1
|
Zhou X, Zhao L, Wang C, Sun W, Jia B, Li D, Fu J. Diverse functions and pathogenetic role of Crumbs in retinopathy. Cell Commun Signal 2024; 22:290. [PMID: 38802833 PMCID: PMC11129452 DOI: 10.1186/s12964-024-01673-z] [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: 02/13/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
The Crumbs protein (CRB) family plays a crucial role in maintaining the apical-basal polarity and integrity of embryonic epithelia. The family comprises different isoforms in different animals and possesses diverse structural, localization, and functional characteristics. Mutations in the human CRB1 or CRB2 gene may lead to a broad spectrum of retinal dystrophies. Various CRB-associated experimental models have recently provided mechanistic insights into human CRB-associated retinopathies. The knowledge obtained from these models corroborates the importance of CRB in retinal development and maintenance. Therefore, complete elucidation of these models can provide excellent therapeutic prospects for human CRB-associated retinopathies. In this review, we summarize the current animal models and human-derived models of different CRB family members and describe the main characteristics of their retinal phenotypes.
Collapse
Affiliation(s)
- Xuebin Zhou
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Liangliang Zhao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Chenguang Wang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Wei Sun
- College of Basic Medical Sciences, Jilin University, Changchun, 130000, China
| | - Bo Jia
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Dan Li
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Jinling Fu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, 130000, China.
| |
Collapse
|
2
|
Fraire CR, Desai K, Obalapuram UA, Mendyka LK, Rajaram V, Sebastian T, Wang Y, Onel K, Lee J, Chen KS. An imbalance between proliferation and differentiation underlies the development of microRNA-defective pineoblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590638. [PMID: 38712047 PMCID: PMC11071395 DOI: 10.1101/2024.04.23.590638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mutations in the microRNA processing genes DICER1 and DROSHA drive several cancers that resemble embryonic progenitors. To understand how microRNAs regulate tumorigenesis, we ablated Drosha or Dicer1 in the developing pineal gland to emulate the pathogenesis of pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. Accordingly, these mice develop pineal tumors marked by loss of microRNAs, including the let-7/miR-98-5p family, and de-repression of microRNA target genes. Pineal tumors driven by loss of Drosha or Dicer1 mimic tumors driven by Rb1 loss, as they exhibit upregulation of S-phase genes and homeobox transcription factors that regulate pineal development. Blocking proliferation of these tumors facilitates expression of pinealocyte maturation markers, with a concomitant reduction in embryonic markers. Select embryonic markers remain elevated, however, as the microRNAs that normally repress these target genes remain absent. One such microRNA target gene is the oncofetal transcription factor Plagl2, which regulates expression of pro-growth genes, and inhibiting their signaling impairs tumor growth. Thus, we demonstrate that tumors driven by loss of microRNA processing may be therapeutically targeted by inhibiting downstream drivers of proliferation.
