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Droll SH, Zhang BJ, Levine MC, Xue C, Ho PJ, Bao X. CASZ1 Is Essential for Skin Epidermal Terminal Differentiation. J Invest Dermatol 2024; 144:2029-2038. [PMID: 38458428 PMCID: PMC11344692 DOI: 10.1016/j.jid.2024.02.014] [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: 10/16/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
The barrier function of skin epidermis is crucial for our bodies to interface with the environment. Because epidermis continuously turns over throughout the lifetime, this barrier must be actively maintained by regeneration. Although several transcription factors have been established as essential activators in epidermal differentiation, it is unclear whether additional factors remain to be identified. In this study, we show that CASZ1, a multi zinc-finger transcription factor previously characterized in nonepithelial cell types, shows highest expression in skin epidermis. CASZ1 expression is upregulated during epidermal terminal differentiation. In addition, CASZ1 expression is impaired in several skin disorders with impaired barrier function, such as atopic dermatitis, psoriasis, and squamous cell carcinoma. Using transcriptome profiling coupled with RNA interference, we identified 674 differentially expressed genes with CASZ1 knockdown. Downregulated genes account for 91.2% of these differentially expressed genes and were enriched for barrier function. In organotypic epidermal regeneration, CASZ1 knockdown promoted proliferation and strongly impaired multiple terminal differentiation markers. Mechanistically, we found that CASZ1 upregulation in differentiation requires the action of both the master transcription factor, p63, and the histone acetyltransferase, p300. Taken together, our findings identify CASZ1 as an essential activator of epidermal differentiation, paving the way for future studies understanding of CASZ1 roles in skin disease.
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Affiliation(s)
- Stephenie H Droll
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Benny J Zhang
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Maxwell C Levine
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Celia Xue
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Patric J Ho
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois, USA; Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA.
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2
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Liu T, Li T, Ke S. Role of the CASZ1 transcription factor in tissue development and disease. Eur J Med Res 2023; 28:562. [PMID: 38053207 DOI: 10.1186/s40001-023-01548-y] [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: 05/08/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
The zinc finger transcription factor gene, CASZ1/Castor (Castor zinc finger 1), initially identified in Drosophila, plays a critical role in neural, cardiac, and cardiovascular development, exerting a complex, multifaceted influence on cell fate and tissue morphogenesis. During neurogenesis, CASZ1 exhibits dynamic expression from early embryonic development to the perinatal period, constituting a key regulator in this process. Additionally, CASZ1 controls the transition between neurogenesis and gliomagenesis. During human cardiovascular system development, CASZ1 is essential for cardiomyocyte differentiation, cardiac morphogenesis, and vascular morphology homeostasis and formation. The deletion or inactivation of CASZ1 mutations can lead to human developmental diseases or tumors, including congenital heart disease, cardiovascular disease, and neuroblastoma. CASZ1 can be used as a biomarker for disease prevention and diagnosis as well as a prognostic indicator for cancer. This review explores the unique functions of CASZ1 in tissue morphogenesis and associated diseases, offering new insights for elucidating the molecular mechanisms underlying diseases and identifying potential therapeutic targets for disease prevention and treatment.
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Affiliation(s)
- Tiantian Liu
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, Henan, China.
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China.
