institute of Biorobotics, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
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3
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Tran M, Askary A, Elowitz MB. Lineage motifs as developmental modules for control of cell type proportions. Dev Cell 2024; 59:812-826.e3. [PMID: 38359830 DOI: 10.1016/j.devcel.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/10/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
In multicellular organisms, cell types must be produced and maintained in appropriate proportions. One way this is achieved is through committed progenitor cells or extrinsic interactions that produce specific patterns of descendant cell types on lineage trees. However, cell fate commitment is probabilistic in most contexts, making it difficult to infer these dynamics and understand how they establish overall cell type proportions. Here, we introduce Lineage Motif Analysis (LMA), a method that recursively identifies statistically overrepresented patterns of cell fates on lineage trees as potential signatures of committed progenitor states or extrinsic interactions. Applying LMA to published datasets reveals spatial and temporal organization of cell fate commitment in zebrafish and rat retina and early mouse embryonic development. Comparative analysis of vertebrate species suggests that lineage motifs facilitate adaptive evolutionary variation of retinal cell type proportions. LMA thus provides insight into complex developmental processes by decomposing them into simpler underlying modules.
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Affiliation(s)
- Martin Tran
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amjad Askary
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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4
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Zheng Y, Stormo GD, Chen S. Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584677. [PMID: 38559186 PMCID: PMC10979960 DOI: 10.1101/2024.03.12.584677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX's cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A's cooperativity defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N's altered biochemical properties disrupt CRX's ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Gary D. Stormo
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
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5
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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6
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Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Campbell LJ, Boyd P, Palazzo I, Nagashima M, Silva NJ, Hitchcock PF, Qian J, Hyde DR, Blackshaw S. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. Nat Commun 2023; 14:8477. [PMID: 38123561 PMCID: PMC10733277 DOI: 10.1038/s41467-023-44142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes through Müller glia (MG) reprogramming and asymmetric cell division that produces a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, do MG reprogram to a developmental retinal progenitor cell (RPC) state? Second, to what extent does regeneration recapitulate retinal development? And finally, does loss of different retinal cell subtypes induce unique MG regeneration responses? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. Here we show that injury induces MG to reprogram to a state similar to late-stage RPCs. However, there are major transcriptional differences between MGPCs and RPCs, as well as major transcriptional differences between activated MG and MGPCs when different retinal cell subtypes are damaged. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Maria Iribarne
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Dmitri Serjanov
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Yijie Zhai
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Thanh Hoang
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Leah J Campbell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Patrick Boyd
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Isabella Palazzo
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Mikiko Nagashima
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Nicholas J Silva
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Peter F Hitchcock
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| | - David R Hyde
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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7
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Celotto L, Rost F, Machate A, Bläsche J, Dahl A, Weber A, Hans S, Brand M. Single-cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration. eLife 2023; 12:RP86507. [PMID: 37988404 PMCID: PMC10662954 DOI: 10.7554/elife.86507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
In the lesioned zebrafish retina, Müller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Müller glia reactivity to progenitor production and neuronal differentiation, we used single-cell RNA sequencing of Müller glia, progenitors and regenerated progeny from uninjured and light-lesioned retinae. We discover an injury-induced Müller glia differentiation trajectory that leads into a cell population with a hybrid identity expressing marker genes of Müller glia and progenitors. A glial self-renewal and a neurogenic trajectory depart from the hybrid cell population. We further observe that neurogenic progenitors progressively differentiate to generate retinal ganglion cells first and bipolar cells last, similar to the events observed during retinal development. Our work provides a comprehensive description of Müller glia and progenitor transcriptional changes and fate decisions in the regenerating retina, which are key to tailor cell differentiation and replacement therapies for retinal dystrophies in humans.
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Affiliation(s)
- Laura Celotto
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Fabian Rost
- Technische Universität Dresden, DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Anja Machate
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Juliane Bläsche
- Technische Universität Dresden, DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Andreas Dahl
- Technische Universität Dresden, DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Anke Weber
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Stefan Hans
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
| | - Michael Brand
- Technische Universität Dresden, CRTD - Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering (CMCB), FetscherstraßeDresdenGermany
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8
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Herrera I, Fernandes JAL, Shir-Mohammadi K, Levesque J, Mattar P. Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration. Cell Death Dis 2023; 14:701. [PMID: 37880237 PMCID: PMC10600220 DOI: 10.1038/s41419-023-06224-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Neurodegenerative diseases are accompanied by dynamic changes in gene expression, including the upregulation of hallmark stress-responsive genes. While the transcriptional pathways that impart adaptive and maladaptive gene expression signatures have been the focus of intense study, the role of higher order nuclear organization in this process is less clear. Here, we examine the role of the nuclear lamina in genome organization during the degeneration of rod photoreceptors. Two proteins had previously been shown to be necessary and sufficient to tether heterochromatin at the nuclear envelope. The lamin B receptor (Lbr) is expressed during development, but downregulates upon rod differentiation. A second tether is the intermediate filament lamin A (LA), which is not normally expressed in murine rods. Here, we show that in the rd1 model of retinitis pigmentosa, LA ectopically upregulates in rod photoreceptors at the onset of degeneration. LA upregulation correlated with increased heterochromatin tethering at the nuclear periphery in rd1 rods, suggesting that LA reorganizes the nucleus. To determine how heterochromatin tethering affects the genome, we used in vivo electroporation to misexpress LA or Lbr in mature rods in the absence of degeneration, resulting in the restoration of conventional nuclear architecture. Using scRNA-seq, we show that reorganizing the nucleus via LA/Lbr misexpression has relatively minor effects on rod gene expression. Next, using ATAC-seq, we show that LA and Lbr both lead to marked increases in genome accessibility. Novel ATAC-seq peaks tended to be associated with stress-responsive genes. Together, our data reveal that heterochromatin tethers have a global effect on genome accessibility, and suggest that heterochromatin tethering primes the photoreceptor genome to respond to stress.
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Affiliation(s)
- Ivana Herrera
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - José Alex Lourenço Fernandes
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Khatereh Shir-Mohammadi
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Jasmine Levesque
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Pierre Mattar
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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9
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Zhang X, Leavey P, Appel H, Makrides N, Blackshaw S. Molecular mechanisms controlling vertebrate retinal patterning, neurogenesis, and cell fate specification. Trends Genet 2023; 39:736-757. [PMID: 37423870 PMCID: PMC10529299 DOI: 10.1016/j.tig.2023.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
This review covers recent advances in understanding the molecular mechanisms controlling neurogenesis and specification of the developing retina, with a focus on insights obtained from comparative single cell multiomic analysis. We discuss recent advances in understanding the mechanisms by which extrinsic factors trigger transcriptional changes that spatially pattern the optic cup (OC) and control the initiation and progression of retinal neurogenesis. We also discuss progress in unraveling the core evolutionarily conserved gene regulatory networks (GRNs) that specify early- and late-state retinal progenitor cells (RPCs) and neurogenic progenitors and that control the final steps in determining cell identity. Finally, we discuss findings that provide insight into regulation of species-specific aspects of retinal patterning and neurogenesis, including consideration of key outstanding questions in the field.