Collapse
Affiliation(s)
- Claudette R. Fraire
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Kavita Desai
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | | | | | - Veena Rajaram
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Teja Sebastian
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Kenan Onel
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| | - Kenneth S. Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX USA
| |
Collapse
|
3
|
Dorgau B, Collin J, Rozanska A, Zerti D, Unsworth A, Crosier M, Hussain R, Coxhead J, Dhanaseelan T, Patel A, Sowden JC, FitzPatrick DR, Queen R, Lako M. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina. Nat Commun 2024; 15:3567. [PMID: 38670973 PMCID: PMC11053058 DOI: 10.1038/s41467-024-47933-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: 07/11/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
Collapse
Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Darin Zerti
- Biosciences Institute, Newcastle University, Newcastle, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Moira Crosier
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Aara Patel
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health and NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
| |
Collapse
|
4
|
Varner LR, Chaya T, Maeda Y, Tsutsumi R, Zhou S, Tsujii T, Okuzaki D, Furukawa T. The deubiquitinase Otud7b suppresses cone photoreceptor degeneration in mouse models of retinal degenerative diseases. iScience 2024; 27:109380. [PMID: 38510130 PMCID: PMC10951987 DOI: 10.1016/j.isci.2024.109380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Primary and secondary cone photoreceptor death in retinal degenerative diseases, including age-related macular degeneration (AMD) and retinitis pigmentosa (RP), leads to severe visual impairment and blindness. Although the cone photoreceptor protection in retinal degenerative diseases is crucial for maintaining vision, the underlying molecular mechanisms are unclear. Here, we found that the deubiquitinase Otud7b/Cezanne is predominantly expressed in photoreceptor cells in the retina. We analyzed Otud7b-/- mice, which were subjected to light-induced damage, a dry AMD model, or were mated with an RP mouse model, and observed increased cone photoreceptor degeneration. Using RNA-sequencing and bioinformatics analysis followed by a luciferase reporter assay, we found that Otud7b downregulates NF-κB activity. Furthermore, inhibition of NF-κB attenuated cone photoreceptor degeneration in the light-exposed Otud7b-/- retina and stress-induced neuronal cell death resulting from Otud7b deficiency. Together, our findings suggest that Otud7b protects cone photoreceptors in retinal degenerative diseases by modulating NF-κB activity.
Collapse
Affiliation(s)
- Leah Rie Varner
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Taro Chaya
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yamato Maeda
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Ryotaro Tsutsumi
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shanshan Zhou
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Toshinori Tsujii
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| |
Collapse
|
5
|
Dorgau B, Collin J, Rozanska A, Boczonadi V, Moya-Molina M, Unsworth A, Hussain R, Coxhead J, Dhanaseelan T, Armstrong L, Queen R, Lako M. Deciphering the spatiotemporal transcriptional and chromatin accessibility of human retinal organoid development at the single-cell level. iScience 2024; 27:109397. [PMID: 38510120 PMCID: PMC10952046 DOI: 10.1016/j.isci.2024.109397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/28/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Molecular information on the early stages of human retinal development remains scarce due to limitations in obtaining early human eye samples. Pluripotent stem cell-derived retinal organoids (ROs) provide an unprecedented opportunity for studying early retinogenesis. Using a combination of single cell RNA-seq and spatial transcriptomics we present for the first-time a single cell spatiotemporal transcriptome of RO development. Our data demonstrate that ROs recapitulate key events of retinogenesis including optic vesicle/cup formation, presence of a putative ciliary margin zone, emergence of retinal progenitor cells and their orderly differentiation to retinal neurons. Combining the scRNA- with scATAC-seq data, we were able to reveal cell-type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development, and to show that chromatin accessibility is highly correlated to the developing human retina, but with some differences in the temporal emergence and abundance of some of the retinal neurons.
Collapse
Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Veronika Boczonadi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Marina Moya-Molina
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
- Newcells Biotech, Newcastle upon Tyne NE4 5BX, UK
| | - Adrienne Unsworth
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Rafiqul Hussain
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Tamil Dhanaseelan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| |
Collapse
|
6
|
Rath MF. Homeobox gene-encoded transcription factors in development and mature circadian function of the rodent pineal gland. J Pineal Res 2024; 76:e12950. [PMID: 38558122 DOI: 10.1111/jpi.12950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Homeobox genes encode transcription factors that are widely known to control developmental processes. This is also the case in the pineal gland, a neuroendocrine brain structure devoted to nighttime synthesis of the hormone melatonin. Thus, in accordance with high prenatal gene expression, knockout studies have identified a specific set of homeobox genes that are essential for development of the pineal gland. However, as a special feature of the pineal gland, homeobox gene expression persists into adulthood, and gene product abundance exhibits 24 h circadian rhythms. Recent lines of evidence show that some homeobox genes even control expression of enzymes catalyzing melatonin synthesis. We here review current knowledge of homeobox genes in the rodent pineal gland and suggest a model for dual functions of homeobox gene-encoded transcription factors in developmental and circadian mature neuroendocrine function.