| | - Tao Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shaorui Ke
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, Henan, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
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3
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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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4
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Gurdita A, Pham Truong VQB, Dolati P, Juric M, Tachibana N, Liu ZC, Ortín-Martínez A, Ibrahimi M, Pokrajac NT, Comanita L, Pacal M, Huang M, Sugita S, Bremner R, Wallace VA. Progenitor division and cell autonomous neurosecretion are required for rod photoreceptor sublaminar positioning. Proc Natl Acad Sci U S A 2023; 120:e2308204120. [PMID: 37812728 PMCID: PMC10589646 DOI: 10.1073/pnas.2308204120] [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: 06/13/2023] [Accepted: 09/06/2023] [Indexed: 10/11/2023] Open
Abstract
Migration is essential for the laminar stratification and connectivity of neurons in the central nervous system. In the retina, photoreceptors (PRs) migrate to positions according to birthdate, with early-born cells localizing to the basal-most side of the outer nuclear layer. It was proposed that apical progenitor mitoses physically drive these basal translocations non-cell autonomously, but direct evidence is lacking, and whether other mechanisms participate is unknown. Here, combining loss- or gain-of-function assays to manipulate cell cycle regulators (Sonic hedgehog, Cdkn1a/p21) with an in vivo lentiviral labelling strategy, we demonstrate that progenitor division is one of two forces driving basal translocation of rod soma. Indeed, replacing Shh activity rescues abnormal rod translocation in retinal explants. Unexpectedly, we show that rod differentiation also promotes rod soma translocation. While outer segment function or formation is dispensable, Crx and SNARE-dependent synaptic function are essential. Thus, both non-cell and cell autonomous mechanisms underpin PR soma sublaminar positioning in the mammalian retina.
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Affiliation(s)
- Akshay Gurdita
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Victor Q. B. Pham Truong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Parnian Dolati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Matey Juric
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Nobuhiko Tachibana
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Zhongda C. Liu
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Arturo Ortín-Martínez
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Mostafa Ibrahimi
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Nenad T. Pokrajac
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Lacrimioara Comanita
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
| | - Marek Pacal
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ONM5G 1X5, Canada
| | - Mengjia Huang
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ONM5T 2S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Shuzo Sugita
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, University Health Network, Toronto, ONM5T 2S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Rod Bremner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ONM5G 1X5, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ONM5T 3A9, Canada
| | - Valerie A. Wallace
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ONM5S 1A8, Canada
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ONM5T 2S8, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ONM5T 3A9, Canada
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5
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Santos-França PL, David LA, Kassem F, Meng XQ, Cayouette M. Time to see: How temporal identity factors specify the developing mammalian retina. Semin Cell Dev Biol 2023; 142:36-42. [PMID: 35760728 DOI: 10.1016/j.semcdb.2022.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Understanding how retinal progenitor cells (RPCs) give rise to the variety of neural cell types of the retina has been a question of major interest over the last few decades. While environmental cues and transcription factor networks have been shown to control specific cell fate decisions, how RPCs alter fate output over time to control proper histogenesis remains poorly understood. In recent years, the identification of "temporal identity factors (TIFs)", which control RPC competence states to ensure that the right cell types are produced at the right time, has contributed to increasing our understanding of temporal patterning in the retina. Here, we review the different TIFs identified to date in the mammalian retina and discuss the underlying mechanisms by which they are thought to operate. We conclude by speculating on how identification of temporal patterning mechanisms might support the development of new therapeutic approaches against visual impairments.
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Affiliation(s)
- Pedro L Santos-França
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Molecular Biology Program, Université de Montréal, Montréal, QC, Canada
| | - Luke Ajay David
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Fatima Kassem
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Xiang Qi Meng
- Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Molecular Biology Program, Université de Montréal, Montréal, QC, Canada; Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada; Department of Medicine, Université de Montréal, QC, Canada; Department of Anatomy and Cell Biology and Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
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6
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Gordon DM, Cunningham D, Zender G, Lawrence PJ, Penaloza JS, Lin H, Fitzgerald-Butt SM, Myers K, Duong T, Corsmeier DJ, Gaither JB, Kuck HC, Wijeratne S, Moreland B, Kelly BJ, Garg V, White P, McBride KL. Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery. PLoS Genet 2022; 18:e1010236. [PMID: 35737725 PMCID: PMC9258875 DOI: 10.1371/journal.pgen.1010236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/06/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant’s effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes. Congenital heart disease is a common group of birth defects that are a leading cause of death in children under one year of age. There is strong evidence that genetics plays a role in causing congenital heart disease. While studies using individual cases have identified causative genes for those with a heart defect when accompanied by other birth defects or intellectual disabilities, for individuals who have only a heart defect without other problems, a genetic cause can be found in fewer than 10%. In this study, we enrolled families where there was more than one individual with a heart defect. This allowed us to take advantage of inheritance by searching for potential disease-causing genetic variants in common among all affected individuals in the family. Among 19 families studied, we were able to find a plausible disease-causing variant in eight of them and identified new genes that may cause or contribute to the presence of a heart defect. Two families had potential disease-causing variants in two different genes. We designed assays to test if the variants led to altered function of the protein coded by the gene, demonstrating a functional consequence that support the gene and variant as contributing to the heart defect. These findings show that studying families may be more effective than using individuals to find causes of heart defects. In addition, this family-based method suggests that changes in more than one gene may be required for a heart defect to occur.