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Affiliation(s)
- Xin Zhang
- Department of Ophthalmology, Columbia University School of Medicine, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University School of Medicine, New York, NY, USA.
| | - Patrick Leavey
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neoklis Makrides
- Department of Ophthalmology, Columbia University School of Medicine, New York, NY, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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10
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Leyva-Díaz E. CUT homeobox genes: transcriptional regulation of neuronal specification and beyond. Front Cell Neurosci 2023; 17:1233830. [PMID: 37744879 PMCID: PMC10515288 DOI: 10.3389/fncel.2023.1233830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
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11
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Bosze B, Suarez-Navarro J, Cajias I, Brzezinski IV JA, Brown NL. Notch pathway mutants do not equivalently perturb mouse embryonic retinal development. PLoS Genet 2023; 19:e1010928. [PMID: 37751417 PMCID: PMC10522021 DOI: 10.1371/journal.pgen.1010928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023] Open
Abstract
In the vertebrate eye, Notch ligands, receptors, and ternary complex components determine the destiny of retinal progenitor cells in part by regulating Hes effector gene activity. There are multiple paralogues for nearly every node in this pathway, which results in numerous instances of redundancy and compensation during development. To dissect such complexity at the earliest stages of eye development, we used seven germline or conditional mutant mice and two spatiotemporally distinct Cre drivers. We perturbed the Notch ternary complex and multiple Hes genes to understand if Notch regulates optic stalk/nerve head development; and to test intracellular pathway components for their Notch-dependent versus -independent roles during retinal ganglion cell and cone photoreceptor competence and fate acquisition. We confirmed that disrupting Notch signaling universally blocks progenitor cell growth, but delineated specific pathway components that can act independently, such as sustained Hes1 expression in the optic stalk/nerve head. In retinal progenitor cells, we found that among the genes tested, they do not uniformly suppress retinal ganglion cell or cone differentiation; which is not due differences in developmental timing. We discovered that shifts in the earliest cell fates correlate with expression changes for the early photoreceptor factor Otx2, but not with Atoh7, a factor required for retinal ganglion cell formation. During photoreceptor genesis we also better defined multiple and simultaneous activities for Rbpj and Hes1 and identify redundant activities that occur downstream of Notch. Given its unique roles at the retina-optic stalk boundary and cone photoreceptor genesis, our data suggest Hes1 as a hub where Notch-dependent and -independent inputs converge.
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Affiliation(s)
- Bernadett Bosze
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Julissa Suarez-Navarro
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Illiana Cajias
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Joseph A. Brzezinski IV
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Nadean L. Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
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12
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Fernández-Suárez E, González-del Pozo M, García-Núñez A, Méndez-Vidal C, Martín-Sánchez M, Mejías-Carrasco JM, Ramos-Jiménez M, Morillo-Sánchez MJ, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. Expanding the phenotype of THRB: a range of macular dystrophies as the major clinical manifestations in patients with a dominant splicing variant. Front Cell Dev Biol 2023; 11:1197744. [PMID: 37547476 PMCID: PMC10401274 DOI: 10.3389/fcell.2023.1197744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of disorders that often severely impair vision. Some patients manifest poor central vision as the first symptom due to cone-dysfunction, which is consistent with cone dystrophy (COD), Stargardt disease (STGD), or macular dystrophy (MD) among others. Here, we aimed to identify the genetic cause of autosomal dominant COD in one family. WGS was performed in 3 affected and 1 unaffected individual using the TruSeq Nano DNA library kit and the NovaSeq 6,000 platform (Illumina). Data analysis identified a novel spliceogenic variant (c.283 + 1G>A) in the thyroid hormone receptor beta gene (THRB) as the candidate disease-associated variant. Further genetic analysis revealed the presence of the same heterozygous variant segregating in two additional unrelated dominant pedigrees including 9 affected individuals with a diagnosis of COD (1), STGD (4), MD (3) and unclear phenotype (1). THRB has been previously reported as a causal gene for autosomal dominant and recessive thyroid hormone resistance syndrome beta (RTHβ); however, none of the IRD patients exhibited RTHβ. Genotype-phenotype correlations showed that RTHβ can be caused by both truncating and missense variants, which are mainly located at the 3' (C-terminal/ligand-binding) region, which is common to both THRB isoforms (TRβ1 and TRβ2). In contrast, the c.283 + 1G>A variant is predicted to disrupt a splice site in the 5'-region of the gene that encodes the N-terminal domain of the TRβ1 isoform protein, leaving the TRβ2 isoform intact, which would explain the phenotypic variability observed between RTHβ and IRD patients. Interestingly, although monochromacy or cone response alterations have already been described in a few RTHβ patients, herein we report the first genetic association between a pathogenic variant in THRB and non-syndromic IRDs. We thereby expand the phenotype of THRB pathogenic variants including COD, STGD, or MD as the main clinical manifestation, which also reflects the extraordinary complexity of retinal functions mediated by the different THRB isoforms.
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Affiliation(s)
- Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - María González-del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Alejandro García-Núñez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - José Manuel Mejías-Carrasco
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Manuel Ramos-Jiménez
- Department of Clinical Neurophysiology, University Hospital Virgen Macarena, Seville, Spain
| | | | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, Seville, Spain
- RETICS Patología Ocular, OFTARED, Instituto de Salud Carlos III, Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
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13
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Nerli E, Kretzschmar J, Bianucci T, Rocha‐Martins M, Zechner C, Norden C. Deterministic and probabilistic fate decisions co-exist in a single retinal lineage. EMBO J 2023; 42:e112657. [PMID: 37184124 PMCID: PMC10350840 DOI: 10.15252/embj.2022112657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
Correct nervous system development depends on the timely differentiation of progenitor cells into neurons. While the output of progenitor differentiation is well investigated at the population and clonal level, how stereotypic or variable fate decisions are during development is still more elusive. To fill this gap, we here follow the fate outcome of single neurogenic progenitors in the zebrafish retina over time using live imaging. We find that neurogenic progenitor divisions produce two daughter cells, one of deterministic and one of probabilistic fate. Interference with the deterministic branch of the lineage affects lineage progression. In contrast, interference with fate probabilities of the probabilistic branch results in a broader range of fate possibilities than in wild-type and involves the production of any neuronal cell type even at non-canonical developmental stages. Combining the interference data with stochastic modelling of fate probabilities revealed that a simple gene regulatory network is able to predict the observed fate decision probabilities during wild-type development. These findings unveil unexpected lineage flexibility that could ensure robust development of the retina and other tissues.
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Affiliation(s)
- Elisa Nerli
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | | | - Tommaso Bianucci
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Physics of Life, Cluster of ExcellenceTU DresdenDresdenGermany
| | - Mauricio Rocha‐Martins
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Christoph Zechner
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Physics of Life, Cluster of ExcellenceTU DresdenDresdenGermany
| | - Caren Norden
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
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14
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Tran M, Askary A, Elowitz MB. Lineage motifs: developmental modules for control of cell type proportions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543925. [PMID: 37333085 PMCID: PMC10274800 DOI: 10.1101/2023.06.06.543925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In multicellular organisms, cell types must be produced and maintained in appropriate proportions. One way this is achieved is through committed progenitor cells that produce specific sets of descendant cell types. However, cell fate commitment is probabilistic in most contexts, making it difficult to infer progenitor states and understand how they establish overall cell type proportions. Here, we introduce Lineage Motif Analysis (LMA), a method that recursively identifies statistically overrepresented patterns of cell fates on lineage trees as potential signatures of committed progenitor states. Applying LMA to published datasets reveals spatial and temporal organization of cell fate commitment in zebrafish and rat retina and early mouse embryo development. Comparative analysis of vertebrate species suggests that lineage motifs facilitate adaptive evolutionary variation of retinal cell type proportions. LMA thus provides insight into complex developmental processes by decomposing them into simpler underlying modules.