Collapse
Affiliation(s)
- Martin F Rath
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
7
|
Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res 2024; 34:243-255. [PMID: 38355306 PMCID: PMC10984388 DOI: 10.1101/gr.278133.123] [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: 05/27/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Dozens of variants in the gene for the homeodomain transcription factor (TF) cone-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation in these mutant Crx retinas corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci are partially predictive of episomal MPRA activity, and distal elements whose accessibility increases later in retinal development are enriched for CREs with silencer activity. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on its cis-regulatory function, leading to misregulation of similar sets of enhancers while having a qualitatively different impact on silencers.
Collapse
Affiliation(s)
- James L Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Ryan Z Friedman
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Inez Y Oh
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| | - Michael A White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA;
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Mahmoudian-Sani MR, Fattahi N, Hashemzadeh Chaleshtori M, Asgharzade S. MIR96 Has Good Potential to Differentiate Human Bone Marrow-Derived Mesenchymal Stem Cells into Photoreceptor-Like Cells. EXP CLIN TRANSPLANT 2024; 22:148-155. [PMID: 38511985 DOI: 10.6002/ect.2023.0300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
OBJECTIVES MicroRNAs play an important role in the development and function of neuron cells. Among these, the miRNA known as MIR96 is abundantly expressed in mammalian retina and significantly affects differentiation, maturation, and survival of human photoreceptor cells. In this study, a mimic to miRNA-96 was transfected into human bone marrowderived mesenchymal stem cells to explore the biological functions of MIR96 at differentiation processing. MATERIALS AND METHODS A mimic to miRNA-96 and a competitive control were transfected into human bone marrow-derived mesenchymal stem cells using Lipofectamine. After 24 and 48 hours, we evaluated changes in expression levels of genes associated with neural progenitor and photoreceptor differentiation (OTX2, NRL, protein kinase C, SLC1A1, and recoverin) by real-time polymerase chain reaction. In addition, we measured expression of mRNA and protein of the CRX gene (neuroretinal progenitor cell marker) and the RHO gene (terminal differentiation marker) using real-time polymerase chain reaction and immunocytochemistry, respectively. RESULTS Real-time polymerase chain reaction results showed increased levels of RHO and recoverin mRNA after 24 hours in transfected cells. In addition, mRNA levels of OTX2, CRX, NRL, RHO, recoverin, and protein kinase C increased after 48 hours in transfected cells. Immunocytochemistry results confirmed these findings by demonstrating RHO and CRX at both 24 and 48 hours in transfected cells. CONCLUSIONS Control of the expression of MIR96 can be a good strategy to promote cell differentiation and can be used in cell therapy for retinal degeneration. Our results showed that human bone marrow-derived mesenchymal stem cells can differentiate into photoreceptor cells after transfection with MIR96. These results support therapeutic use of MIR96 in retinal degeneration and suggest human bone marrowderived mesenchymal stem cells as a promising tool for interventions.