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Affiliation(s)
- David M. Gordon
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - David Cunningham
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Gloria Zender
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Patrick J. Lawrence
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jacqueline S. Penaloza
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Hui Lin
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Sara M. Fitzgerald-Butt
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Katherine Myers
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Tiffany Duong
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Donald J. Corsmeier
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jeffrey B. Gaither
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Harkness C. Kuck
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Saranga Wijeratne
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Blythe Moreland
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Benjamin J. Kelly
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | | | - Vidu Garg
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (PW); (KLM)
| | - Peter White
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (PW); (KLM)
| | - Kim L. McBride
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (PW); (KLM)
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7
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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8
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Hench K, Helmkampf M, McMillan WO, Puebla O. Rapid radiation in a highly diverse marine environment. Proc Natl Acad Sci U S A 2022; 119:e2020457119. [PMID: 35042790 PMCID: PMC8794831 DOI: 10.1073/pnas.2020457119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
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Affiliation(s)
- Kosmas Hench
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
| | - Martin Helmkampf
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
| | - Oscar Puebla
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
- Institute for Chemistry and Biology of the Marine Environment, 26111 Oldenburg, Germany
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
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9
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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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10
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Smith CL, Lan Y, Jain R, Epstein JA, Poleshko A. Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. SCIENCE ADVANCES 2021; 7:eabj3035. [PMID: 34559565 PMCID: PMC8462898 DOI: 10.1126/sciadv.abj3035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The nuclear architecture of rod photoreceptor cells in nocturnal mammals is unlike that of other animal cells. Murine rod cells have an “inverted” chromatin organization with euchromatin at the nuclear periphery and heterochromatin packed in the center of the nucleus. In conventional nuclear architecture, euchromatin is mostly in the interior, and heterochromatin is largely at the nuclear periphery. We demonstrate that inverted nuclear architecture is achieved through global relabeling of the rod cell epigenome. During rod cell maturation, H3K9me2-labeled nuclear peripheral heterochromatin is relabeled with H3K9me3 and repositioned to the nuclear center, while transcriptionally active euchromatin is labeled with H3K9me2 and positioned at the nuclear periphery. Global chromatin relabeling is correlated with spatial rearrangement, suggesting a critical role for histone modifications, specifically H3K9 methylation, in nuclear architecture. These results reveal a dramatic example of genome-wide epigenetic relabeling of chromatin that accompanies altered nuclear architecture in a postnatal, postmitotic cell.
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Affiliation(s)
- Cheryl L. Smith
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute, and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute, and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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11
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Ogawa Y, Corbo JC. Partitioning of gene expression among zebrafish photoreceptor subtypes. Sci Rep 2021; 11:17340. [PMID: 34462505 PMCID: PMC8405809 DOI: 10.1038/s41598-021-96837-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Vertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- and bright-light vision, respectively. While many molecular features that distinguish rods and cones are known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes are renowned for the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult photoreceptors in zebrafish, a teleost. We found that in addition to the four canonical zebrafish cone types, there exist subpopulations of green and red cones (previously shown to be located in the ventral retina) that express red-shifted opsin paralogs (opn1mw4 or opn1lw1) as well as a unique combination of cone phototransduction genes. Furthermore, the expression of many paralogous phototransduction genes is partitioned among cone subtypes, analogous to the partitioning of the phototransduction paralogs between rods and cones seen across vertebrates. The partitioned cone-gene pairs arose via the teleost-specific whole-genome duplication or later clade-specific gene duplications. We also discovered that cone subtypes express distinct transcriptional regulators, including many factors not previously implicated in photoreceptor development or differentiation. Overall, our work suggests that partitioning of paralogous gene expression via the action of differentially expressed transcriptional regulators enables diversification of cone subtypes in teleosts.