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Affiliation(s)
- Martin Tran
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amjad Askary
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael B. Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lead contact
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15
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Rusin LY. Evolution of homology: From archetype towards a holistic concept of cell type. J Morphol 2023; 284:e21569. [PMID: 36789784 DOI: 10.1002/jmor.21569] [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] [Received: 08/17/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life.
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Affiliation(s)
- Leonid Y Rusin
- Laboratory for Mathematic Methods and Models in Bioinformatics, Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- EvoGenome Analytics LLC, Odintsovo, Moscow Region, Russia
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16
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Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res 2023; 51:2151-2176. [PMID: 36715342 PMCID: PMC10018358 DOI: 10.1093/nar/gkad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2 and Isl1, including those dependent on Atoh7, and uncover the sequential and combinatorial interactions of these factors with the epigenetic landscape to control gene expression along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xushen Chen
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Nan Nan
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Correspondence may also be addressed to Jie Wang.
| | - Xiuqian Mu
- To whom correspondence should be addressed. Tel: +1 716 881 7463; Fax: +1 716 887 2991;
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17
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Cohen-Gulkar M, David A, Messika-Gold N, Eshel M, Ovadia S, Zuk-Bar N, Idelson M, Cohen-Tayar Y, Reubinoff B, Ziv T, Shamay M, Elkon R, Ashery-Padan R. The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration. PLoS Biol 2023; 21:e3001924. [PMID: 36649236 PMCID: PMC9844853 DOI: 10.1371/journal.pbio.3001924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/16/2022] [Indexed: 01/18/2023] Open
Abstract
Tissue-specific transcription factors (TFs) control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of TFs that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here, we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental TFs LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data from human RPE, and AMD genome-wide association study (GWAS) data, followed by functional validation using a reporter assay, revealed a causal genetic variant that affects AMD risk by altering TRPM1 expression in the RPE through modulation of LHX2 transcriptional activity on its promoter. Taken together, the reported cistrome of LHX2 and OTX2, the identified downstream genes and interacting co-factors reveal the RPE transcription module and uncover a causal regulatory risk single-nucleotide polymorphism (SNP) in the multifactorial common blinding disease AMD.
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Affiliation(s)
- Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Mai Eshel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Shai Ovadia
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Nitay Zuk-Bar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Maria Idelson
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and Department of Gynecology, Jerusalem, Israel
| | - Yamit Cohen-Tayar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Benjamin Reubinoff
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and Department of Gynecology, Jerusalem, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Meir Shamay
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RE); (RAP)
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RE); (RAP)
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18
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Javed A, Santos-França PL, Mattar P, Cui A, Kassem F, Cayouette M. Ikaros family proteins redundantly regulate temporal patterning in the developing mouse retina. Development 2023; 150:286611. [PMID: 36537580 DOI: 10.1242/dev.200436] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Temporal identity factors regulate competence of neural progenitors to generate specific cell types in a time-dependent manner, but how they operate remains poorly defined. In the developing mouse retina, the Ikaros zinc-finger transcription factor Ikzf1 regulates production of early-born cell types, except cone photoreceptors. In this study we show that, during early stages of retinal development, another Ikaros family protein, Ikzf4, functions redundantly with Ikzf1 to regulate cone photoreceptor production. Using CUT&RUN and functional assays, we show that Ikzf4 binds and represses genes involved in late-born rod photoreceptor specification, hence favoring cone production. At late stages, when Ikzf1 is no longer expressed in progenitors, we show that Ikzf4 re-localizes to target genes involved in gliogenesis and is required for Müller glia production. We report that Ikzf4 regulates Notch signaling genes and is sufficient to activate the Hes1 promoter through two Ikzf GGAA-binding motifs, suggesting a mechanism by which Ikzf4 may influence gliogenesis. These results uncover a combinatorial role for Ikaros family members during nervous system development and provide mechanistic insights on how they temporally regulate cell fate output.
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Affiliation(s)
- Awais Javed
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
| | - Pedro L Santos-França
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
| | - Allie Cui
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
| | - Fatima Kassem
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 0G4, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 0G4, Canada
- Department of Medicine, Université de Montréal, Montreal H3T 1J4, Canada
- Department of Anatomy and Cell Biology, Division of Experimental Medicine, McGill University, Montreal H3A 0G4, Canada
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19
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Bosze B, Suarez-Navarro J, Cajias I, Brzezinski JA, Brown NL. Not all Notch pathway mutations are equal in the embryonic mouse retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523641. [PMID: 36711950 PMCID: PMC9882158 DOI: 10.1101/2023.01.11.523641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In the vertebrate retina, combinations of Notch ligands, receptors, and ternary complex components determine the destiny of retinal progenitor cells by regulating Hes effector gene activity. Owing to reiterated Notch signaling in numerous tissues throughout development, there are multiple vertebrate paralogues for nearly every node in this pathway. These Notch signaling components can act redundantly or in a compensatory fashion during development. To dissect the complexity of this pathway during retinal development, we used seven germline or conditional mutant mice and two spatiotemporally distinct Cre drivers. We perturbed the Notch ternary complex and multiple Hes genes with two overt goals in mind. First, we wished to determine if Notch signaling is required in the optic stalk/nerve head for Hes1 sustained expression and activity. Second, we aimed to test if Hes1, 3 and 5 genes are functionally redundant during early retinal histogenesis. With our allelic series, we found that disrupting Notch signaling consistently blocked mitotic growth and overproduced ganglion cells, but we also identified two significant branchpoints for this pathway. In the optic stalk/nerve head, sustained Hes1 is regulated independent of Notch signaling, whereas during photoreceptor genesis both Notch-dependent and -independent roles for Rbpj and Hes1 impact photoreceptor genesis in opposing manners.
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Affiliation(s)
- Bernadett Bosze
- Department of Cell Biology & Human Anatomy, University of California, Davis, CA 95616
| | | | - Illiana Cajias
- Department of Cell Biology & Human Anatomy, University of California, Davis, CA 95616
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Nadean L Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis, CA 95616
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20
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Liu H, Lu A, Kelley KA, Forrest D. Noncoding Mutations in a Thyroid Hormone Receptor Gene That Impair Cone Photoreceptor Function. Endocrinology 2023; 164:6984996. [PMID: 36631163 PMCID: PMC10091487 DOI: 10.1210/endocr/bqad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
The function of a hormone receptor requires mechanisms to control precisely where, when, and at what level the receptor gene is expressed. An intriguing case concerns the selective induction of thyroid hormone receptor β2 (TRβ2), encoded by Thrb, in the pituitary and also in cone photoreceptors, in which it critically regulates expression of the opsin photopigments that mediate color vision. Here, we investigate the physiological significance of a candidate enhancer for induction of TRβ2 by mutagenesis of a conserved intron region in its natural context in the endogenous Thrb gene in mice. Mutation of e-box sites for bHLH (basic-helix-loop-helix) transcription factors preferentially impairs TRβ2 expression in cones whereas mutation of nearby sequences preferentially impairs expression in pituitary. A deletion encompassing all sites impairs expression in both tissues, indicating bifunctional activity. In cones, the e-box mutations disrupt chromatin acetylation, blunt the developmental induction of TRβ2, and ultimately impair cone opsin expression and sensitivity to longer wavelengths of light. These results demonstrate the necessity of studying an enhancer in its natural chromosomal context for defining biological relevance and reveal surprisingly critical nuances of level and timing of enhancer function. Our findings illustrate the influence of noncoding sequences over thyroid hormone functions.