Collapse
Affiliation(s)
- Mohammad-Reza Mahmoudian-Sani
- From the Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | | | | |
Collapse
|
10
|
Zheng J, Song W, Zhou Y, Li X, Wang M, Zhang C. Cross-species single-cell landscape of vertebrate pineal gland. J Pineal Res 2024; 76:e12927. [PMID: 38018267 DOI: 10.1111/jpi.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
The pineal gland has evolved from a photoreceptive organ in fish to a neuroendocrine organ in mammals. This study integrated multiple daytime single-cell RNA-seq datasets from the pineal glands of zebrafish, rats, and monkeys, providing a detailed examination of the evolutionary transition at single-cell resolution. We identified key factors responsible for the anatomical and functional transformation of the pineal gland. We retrieved and integrated daytime single-cell transcriptomic datasets from the pineal glands of zebrafish, rats, and monkeys, resulting in a total of 22 431 cells after rigorous quality filtering. Comparative analysis was then conducted to elucidate the evolution of pineal cells, their photosensitivity, their role in melatonin production, and the signaling processes within the glands of these species. Our analysis identified distinct cellular compositions of the pineal gland in zebrafish, rats, and monkeys. Zebrafish photoreceptors exhibited comprehensive phototransduction gene expression, while specific genes, including transducin (Gngt1, Gnb3, and Gngt2) and phosducin (Pdc), were consistently present in mammalian pinealocytes. We found transcriptional similarities between the pineal gland and retina, underscoring shared evolutionary and functional pathways. Zebrafish displayed unique light-responsive circadian gene activity compared to rats and monkeys. Key ligand-receptor interactions were identified, especially involving MDK and PTN, influencing melatonin synthesis across species. Furthermore, we observed species-specific GPCR (G protein-coupled receptors) expressions related to melatonin synthesis and their alignment with retinal expressions. Our findings also highlighted specific transcription factors (TFs) and regulatory networks associated with pineal gland evolution and function. Our study provides a detailed analysis of the pineal gland's evolution from fish to mammals. We identified key transcriptional changes and controls that highlight the gland's functional diversity. Notably, we found significant ligand-receptor interactions influencing melatonin synthesis and demonstrated parallels between pineal and retinal expressions. These insights enhance our understanding of the pineal gland's role in phototransduction, melatonin production, and circadian rhythms in vertebrates.
Collapse
Affiliation(s)
- Jihong Zheng
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenqi Song
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yihang Zhou
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xuan Li
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Meng Wang
- Songjiang Research Institute, Songjiang District Central Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Zhang
- Fundamental Research Center, Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| |
Collapse
|
11
|
Rocha-Martins M. Cell behaviors that pattern developing tissues: the case of the vertebrate nervous system. Curr Top Dev Biol 2023; 159:30-58. [PMID: 38729679 DOI: 10.1016/bs.ctdb.2023.11.003] [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] [Indexed: 05/12/2024]
Abstract
Morphogenesis from cells to tissue gives rise to the complex architectures that make our organs. How cells and their dynamic behavior are translated into functional spatial patterns is only starting to be understood. Recent advances in quantitative imaging revealed that, although highly heterogeneous, cellular behaviors make reproducible tissue patterns. Emerging evidence suggests that mechanisms of cellular coordination, intrinsic variability and plasticity are critical for robust pattern formation. While pattern development shows a high level of fidelity, tissue organization has undergone drastic changes throughout the course of evolution. In addition, alterations in cell behavior, if unregulated, can cause developmental malformations that disrupt function. Therefore, comparative studies of different species and of disease models offer a powerful approach for understanding how novel spatial configurations arise from variations in cell behavior and the fundamentals of successful pattern formation. In this chapter, I dive into the development of the vertebrate nervous system to explore efforts to dissect pattern formation beyond molecules, the emerging core principles and open questions.
Collapse
|
12
|
Wahle P, Brancati G, Harmel C, He Z, Gut G, Del Castillo JS, Xavier da Silveira Dos Santos A, Yu Q, Noser P, Fleck JS, Gjeta B, Pavlinić D, Picelli S, Hess M, Schmidt GW, Lummen TTA, Hou Y, Galliker P, Goldblum D, Balogh M, Cowan CS, Scholl HPN, Roska B, Renner M, Pelkmans L, Treutlein B, Camp JG. Multimodal spatiotemporal phenotyping of human retinal organoid development. Nat Biotechnol 2023; 41:1765-1775. [PMID: 37156914 PMCID: PMC10713453 DOI: 10.1038/s41587-023-01747-2] [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: 03/03/2022] [Accepted: 03/13/2023] [Indexed: 05/10/2023]
Abstract
Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales and molecular modalities are lacking. In this study, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation.