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Affiliation(s)
- Yohey Ogawa
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA.
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12
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Tidswell ORA, Benton MA, Akam M. The neuroblast timer gene nubbin exhibits functional redundancy with gap genes to regulate segment identity in Tribolium. Development 2021; 148:271199. [PMID: 34351412 PMCID: PMC8406537 DOI: 10.1242/dev.199719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/23/2021] [Indexed: 12/05/2022]
Abstract
The neuroblast timer genes hunchback, Krüppel, nubbin and castor are expressed in temporal sequence in neural stem cells, and in corresponding spatial sequence along the Drosophila blastoderm. As canonical gap genes, hunchback and Krüppel play a crucial role in insect segmentation, but the roles of nubbin and castor in this process remain ambiguous. We have investigated the expression and functions of nubbin and castor during segmentation in the beetle Tribolium. We show that Tc-hunchback, Tc-Krüppel, Tc-nubbin and Tc-castor are expressed sequentially in the segment addition zone, and that Tc-nubbin regulates segment identity redundantly with two previously described gap/gap-like genes, Tc-giant and Tc-knirps. Simultaneous knockdown of Tc-nubbin, Tc-giant and Tc-knirps results in the formation of ectopic legs on abdominal segments. This homeotic transformation is caused by loss of abdominal Hox gene expression, likely due to expanded Tc-Krüppel expression. Our findings support the theory that the neuroblast timer series was co-opted for use in insect segment patterning, and contribute to our growing understanding of the evolution and function of the gap gene network outside of Drosophila. Summary:nubbin and the gap genes knirps and giant redundantly repress Krüppel expression during segmentation. Simultaneous knockdown of all three genes causes ectopic Krüppel expression and loss of abdominal segment identity.
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Affiliation(s)
| | - Matthew A Benton
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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13
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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14
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Burger CA, Jiang D, Mackin RD, Samuel MA. Development and maintenance of vision's first synapse. Dev Biol 2021; 476:218-239. [PMID: 33848537 DOI: 10.1016/j.ydbio.2021.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/21/2022]
Abstract
Synapses in the outer retina are the first information relay points in vision. Here, photoreceptors form synapses onto two types of interneurons, bipolar cells and horizontal cells. Because outer retina synapses are particularly large and highly ordered, they have been a useful system for the discovery of mechanisms underlying synapse specificity and maintenance. Understanding these processes is critical to efforts aimed at restoring visual function through repairing or replacing neurons and promoting their connectivity. We review outer retina neuron synapse architecture, neural migration modes, and the cellular and molecular pathways that play key roles in the development and maintenance of these connections. We further discuss how these mechanisms may impact connectivity in the retina.
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Affiliation(s)
- Courtney A Burger
- Huffington Center on Aging, Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Danye Jiang
- Huffington Center on Aging, Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert D Mackin
- Huffington Center on Aging, Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melanie A Samuel
- Huffington Center on Aging, Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA.
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15
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Mattar P, Jolicoeur C, Dang T, Shah S, Clark BS, Cayouette M. A Casz1-NuRD complex regulates temporal identity transitions in neural progenitors. Sci Rep 2021; 11:3858. [PMID: 33594190 PMCID: PMC7886867 DOI: 10.1038/s41598-021-83395-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Neural progenitor cells undergo identity transitions during development to ensure the generation different types of neurons and glia in the correct sequence and proportions. A number of temporal identity factors that control these transitions in progenitor competence have been identified, but the molecular mechanisms underlying their function remain unclear. Here, we asked how Casz1, the mammalian orthologue of Drosophila castor, regulates competence during retinal development. We show that Casz1 is required to control the transition between neurogenesis and gliogenesis. Using BioID proteomics, we reveal that Casz1 interacts with the nucleosome remodeling and deacetylase (NuRD) complex in retinal cells. Finally, we show that both the NuRD and the polycomb repressor complexes are required for Casz1 to promote the rod fate and suppress gliogenesis. As additional temporal identity factors have been found to interact with the NuRD complex in other contexts, we propose that these factors might act through this common biochemical process to regulate neurogenesis.