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Affiliation(s)
- Hong Liu
- NIDDK, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ailing Lu
- NIDDK, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin A Kelley
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Douglas Forrest
- NIDDK, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD 20892, USA
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21
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Ng L, Liu H, Liu Y, Forrest D. Biphasic expression of thyroid hormone receptor TRβ1 in mammalian retina and anterior ocular tissues. Front Endocrinol (Lausanne) 2023; 14:1174600. [PMID: 37033230 PMCID: PMC10076699 DOI: 10.3389/fendo.2023.1174600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
The retina is increasingly recognized as a target of thyroid hormone. We previously reported critical functions for thyroid hormone receptor TRβ2, encoded by Thrb, in cones, the photoreceptors that mediate color vision. TRβ1, another Thrb receptor isoform, is widely expressed in other tissues but little studied in the retina. Here, we investigate these N-terminal isoforms by RNA-sequencing analysis and reveal a striking biphasic profile for TRβ1 in mouse and human retina. In contrast to the early TRβ2 peak, TRβ1 peaks later during retinal maturation or later differentiation of human retinal organoids. This switch in receptor expression profiles was confirmed using lacZ reporter mice. TRβ1 localized in cones, amacrine cells and ganglion cells in contrast to the restricted expression of TRβ2 in cones. Intriguingly, TRβ1 was also detected in the retinal pigmented epithelium and in anterior structures in the ciliary margin zone, ciliary body and iris, suggesting novel functions in non-retinal eye tissues. Although TRβ1 was detected in cones, TRβ1-knockout mice displayed only minor changes in opsin photopigment expression and normal electroretinogram responses. Our results suggest that strikingly different temporal and cell-specific controls over TRβ1 and TRβ2 expression may underlie thyroid hormone actions in a range of ocular cell types. The TRβ1 expression pattern suggests novel functions in retinal and non-neural ocular tissues.
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Affiliation(s)
- Lily Ng
- National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD, United States
| | - Hong Liu
- National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD, United States
| | - Ye Liu
- National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD, United States
| | - Douglas Forrest
- National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Endocrinology and Receptor Biology, National Institutes of Health, Bethesda, MD, United States
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22
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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23
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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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24
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Bachu VS, Kandoi S, Park KU, Kaufman ML, Schwanke M, Lamba DA, Brzezinski JA. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas. Dev Biol 2022; 488:131-150. [PMID: 35644251 PMCID: PMC10676565 DOI: 10.1016/j.ydbio.2022.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
How cone photoreceptors are formed during retinal development is only partially known. This is in part because we do not fully understand the gene regulatory network responsible for cone genesis. We reasoned that cis-regulatory elements (enhancers) active in nascent cones would be regulated by the same upstream network that controls cone formation. To dissect this network, we searched for enhancers active in developing cones. By electroporating enhancer-driven fluorescent reporter plasmids, we observed that a sequence within an intron of the cone-specific Pde6c gene acted as an enhancer in developing mouse cones. Similar fluorescent reporter plasmids were used to generate stable transgenic human induced pluripotent stem cells that were then grown into three-dimensional human retinal organoids. These organoids contained fluorescently labeled cones, demonstrating that the Pde6c enhancer was also active in human cones. We observed that enhancer activity was transient and labeled a minor population of developing rod photoreceptors in both mouse and human systems. This cone-enriched pattern argues that the Pde6c enhancer is activated in cells poised between rod and cone fates. Additionally, it suggests that the Pde6c enhancer is activated by the same regulatory network that selects or stabilizes cone fate choice. To further understand this regulatory network, we identified essential enhancer sequence regions through a series of mutagenesis experiments. This suggested that the Pde6c enhancer was regulated by transcription factor binding at five or more locations. Binding site predictions implicated transcription factor families known to control photoreceptor formation and families not previously associated with cone development. These results provide a framework for deciphering the gene regulatory network that controls cone genesis in both human and mouse systems. Our new transgenic human stem cell lines provide a tool for determining which cone developmental mechanisms are shared and distinct between mice and humans.
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Affiliation(s)
- Vismaya S Bachu
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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25
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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma. Oncogenesis 2022; 11:34. [PMID: 35729105 PMCID: PMC9213451 DOI: 10.1038/s41389-022-00409-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
Retinoblastoma is a rare, intraocular paediatric cancer that originates in the neural retina and is most frequently caused by bi-allelic loss of RB1 gene function. Other oncogenic mutations, such as amplification and increased expression of the MYCN gene, have been found even with proficient RB1 function. In this study, we investigated whether MYCN over-expression can drive carcinogenesis independently of RB1 loss-of-function mutations. The aim was to elucidate the events that result in carcinogenesis and identify the cancer cell-of-origin. We used the chicken retina, a well-established model for studying retinal neurogenesis, and established human embryonic stem cell-derived retinal organoids as model systems. We over-expressed MYCN by electroporation of piggyBac genome-integrating expression vectors. We found that over-expression of MYCN induced tumorigenic growth with high frequency in RB1-proficient chicken retinas and human organoids. In both systems, the tumorigenic cells expressed markers for undifferentiated cone photoreceptor/horizontal cell progenitors. The over-expression resulted in metastatic retinoblastoma within 7–9 weeks in chicken. Cells expressing MYCN could be grown in vitro and, when orthotopically injected, formed tumours that infiltrated the sclera and optic nerve and expressed markers for cone progenitors. Investigation of the tumour cell phenotype determined that the potential for neoplastic growth was embryonic stage-dependent and featured a cell-specific resistance to apoptosis in the cone/horizontal cell lineage, but not in ganglion or amacrine cells. We conclude that MYCN over-expression is sufficient to drive tumorigenesis and that a cell-specific resistance to apoptosis in the cone/horizontal cell lineage mediates the cancer phenotype. ![]()
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26
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Hussey KA, Hadyniak SE, Johnston RJ. Patterning and Development of Photoreceptors in the Human Retina. Front Cell Dev Biol 2022; 10:878350. [PMID: 35493094 PMCID: PMC9049932 DOI: 10.3389/fcell.2022.878350] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/25/2022] [Indexed: 01/04/2023] Open
Abstract
Humans rely on visual cues to navigate the world around them. Vision begins with the detection of light by photoreceptor cells in the retina, a light-sensitive tissue located at the back of the eye. Photoreceptor types are defined by morphology, gene expression, light sensitivity, and function. Rod photoreceptors function in low-light vision and motion detection, and cone photoreceptors are responsible for high-acuity daytime and trichromatic color vision. In this review, we discuss the generation, development, and patterning of photoreceptors in the human retina. We describe our current understanding of how photoreceptors are patterned in concentric regions. We conclude with insights into mechanisms of photoreceptor differentiation drawn from studies of model organisms and human retinal organoids.