Collapse
Affiliation(s)
- Philipp Wahle
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giovanna Brancati
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Gabriele Gut
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Aline Xavier da Silveira Dos Santos
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Pascal Noser
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Bruno Gjeta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Dinko Pavlinić
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Max Hess
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tom T A Lummen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Yanyan Hou
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Patricia Galliker
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - David Goldblum
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marton Balogh
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Department of Ophthalmology, University of Basel, Basel, Switzerland.
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| |
Collapse
|
13
|
Terrinoni A, Micheloni G, Moretti V, Caporali S, Bernardini S, Minieri M, Pieri M, Giaroni C, Acquati F, Costantino L, Ferrara F, Valli R, Porta G. OTX Genes in Adult Tissues. Int J Mol Sci 2023; 24:16962. [PMID: 38069286 PMCID: PMC10707059 DOI: 10.3390/ijms242316962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
OTX homeobox genes have been extensively studied for their role in development, especially in neuroectoderm formation. Recently, their expression has also been reported in adult physiological and pathological tissues, including retina, mammary and pituitary glands, sinonasal mucosa, in several types of cancer, and in response to inflammatory, ischemic, and hypoxic stimuli. Reactivation of OTX genes in adult tissues supports the notion of the evolutionary amplification of functions of genes by varying their temporal expression, with the selection of homeobox genes from the "toolbox" to drive or contribute to different processes at different stages of life. OTX involvement in pathologies points toward these genes as potential diagnostic and/or prognostic markers as well as possible therapeutic targets.
Collapse
Affiliation(s)
- Alessandro Terrinoni
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Giovanni Micheloni
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Vittoria Moretti
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Sabrina Caporali
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Marilena Minieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Massimo Pieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Cristina Giaroni
- Department of Medicina e Innovazione Tecnologica, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Francesco Acquati
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
- Department of Biotechnology and Life Science, University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
| | - Lucy Costantino
- Department of Molecular Genetics, Centro Diagnostico Italiano, Via Saint Bon 20, 20147 Milano, Italy
| | - Fulvio Ferrara
- Department of Molecular Genetics, Centro Diagnostico Italiano, Via Saint Bon 20, 20147 Milano, Italy
| | - Roberto Valli
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| | - Giovanni Porta
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5, 21100 Varese, Italy
| |
Collapse
|
14
|
Honnell V, Sweeney S, Norrie J, Ramirez C, Xu B, Teubner B, Lee AY, Bell C, Dyer MA. Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562742. [PMID: 37905144 PMCID: PMC10614883 DOI: 10.1101/2023.10.17.562742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. Recently, we found that distinct modules within a murine SE regulate gene expression of master regulatory transcription factor Vsx2 in a developmental stage- and cell-type specific manner. Vsx2 is expressed in retinal progenitor cells as well as differentiated bipolar neurons and Müller glia. Mutations in VSX2 in humans and mice lead to microphthalmia due to a defect in retinal progenitor cell proliferation. Deletion of a single module within the Vsx2 SE leads to microphthalmia. Deletion of a separate module within the SE leads to a complete loss of bipolar neurons, yet the remainder of the retina develops normally. Furthermore, the Vsx2 SE is evolutionarily conserved in vertebrates, suggesting that these modules are important for retinal development across species. In the present study, we examine the ability of these modules to drive retinal development between species. By inserting the human build of one Vsx2 SE module into a mouse with microphthalmia, eye size was rescued. To understand the implications of these SE modules in a model of human development, we generated human retinal organoids. Deleting one module results in small organoids, recapitulating the small-eyed phenotype of mice with microphthalmia, while deletion of the other module leads to a complete loss of ON cone bipolar neurons. This prototypical SE serves as a model for uncoupling developmental stage- and cell-type specific effects of neurogenic transcription factors with complex expression patterns. Moreover, by elucidating the gene regulatory mechanisms, we can begin to examine how dysregulation of these mechanisms contributes to phenotypic diversity and disease.