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Affiliation(s)
- Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada. .,Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada. .,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Thanh Dang
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Brian S Clark
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada. .,Department of Anatomy and Cell Biology, and Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada. .,Department of Medicine, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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16
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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17
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Burger CA, Albrecht NE, Jiang D, Liang JH, Poché RA, Samuel MA. LKB1 and AMPK instruct cone nuclear position to modify visual function. Cell Rep 2021; 34:108698. [PMID: 33535040 PMCID: PMC7906279 DOI: 10.1016/j.celrep.2021.108698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/06/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Cone photoreceptors detect light and are responsible for color vision. These cells display a distinct polarized morphology where nuclei are precisely aligned in the apical retina. However, little is known about the mechanisms involved in cone nuclear positioning or the impact of this organization on retina function. We show that the serine/threonine kinase LKB1 and one of its substrates, AMPK, regulate cone nuclear positioning. In the absence of either molecule, cone nuclei are misplaced along the axon, resulting in altered nuclear lamination. LKB1 is required specifically in cones to mediate this process, and disruptions in nuclear alignment result in reduced cone function. Together, these results identify molecular determinants of cone nuclear position and indicate that cone nuclear position alignment enables proper visual function.
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Affiliation(s)
- Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justine H Liang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ross A Poché
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA.
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18
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Wright CM, Schneider S, Smith-Edwards KM, Mafra F, Leembruggen AJL, Gonzalez MV, Kothakapa DR, Anderson JB, Maguire BA, Gao T, Missall TA, Howard MJ, Bornstein JC, Davis BM, Heuckeroth RO. scRNA-Seq Reveals New Enteric Nervous System Roles for GDNF, NRTN, and TBX3. Cell Mol Gastroenterol Hepatol 2021; 11:1548-1592.e1. [PMID: 33444816 PMCID: PMC8099699 DOI: 10.1016/j.jcmgh.2020.12.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Bowel function requires coordinated activity of diverse enteric neuron subtypes. Our aim was to define gene expression in these neuron subtypes to facilitate development of novel therapeutic approaches to treat devastating enteric neuropathies, and to learn more about enteric nervous system function. METHODS To identify subtype-specific genes, we performed single-nucleus RNA-seq on adult mouse and human colon myenteric plexus, and single-cell RNA-seq on E17.5 mouse ENS cells from whole bowel. We used immunohistochemistry, select mutant mice, and calcium imaging to validate and extend results. RESULTS RNA-seq on 635 adult mouse colon myenteric neurons and 707 E17.5 neurons from whole bowel defined seven adult neuron subtypes, eight E17.5 neuron subtypes and hundreds of differentially expressed genes. Manually dissected human colon myenteric plexus yielded RNA-seq data from 48 neurons, 3798 glia, 5568 smooth muscle, 377 interstitial cells of Cajal, and 2153 macrophages. Immunohistochemistry demonstrated differential expression for BNC2, PBX3, SATB1, RBFOX1, TBX2, and TBX3 in enteric neuron subtypes. Conditional Tbx3 loss reduced NOS1-expressing myenteric neurons. Differential Gfra1 and Gfra2 expression coupled with calcium imaging revealed that GDNF and neurturin acutely and differentially regulate activity of ∼50% of myenteric neurons with distinct effects on smooth muscle contractions. CONCLUSION Single cell analyses defined genes differentially expressed in myenteric neuron subtypes and new roles for TBX3, GDNF and NRTN. These data facilitate molecular diagnostic studies and novel therapeutics for bowel motility disorders.