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27
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Nazlamova L, Cassidy EJ, Sowden JC, Lotery A, Lakowski J. Generation of a Cone Photoreceptor-specific GNGT2 Reporter Line in Human Pluripotent Stem Cells. Stem Cells 2022; 40:190-203. [PMID: 35293574 DOI: 10.1093/stmcls/sxab015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/23/2021] [Indexed: 11/14/2022]
Abstract
Fluorescent reporter lines generated in human pluripotent stem cells are a highly useful tool to track, isolate, and analyze cell types and lineages in live cultures. Here, we generate the first human cone photoreceptor reporter cell line by CRISPR/Cas9 genome editing of a human embryonic stem cell (hESC) line to tag both alleles of the Guanine nucleotide-binding protein subunit gamma-T2 (GNGT2) gene with a mCherry reporter cassette. Three-dimensional optic vesicle-like structures were produced to verify reporter fidelity and track cones throughout their development in culture. The GNGT2-T2A-mCherry hESC line faithfully and robustly labels GNGT2-expressing cones throughout the entirety of their differentiation in vitro, recapitulating normal fetal expression of this gene. Our observations indicate that human cones undergo significant migratory activity during the course of differentiation in vitro. Consistent with this, our analysis of human fetal retinae from different stages of development finds positional differences of the cone population depending on their state of maturation. This novel reporter line will provide a useful tool for investigating human cone development and disease.
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Affiliation(s)
- Liliya Nazlamova
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emma-Jane Cassidy
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health, University College London and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Andrew Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jörn Lakowski
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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28
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Sun C, Zhang X, Ruzycki PA, Chen S. Essential Functions of MLL1 and MLL2 in Retinal Development and Cone Cell Maintenance. Front Cell Dev Biol 2022; 10:829536. [PMID: 35223853 PMCID: PMC8864151 DOI: 10.3389/fcell.2022.829536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
MLL1 (KMT2A) and MLL2 (KMT2B) are homologous members of the mixed-lineage leukemia (MLL) family of histone methyltransferases involved in epigenomic transcriptional regulation. Their sequence variants have been associated with neurological and psychological disorders, but little is known about their roles and mechanism of action in CNS development. Using mouse retina as a model, we previously reported MLL1’s role in retinal neurogenesis and horizontal cell maintenance. Here we determine roles of MLL2 and MLL1/MLL2 together in retinal development using conditional knockout (CKO) mice. Deleting Mll2 from Chx10+ retinal progenitors resulted in a similar phenotype as Mll1 CKO, but removal of both alleles produced much more severe deficits than each single CKO: 1-month double CKO mutants displayed null light responses in electroretinogram; thin retinal layers, including shorter photoreceptor outer segments with impaired phototransduction gene expression; and reduced numbers of M-cones, horizontal and amacrine neurons, followed by fast retinal degeneration. Despite moderately reduced progenitor cell proliferation at P0, the neurogenic capacity was largely maintained in double CKO mutants. However, upregulated apoptosis and reactive gliosis were detected during postnatal retinal development. Finally, the removal of both MLLs in fated rods produced a normal phenotype, but the CKO in M-cones impaired M-cone function and survival, indicating both cell non-autonomous and autonomous mechanisms. Altogether, our results suggest that MLL1/MLL2 play redundant roles in maintaining specific retinal neurons after cell fate specification and are essential for establishing functional neural networks.
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Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, St. Louis, MO, United States
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, St. Louis, MO, United States
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, St. Louis, MO, United States
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, St. Louis, MO, United States
- Department of Developmental Biology, Washington University, St. Louis, MO, United States
- *Correspondence: Shiming Chen,
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29
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Bery A, Bagchi U, Bergen AA, Felder-Schmittbuhl MP. Circadian clocks, retinogenesis and ocular health in vertebrates: new molecular insights. Dev Biol 2022; 484:40-56. [DOI: 10.1016/j.ydbio.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 12/22/2022]
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30
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West ER, Lapan SW, Lee C, Kajderowicz KM, Li X, Cepko CL. Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity. Cell Rep 2022; 38:110191. [PMID: 34986354 DOI: 10.1016/j.celrep.2021.110191] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
How do neuronal subtypes emerge during development? Recent molecular studies have profiled existing neuronal diversity, but neuronal subtype genesis remains elusive. The 15 types of mouse retinal bipolar interneurons are characterized by distinct functions, morphologies, and transcriptional profiles. Here, we develop a comprehensive spatiotemporal map of bipolar subtype genesis in the murine retina. Combining multiplexed detection of 16 RNA markers with timed delivery of 5-ethynyl uridine (EdU) and bromodeoxyuridine (BrdU), we analyze more than 30,000 single cells in full retinal sections to classify all bipolar subtypes and their birthdates. We find that bipolar subtype birthdates are ordered and follow a centrifugal developmental axis. Spatial analysis reveals a striking wave pattern of bipolar subtype birthdates, and lineage analyses suggest clonal restriction on homotypic subtype production. These results inspire a hierarchical developmental model, with ordered subtype genesis within lineages. Our results provide insight into neuronal subtype development and establish a framework for studying subtype diversification.
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Affiliation(s)
- Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Sylvain W Lapan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - ChangHee Lee
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kathrin M Kajderowicz
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Constance L Cepko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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31
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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32
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Tainika B, Bayraktar ÖH. Lighted incubation: embryonic development, hatchability and hatching quality of broiler chicks. WORLD POULTRY SCI J 2021. [DOI: 10.1080/00439339.2022.1988806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Brian Tainika
- Department of Animal Production and Technologies, Faculty of Ayhan Şahenk Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Özer Hakan Bayraktar
- Department of Animal Science, Faculty of Agriculture, Ege University, İzmir, Turkey
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33
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Gabriel E, Albanna W, Pasquini G, Ramani A, Josipovic N, Mariappan A, Schinzel F, Karch CM, Bao G, Gottardo M, Suren AA, Hescheler J, Nagel-Wolfrum K, Persico V, Rizzoli SO, Altmüller J, Riparbelli MG, Callaini G, Goureau O, Papantonis A, Busskamp V, Schneider T, Gopalakrishnan J. Human brain organoids assemble functionally integrated bilateral optic vesicles. Cell Stem Cell 2021; 28:1740-1757.e8. [PMID: 34407456 DOI: 10.1016/j.stem.2021.07.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/23/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
During embryogenesis, optic vesicles develop from the diencephalon via a multistep process of organogenesis. Using induced pluripotent stem cell (iPSC)-derived human brain organoids, we attempted to simplify the complexities and demonstrate formation of forebrain-associated bilateral optic vesicles, cellular diversity, and functionality. Around day 30, brain organoids attempt to assemble optic vesicles, which develop progressively as visible structures within 60 days. These optic vesicle-containing brain organoids (OVB-organoids) constitute a developing optic vesicle's cellular components, including primitive corneal epithelial and lens-like cells, retinal pigment epithelia, retinal progenitor cells, axon-like projections, and electrically active neuronal networks. OVB-organoids also display synapsin-1, CTIP-positive myelinated cortical neurons, and microglia. Interestingly, various light intensities could trigger photosensitive activity of OVB-organoids, and light sensitivities could be reset after transient photobleaching. Thus, brain organoids have the intrinsic ability to self-organize forebrain-associated primitive sensory structures in a topographically restricted manner and can allow interorgan interaction studies within a single organoid.
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Affiliation(s)
- Elke Gabriel
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Walid Albanna
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; Department of Neurosurgery, RWTH Aachen University, 52074 Aachen, Germany
| | - Giovanni Pasquini
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Anand Ramani
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, 37075 Göttingen, Germany; Center for molecular medicine, Cologne, Universität zu Köln, 50931 Köln, Germany
| | - Aruljothi Mariappan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Friedrich Schinzel
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO 63116, USA
| | - Guobin Bao
- Institute of Neurophysiology and Cellular Biophysics, University Medicine Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Marco Gottardo
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Ata Alp Suren
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Veronica Persico
- Department of Life Sciences and Medical Biotechnology University of Siena, Siena 53100, Italy
| | - Silvio O Rizzoli
- Institute of Neurophysiology and Cellular Biophysics, University Medicine Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Universität zu Köln, Köln, Germany; Center for molecular medicine, Cologne, Universität zu Köln, 50931 Köln, Germany
| | | | - Giuliano Callaini
- Department of Life Sciences and Medical Biotechnology University of Siena, Siena 53100, Italy
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Argyris Papantonis
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, 37075 Göttingen, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Toni Schneider
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany.
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34
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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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35
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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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36
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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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37
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Kaufman ML, Goodson NB, Park KU, Schwanke M, Office E, Schneider SR, Abraham J, Hensley A, Jones KL, Brzezinski JA. Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity. Development 2021; 148:dev199399. [PMID: 34143204 PMCID: PMC8254865 DOI: 10.1242/dev.199399] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/10/2021] [Indexed: 11/20/2022]
Abstract
During retinal development, a large subset of progenitors upregulates the transcription factor Otx2, which is required for photoreceptor and bipolar cell formation. How these retinal progenitor cells initially activate Otx2 expression is unclear. To address this, we investigated the cis-regulatory network that controls Otx2 expression in mice. We identified a minimal enhancer element, DHS-4D, that drove expression in newly formed OTX2+ cells. CRISPR/Cas9-mediated deletion of DHS-4D reduced OTX2 expression, but this effect was diminished in postnatal development. Systematic mutagenesis of the enhancer revealed that three basic helix-loop-helix (bHLH) transcription factor-binding sites were required for its activity. Single cell RNA-sequencing of nascent Otx2+ cells identified the bHLH factors Ascl1 and Neurog2 as candidate regulators. CRISPR/Cas9 targeting of these factors showed that only the simultaneous loss of Ascl1 and Neurog2 prevented OTX2 expression. Our findings suggest that Ascl1 and Neurog2 act either redundantly or in a compensatory fashion to activate the DHS-4D enhancer and Otx2 expression. We observed redundancy or compensation at both the transcriptional and enhancer utilization levels, suggesting that the mechanisms governing Otx2 regulation in the retina are flexible and robust.
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Affiliation(s)
- Michael L. Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Noah B. Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emma Office
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sophia R. Schneider
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joy Abraham
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Austin Hensley
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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38
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Lonfat N, Wang S, Lee C, Garcia M, Choi J, Park PJ, Cepko C. Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. Development 2021; 148:261747. [PMID: 33929509 DOI: 10.1242/dev.198549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/31/2021] [Indexed: 11/20/2022]
Abstract
The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC RPC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.
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Affiliation(s)
- Nicolas Lonfat
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA.,Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Su Wang
- Department of Biomedical Informatics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - ChangHee Lee
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Mauricio Garcia
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA.,Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Jiho Choi
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA.,Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Connie Cepko
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA.,Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Schick E, Gonzalez KC, Dutta P, Hossain K, Ghinia Tegla MG, Emerson MM. Early cis-regulatory events in the formation of retinal horizontal cells. Dev Biol 2021; 476:88-100. [PMID: 33774011 DOI: 10.1016/j.ydbio.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022]
Abstract
During retinal development, multipotent and restricted progenitor cells generate all of the neuronal cells of the retina. Among these are horizontal cells, which are interneurons that modulate the light-induced signal from photoreceptors. This study utilizes the identification of novel cis-regulatory elements as a method to examine the gene regulatory networks that direct the development of horizontal cells. Here we describe a screen for cis-regulatory elements, or enhancers, for the horizontal cell-associated genes PTF1A, ONECUT1 (OC1), TFAP2A (AP2A), and LHX1. The OC1ECR22 and Tfap2aACR5 elements were shown to be potential enhancers for OC1 and TFAP2A, respectively, and to be specifically active in developing horizontal cells. The OC1ECR22 element is activated by PTF1A and RBPJ, which translates to regulation of OC1 expression and suggests that PTF1A is a direct activator of OC1 expression in developing horizontal cells. The region within the Tfap2aACR5 element that is responsible for its activation was determined to be a 100 bp sequence named Motif 4. Both OC1ECR22 and Tfap2aACR5 are negatively regulated by the nuclear receptors THRB and RXRG, as is the expression of OC1 and AP2A, suggesting that nuclear receptors may have a role in the negative regulation of horizontal cell development.
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Affiliation(s)
- Estie Schick
- Biology PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Kevin C Gonzalez
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Pooja Dutta
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Kazi Hossain
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Miruna G Ghinia Tegla
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA; Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA; Biochemistry PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA.
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40
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Vassalli QA, Colantuono C, Nittoli V, Ferraioli A, Fasano G, Berruto F, Chiusano ML, Kelsh RN, Sordino P, Locascio A. Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation. Front Cell Dev Biol 2021; 9:602450. [PMID: 33816460 PMCID: PMC8012850 DOI: 10.3389/fcell.2021.602450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Photoreceptor cells (PRC) are neurons highly specialized for sensing light stimuli and have considerably diversified during evolution. The genetic mechanisms that underlie photoreceptor differentiation and accompanied the progressive increase in complexity and diversification of this sensory cell type are a matter of great interest in the field. A role of the homeodomain transcription factor Onecut (Oc) in photoreceptor cell formation is proposed throughout multicellular organisms. However, knowledge of the identity of the Oc downstream-acting factors that mediate specific tasks in the differentiation of the PRC remains limited. Here, we used transgenic perturbation of the Ciona robusta Oc protein to show its requirement for ciliary PRC differentiation. Then, transcriptome profiling between the trans-activation and trans-repression Oc phenotypes identified differentially expressed genes that are enriched in exocytosis, calcium homeostasis, and neurotransmission. Finally, comparison of RNA-Seq datasets in Ciona and mouse identifies a set of Oc downstream genes conserved between tunicates and vertebrates. The transcription factor Oc emerges as a key regulator of neurotransmission in retinal cell types.