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Affiliation(s)
- Christina M Wright
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sabine Schneider
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristen M Smith-Edwards
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Neuroscience at the University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fernanda Mafra
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
| | | | - Michael V Gonzalez
- Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania
| | - Deepika R Kothakapa
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jessica B Anderson
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Beth A Maguire
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tao Gao
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tricia A Missall
- Department of Dermatology, University of Florida, Gainesville, Florida
| | - Marthe J Howard
- Department of Neurosciences, University of Toledo Health Sciences Campus, Toledo, Ohio
| | - Joel C Bornstein
- Department of Physiology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian M Davis
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Neuroscience at the University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert O Heuckeroth
- Department of Pediatrics, Abramson Research Center, Children's Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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20
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Mighty J, Zhou J, Benito-Martin A, Sauma S, Hanna S, Onwumere O, Shi C, Muntzel M, Sauane M, Young M, Molina H, Cox D, Redenti S. Analysis of Adult Neural Retina Extracellular Vesicle Release, RNA Transport and Proteomic Cargo. Invest Ophthalmol Vis Sci 2020; 61:30. [PMID: 32084266 PMCID: PMC7326611 DOI: 10.1167/iovs.61.2.30] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Purpose Extracellular vesicles (EVs) contain RNA and protein cargo reflective of the genotype and phenotype of the releasing cell of origin. Adult neural retina EV release, RNA transfer, and proteomic cargo are the focus of this study. Methods Adult wild-type mouse retinae were cultured and released EV diameters and concentrations quantified using Nanosight. Immunogold transmission electron microscopy (TEM) was used to image EV ultrastructure and marker protein localization. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze retinal cell transcripts present in EVs. Super-resolution microscopy was used to image fluorescent (green) RNA and (red) lipid membrane labeled EVs, released by adult retina, and internalized by isolated retinal cells. Mass spectrometry was used to characterize the proteomes of adult retina and EVs. Results Adult neural retina released EVs at a rate of 1.42 +/- 0.08 × 108/mL over 5 days, with diameters ranging from 30 to 910 nm. The canonical EV markers CD63 and Tsg101 localized to retinal EVs. Adult retinal and neuronal mRNA species present in both retina and EVs included rhodopsin and the neuronal nuclei marker NeuN. Fluorescently labeled RNA in retinal cells was enclosed in EVs, transported to, and uptaken by co-cultured adult retinal cells. Proteomic analysis revealed 1696 protein species detected only in retinal cells, 957 species shared between retina and EVs, and 82 detected only in EVs. Conclusions The adult neural retina constitutively releases EVs with molecular cargo capable of intercellular transport and predicted involvement in biological processes including retinal physiology, mRNA processing, and transcription regulation within the retinal microenvironment.
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21
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Feodorova Y, Falk M, Mirny LA, Solovei I. Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. Trends Cell Biol 2020; 30:276-289. [PMID: 31980345 DOI: 10.1016/j.tcb.2019.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023]
Abstract
The cell nucleus is a remarkably well-organized organelle with membraneless but distinct compartments of various functions. The largest of them, euchromatin and heterochromatin, are spatially segregated in such a way that the transcriptionally active genome occupies the nuclear interior, whereas silent genomic loci are preferentially associated with the nuclear envelope. This rule is broken by rod photoreceptor cells of nocturnal mammals, in which the two major compartments have inverted positions. The inversion and dense compaction of heterochromatin converts these nuclei into microlenses that focus light and facilitate nocturnal vision. As is often the case in biology, when a mutation helps to understand normal processes and structures, inverted nuclei have served as a tool to unravel general principles of nuclear organization, including mechanisms of heterochromatin tethering to the nuclear envelope, autonomous behavior of small genomic segments, and euchromatin-heterochromatin segregation.
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Affiliation(s)
- Yana Feodorova
- Biozentrum, Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
| | - Martin Falk
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, University of Chicago, 929 E 57th St, Chicago, IL 60637, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Irina Solovei
- Biozentrum, Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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Subramanian K, Weigert M, Borsch O, Petzold H, Garcia-Ulloa A, Myers EW, Ader M, Solovei I, Kreysing M. Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice. eLife 2019; 8:49542. [PMID: 31825309 PMCID: PMC6974353 DOI: 10.7554/elife.49542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/11/2019] [Indexed: 01/06/2023] Open
Abstract
Rod photoreceptors of nocturnal mammals display a striking inversion of nuclear architecture, which has been proposed as an evolutionary adaptation to dark environments. However, the nature of visual benefits and the underlying mechanisms remains unclear. It is widely assumed that improvements in nocturnal vision would depend on maximization of photon capture at the expense of image detail. Here, we show that retinal optical quality improves 2-fold during terminal development, and that this enhancement is caused by nuclear inversion. We further demonstrate that improved retinal contrast transmission, rather than photon-budget or resolution, enhances scotopic contrast sensitivity by 18–27%, and improves motion detection capabilities up to 10-fold in dim environments. Our findings therefore add functional significance to a prominent exception of nuclear organization and establish retinal contrast transmission as a decisive determinant of mammalian visual perception.