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Affiliation(s)
- Quirino Attilio Vassalli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Chiara Colantuono
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Valeria Nittoli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Anna Ferraioli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Giulia Fasano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Federica Berruto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agriculture, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Robert Neil Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, London, United Kingdom
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Annamaria Locascio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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41
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Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun 2021; 12:1465. [PMID: 33674582 PMCID: PMC7935890 DOI: 10.1038/s41467-021-21704-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Atoh7 has been believed to be essential for establishing the retinal ganglion cell (RGC) lineage, and Pou4f2 and Isl1 are known to regulate RGC specification and differentiation. Here we report our further study of the roles of these transcription factors. Using bulk RNA-seq, we identify genes regulated by the three transcription factors, which expand our understanding of the scope of downstream events. Using scRNA-seq on wild-type and mutant retinal cells, we reveal a transitional cell state of retinal progenitor cells (RPCs) co-marked by Atoh7 and other genes for different lineages and shared by all early retinal lineages. We further discover the unexpected emergence of the RGC lineage in the absence of Atoh7. We conclude that competence of RPCs for different retinal fates is defined by lineage-specific genes co-expressed in the transitional state and that Atoh7 defines the RGC competence and collaborates with other factors to shepherd transitional RPCs to the RGC lineage.
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Affiliation(s)
- Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jonathan E Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Julien Kann
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zihua Hu
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA.
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.
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42
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Dose-dependent regulation of horizontal cell fate by Onecut family of transcription factors. PLoS One 2020; 15:e0237403. [PMID: 32790713 PMCID: PMC7425962 DOI: 10.1371/journal.pone.0237403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/24/2020] [Indexed: 11/19/2022] Open
Abstract
Genome duplication leads to an emergence of gene paralogs that are essentially free to undergo the process of neofunctionalization, subfunctionalization or degeneration (gene loss). Onecut1 (Oc1) and Onecut2 (Oc2) transcription factors, encoded by paralogous genes in mammals, are expressed in precursors of horizontal cells (HCs), retinal ganglion cells and cone photoreceptors. Previous studies have shown that ablation of either Oc1 or Oc2 gene in the mouse retina results in a decreased number of HCs, while simultaneous deletion of Oc1 and Oc2 leads to a complete loss of HCs. Here we study the genetic redundancy between Oc1 and Oc2 paralogs and focus on how the dose of Onecut transcription factors influences abundance of individual retinal cell types and overall retina physiology. Our data show that reducing the number of functional Oc alleles in the developing retina leads to a gradual decrease in the number of HCs, progressive thinning of the outer plexiform layer and diminished electrophysiology responses. Taken together, these observations indicate that in the context of HC population, the alleles of Oc1/Oc2 paralogous genes are mutually interchangeable, function additively to support proper retinal function and their molecular evolution does not follow one of the typical routes after gene duplication.
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43
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Chan CSY, Lonfat N, Zhao R, Davis AE, Li L, Wu MR, Lin CH, Ji Z, Cepko CL, Wang S. Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina. Development 2020; 147:dev.187922. [PMID: 32631829 DOI: 10.1242/dev.187922] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
Transcription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the mouse retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs, respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells use a cohort of TFs with different expression patterns and multiple CRMs with different chromatin configurations to regulate the expression of Otx2 precisely.
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Affiliation(s)
- Candace S Y Chan
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Nicolas Lonfat
- Departments of Genetics and Ophthalmology, Blavatnik Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rong Zhao
- Departments of Genetics and Ophthalmology, Blavatnik Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander E Davis
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Liang Li
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA.,Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Man-Ru Wu
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Cheng-Hui Lin
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Zhe Ji
- Department of Bioengineering, Northwestern University, Evanston, IL 60208, USA
| | - Constance L Cepko
- Departments of Genetics and Ophthalmology, Blavatnik Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sui Wang
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
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44
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Hydrogel-based milliwell arrays for standardized and scalable retinal organoid cultures. Sci Rep 2020; 10:10275. [PMID: 32581233 PMCID: PMC7314858 DOI: 10.1038/s41598-020-67012-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 06/01/2020] [Indexed: 12/31/2022] Open
Abstract
The development of improved methods to culture retinal organoids is relevant for the investigation of mechanisms of retinal development under pathophysiological conditions, for screening of neuroprotective compounds, and for providing a cellular source for clinical transplantation. We report a tissue-engineering approach to accelerate and standardize the production of retinal organoids by culturing mouse embryonic stem cells (mESC) in optimal physico-chemical microenvironments. Arrayed round-bottom milliwells composed of biomimetic hydrogels, combined with an optimized medium formulation, promoted the rapid generation of retina-like tissue from mESC aggregates in a highly efficient and stereotypical manner: ∼93% of the aggregates contained retinal organoid structures. 26 day-old retinal organoids were composed of ∼80% of photoreceptors, of which ∼22% are GNAT2-positive cones, an important and rare sensory cell type that is difficult to study in rodent models. The compartmentalization of retinal organoids into predefined locations on a two-dimensional array not only allowed us to derive almost all aggregates into retinal organoids, but also to reliably capture the dynamics of individual organoids, an advantageous requirement for high-throughput experimentation. Our improved retinal organoid culture system should be useful for applications that require scalability and single-organoid traceability.
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45
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Ghinia Tegla MG, Buenaventura DF, Kim DY, Thakurdin C, Gonzalez KC, Emerson MM. OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification. eLife 2020; 9:e54279. [PMID: 32347797 PMCID: PMC7237216 DOI: 10.7554/elife.54279] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
During vertebrate retinal development, subsets of progenitor cells generate progeny in a non-stochastic manner, suggesting that these decisions are tightly regulated. However, the gene-regulatory network components that are functionally important in these progenitor cells are largely unknown. Here we identify a functional role for the OTX2 transcription factor in this process. CRISPR/Cas9 gene editing was used to produce somatic mutations of OTX2 in the chick retina and identified similar phenotypes to those observed in human patients. Single cell RNA sequencing was used to determine the functional consequences OTX2 gene editing on the population of cells derived from OTX2-expressing retinal progenitor cells. This confirmed that OTX2 is required for the generation of photoreceptors, but also for repression of specific retinal fates and alternative gene regulatory networks. These include specific subtypes of retinal ganglion and horizontal cells, suggesting that in this context, OTX2 functions to repress sister cell fate choices.
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Affiliation(s)
| | - Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
- PhD Program in Biology, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
| | - Diana Y Kim
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Cassandra Thakurdin
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Kevin C Gonzalez
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
- PhD Program in Biology, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
- PhD Program in Biochemistry, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
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46
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Patoori S, Jean-Charles N, Gopal A, Sulaiman S, Gopal S, Wang B, Souferi B, Emerson MM. Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. Neural Dev 2020; 15:5. [PMID: 32192535 PMCID: PMC7082998 DOI: 10.1186/s13064-020-00142-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/27/2020] [Indexed: 01/03/2023] Open
Abstract
Background The vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. These cells do not express Vsx2, but co-express the transcription factors (TFs) Onecut1 and Otx2, which bind to ThrbCRM1. The components of the gene regulatory networks that control the transition from multipotent to fate-restricted gene expression are not known. This work aims to identify and evaluate cis-regulatory elements proximal to Onecut1 to identify the gene regulatory networks involved in RPC fate-restriction. Method We identified regulatory elements through ATAC-seq and conservation, followed by reporter assays to screen for activity based on temporal and spatial criteria. The regulatory elements of interest were subject to deletion and mutation analysis to identify functional sequences and evaluated by quantitative flow cytometry assays. Finally, we combined the enhancer::reporter assays with candidate TF overexpression to evaluate the relationship between the TFs, the enhancers, and early vertebrate retinal development. Statistical tests included ANOVA, Kruskal-Wallis, or unpaired t-tests. Results Two regulatory elements, ECR9 and ECR65, were identified to be active in ThrbCRM1(+) restricted RPCs. Candidate bHLH binding sites were identified as critical sequences in both elements. Overexpression of candidate bHLH TFs revealed specific enhancer-bHLH interactions. Nhlh1 overexpression expanded ECR65 activity into the Vsx2(+) RPC population, and overexpression of NeuroD1/NeuroG2/NeuroD4 had a similar effect on ECR9. Furthermore, bHLHs that were able to activate ectopic ECR9 reporter were able to induce endogenous Otx2 expression. Conclusions This work reports a large-scale screen to identify spatiotemporally specific regulatory elements near the Onecut1 locus. These elements were used to identify distinct populations in the developing retina. In addition, fate-restricted regulatory elements responded differentially to bHLH factors, and suggest a role for retinal bHLHs upstream of the Otx2 and Onecut1 genes during the formation of restricted RPCs from multipotent RPCs.
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Affiliation(s)
- Sruti Patoori
- 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
| | - Nathalie Jean-Charles
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Ariana Gopal
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Sacha Sulaiman
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Sneha Gopal
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.,Present Address: Doctoral program in Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Brian Wang
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Benjamin Souferi
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.,Present Address: Touro College of Osteopathic Medicine, New York, NY, 10027, 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, Graduate Center, City University of New York, New York, NY, 10016, USA.
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47
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Perez-Cervantes C, Smith LA, Nadadur RD, Hughes AEO, Wang S, Corbo JC, Cepko C, Lonfat N, Moskowitz IP. Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development 2020; 147:dev184432. [PMID: 31915147 PMCID: PMC7033740 DOI: 10.1242/dev.184432] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) NrlNrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.
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Affiliation(s)
- Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Linsin A Smith
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rangarajan D Nadadur
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sui Wang
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Constance Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicolas Lonfat
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
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Javed A, Mattar P, Lu S, Kruczek K, Kloc M, Gonzalez-Cordero A, Bremner R, Ali RR, Cayouette M. Pou2f1 and Pou2f2 cooperate to control the timing of cone photoreceptor production in the developing mouse retina. Development 2020; 147:dev.188730. [DOI: 10.1242/dev.188730] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022]
Abstract
Multipotent retinal progenitor cells (RPCs) generate various cell types in a precise chronological order, but how exactly cone photoreceptor production is restricted to early stages remains unclear. Here, we show that the POU-homeodomain factors Pou2f1/Pou2f2, the homologs of Drosophila temporal identity factors nub/pdm2, regulate the timely production of cones in mice. Forcing sustained expression of Pou2f1 or Pou2f2 in RPCs expands the period of cone production, whereas misexpression in late-stage RPCs triggers ectopic cone production at the expense of late-born fates. Mechanistically, we report that Pou2f1 induces Pou2f2 expression, which binds to a POU motif in the promoter of the rod-inducing factor Nrl to repress its expression. Conversely, conditional inactivation of Pou2f2 in RPCs increases Nrl expression and reduces cone production. Finally, we provide evidence that Pou2f1 is part of a cross-regulatory cascade with the other temporal identity factors Ikzf1 and Casz1. These results uncover Pou2f1/2 as regulators of the temporal window for cone genesis and, given their widespread expression in the nervous system, raise the possibility of a general role in temporal patterning.
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Affiliation(s)
- Awais Javed
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montreal (IRCM), Canada
- Molecular Biology Program, Université de Montréal, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montreal (IRCM), Canada
| | - Suying Lu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada. Department of Ophthalmology and Vision Science, Department of Lab Medicine and Pathobiology, University of Toronto
| | | | | | | | - Rod Bremner
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada. Department of Ophthalmology and Vision Science, Department of Lab Medicine and Pathobiology, University of Toronto
| | - Robin R. Ali
- UCL Institute of Ophthalmology, London, UK
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montreal (IRCM), Canada
- Molecular Biology Program, Université de Montréal, Canada
- Department of Medicine, Université de Montréal, Canada
- Department of Anatomy and Cell Biology; Division of Experimental Medicine, McGill University, Canada
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49
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Buenaventura DF, Corseri A, Emerson MM. Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors. Invest Ophthalmol Vis Sci 2019; 60:2787-2799. [PMID: 31260032 PMCID: PMC6607928 DOI: 10.1167/iovs.19-26951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose The early transcriptional events that occur in newly generated cone photoreceptors are not well described. Knowledge of these events is critical to provide benchmarks for in vitro-derived cone photoreceptors and to understand the process of cone and rod photoreceptor diversification. We sought to identify genes with differential gene expression in embryonic mouse cone photoreceptors. Methods The specificity of expression of the LHX4 transcription factor in developing cone photoreceptors was examined using immunofluorescence visualization in both mouse and chicken retinas. A LHX4 transgenic reporter line with high specificity for developing mouse cone photoreceptors was identified and used to purify early-stage cone photoreceptors for profiling by single-cell RNA sequencing. Comparisons were made to previous datasets targeting photoreceptors. Results The LHX4 transcription factor and a transgenic reporter were determined to be highly specific to early developing cone photoreceptors in the mouse. Single-cell transcriptional profiling identified new genes with enriched expression in cone photoreceptors relative to concurrent cell populations. Comparison to previous profiling datasets allowed for further characterization of these genes across developmental time, species, photoreceptor type, and gene regulatory network. Conclusions The LHX4 gene is highly enriched in developing cone photoreceptors as are several new genes identified through transcriptional profiling, some of which are expressed in subclusters of cones. Many of these cone-enriched genes do not show obvious de-repression in profiling of retinas mutant for the rod-specific transcription factor NRL, highlighting differences between endogenous cones and those induced in NRL mutants.
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Affiliation(s)
- Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States
| | - Adrianne Corseri
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States.,Biochemistry PhD Program, Graduate Center, City University of New York, New York, New York, United States
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Retinogenesis of the Human Fetal Retina: An Apical Polarity Perspective. Genes (Basel) 2019; 10:genes10120987. [PMID: 31795518 PMCID: PMC6947654 DOI: 10.3390/genes10120987] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
The Crumbs complex has prominent roles in the control of apical cell polarity, in the coupling of cell density sensing to downstream cell signaling pathways, and in regulating junctional structures and cell adhesion. The Crumbs complex acts as a conductor orchestrating multiple downstream signaling pathways in epithelial and neuronal tissue development. These pathways lead to the regulation of cell size, cell fate, cell self-renewal, proliferation, differentiation, migration, mitosis, and apoptosis. In retinogenesis, these are all pivotal processes with important roles for the Crumbs complex to maintain proper spatiotemporal cell processes. Loss of Crumbs function in the retina results in loss of the stratified appearance resulting in retinal degeneration and loss of visual function. In this review, we begin by discussing the physiology of vision. We continue by outlining the processes of retinogenesis and how well this is recapitulated between the human fetal retina and human embryonic stem cell (ESC) or induced pluripotent stem cell (iPSC)-derived retinal organoids. Additionally, we discuss the functionality of in utero and preterm human fetal retina and the current level of functionality as detected in human stem cell-derived organoids. We discuss the roles of apical-basal cell polarity in retinogenesis with a focus on Leber congenital amaurosis which leads to blindness shortly after birth. Finally, we discuss Crumbs homolog (CRB)-based gene augmentation.
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