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Affiliation(s)
- Kaushikaram Subramanian
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Oliver Borsch
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heike Petzold
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany.,Department of Computer Science, Technische Universität Dresden, Dresden, Germany
| | - Marius Ader
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Irina Solovei
- Biozentrum, Ludwig Maximilians Universität, München, Germany
| | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
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23
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Overbey EG, da Silveira WA, Stanbouly S, Nishiyama NC, Roque-Torres GD, Pecaut MJ, Zawieja DC, Wang C, Willey JS, Delp MD, Hardiman G, Mao XW. Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina. Sci Rep 2019; 9:13304. [PMID: 31527661 PMCID: PMC6746706 DOI: 10.1038/s41598-019-49453-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/19/2019] [Indexed: 11/08/2022] Open
Abstract
Extended spaceflight has been shown to adversely affect astronaut visual acuity. The purpose of this study was to determine whether spaceflight alters gene expression profiles and induces oxidative damage in the retina. Ten week old adult C57BL/6 male mice were flown aboard the ISS for 35 days and returned to Earth alive. Ground control mice were maintained on Earth under identical environmental conditions. Within 38 (+/-4) hours after splashdown, mice ocular tissues were collected for analysis. RNA sequencing detected 600 differentially expressed genes (DEGs) in murine spaceflight retinas, which were enriched for genes related to visual perception, the phototransduction pathway, and numerous retina and photoreceptor phenotype categories. Twelve DEGs were associated with retinitis pigmentosa, characterized by dystrophy of the photoreceptor layer rods and cones. Differentially expressed transcription factors indicated changes in chromatin structure, offering clues to the observed phenotypic changes. Immunofluorescence assays showed degradation of cone photoreceptors and increased retinal oxidative stress. Total retinal, retinal pigment epithelium, and choroid layer thickness were significantly lower after spaceflight. These results indicate that retinal performance may decrease over extended periods of spaceflight and cause visual impairment.
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Affiliation(s)
- Eliah G Overbey
- University of Washington, Department of Genome Sciences, Seattle, WA, USA.
| | - Willian Abraham da Silveira
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Seta Stanbouly
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Nina C Nishiyama
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
| | | | - Michael J Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
| | - David Carl Zawieja
- Department of Medical Physiology, Texas A&M University, College Station, Texas, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Jeffrey S Willey
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Michael D Delp
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Gary Hardiman
- Queen's University Belfast, Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Xiao Wen Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University, Loma Linda, CA, 92350, USA
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24
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Lucas T, Kohwi M. From insects to mammals: regulation of genome architecture in neural development. Curr Opin Neurobiol 2019; 59:146-156. [PMID: 31299459 DOI: 10.1016/j.conb.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
One of the hallmarks of the metazoan genome is that genes are non-randomly positioned within the cell nucleus; in fact, the entire genome is packaged in a highly organized manner to orchestrate proper gene expression for each cell type. This is an especially daunting task for the development of the brain, which consists of an incredibly diverse population of neural cells. How genome architecture is established, maintained, and regulated to promote diverse cell fates and functions are fascinating questions with important implications in development and disease. The explosion in various biochemical and imaging techniques to analyze chromatin is now making it possible to interrogate the genome at an unprecedented resolution. Here we will focus on current advances in understanding genome architecture and gene regulation in the context of neural development.
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Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute for Mind Brain Behavior, Kavli Institute for Brain Sciences, Columbia University, New York, NY, United States
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute for Mind Brain Behavior, Kavli Institute for Brain Sciences, Columbia University, New York, NY, United States.
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