Collapse
Affiliation(s)
- Victoria Honnell
- Department of Developmental Neurobiology at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
- Graduate School of Biomedical Sciences at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Shannon Sweeney
- Department of Developmental Neurobiology at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Jackie Norrie
- Department of Developmental Neurobiology at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Cody Ramirez
- Department of Developmental Neurobiology at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Brett Teubner
- Department of Developmental Neurobiology at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Ah Young Lee
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Claire Bell
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Michael A. Dyer
- Department of Developmental Neurobiology at St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| |
Collapse
|
15
|
Kerschensteiner D. Losing, preserving, and restoring vision from neurodegeneration in the eye. Curr Biol 2023; 33:R1019-R1036. [PMID: 37816323 PMCID: PMC10575673 DOI: 10.1016/j.cub.2023.08.044] [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] [Indexed: 10/12/2023]
Abstract
The retina is a part of the brain that sits at the back of the eye, looking out onto the world. The first neurons of the retina are the rod and cone photoreceptors, which convert changes in photon flux into electrical signals that are the basis of vision. Rods and cones are frequent targets of heritable neurodegenerative diseases that cause visual impairment, including blindness, in millions of people worldwide. This review summarizes the diverse genetic causes of inherited retinal degenerations (IRDs) and their convergence onto common pathogenic mechanisms of vision loss. Currently, there are few effective treatments for IRDs, but recent advances in disparate areas of biology and technology (e.g., genome editing, viral engineering, 3D organoids, optogenetics, semiconductor arrays) discussed here enable promising efforts to preserve and restore vision in IRD patients with implications for neurodegeneration in less approachable brain areas.
Collapse
Affiliation(s)
- Daniel Kerschensteiner
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
16
|
Ramachandra Rao S, Fliesler SJ. A simple, rapid fluorescent reporter-based method for detection of ectopic cre recombinase expression in presumed retinal cell type-targeted mouse lines. Exp Eye Res 2023; 235:109637. [PMID: 37659708 PMCID: PMC10756212 DOI: 10.1016/j.exer.2023.109637] [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: 06/12/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023]
Abstract
Although cell type-specific Cre recombinase-expressing mouse lines are commonly used to generate conditional knockout of genes of interest, germline recombination and ectopic "leakiness" in Cre recombinase expression in non-specific cell types has been observed in several neuronal and glial-specific Cre lines. This often leads to inadvertent loss of conditional mouse lines, requiring rederivation. It is therefore imperative to be able to monitor and validate cell type-specific Cre recombinase-mediated gene editing. Herein, we describe a simple, inexpensive, rapid ZsGreen fluor-reporter-based strategy for genotype-free identification of ectopic leakiness using a custom-designed, 3-D blue LED light box. We assessed cell type-specific expression in several allegedly specific Cre recombinase mouse lines commonly used in vision research: retinal pigment epithelium (RPE)-specific (VMD2 (Best1) Cre, RPE65 Cre); astrocyte-specific (GFAP Cre); as well as photoreceptor-bipolar progenitor cell-specific (CRX Cre). Our standardized workflow allows facile, rapid identification of ectopic and non-specific Cre recombinase expression in any presume specific Cre mouse line, without the need for genotyping and without causing animal distress.
Collapse
Affiliation(s)
- Sriganesh Ramachandra Rao
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Sciences, The State University of New York - University at Buffalo, Buffalo, NY, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, The State University of New York - University at Buffalo, Buffalo, NY, USA; Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, The State University of New York - University at Buffalo, Buffalo, NY, USA; Research Service, VA Western New York Healthcare System, Buffalo, NY, USA
| | - Steven J Fliesler
- Department of Ophthalmology, Jacobs School of Medicine and Biomedical Sciences, The State University of New York - University at Buffalo, Buffalo, NY, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, The State University of New York - University at Buffalo, Buffalo, NY, USA; Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, The State University of New York - University at Buffalo, Buffalo, NY, USA; Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Fogliano C, Carotenuto R, Rusciano G, Sasso A, Motta CM, Agnisola C, Avallone B. Structural and functional damage to the retina and skeletal muscle in Xenopus laevis embryos exposed to the commonly used psychotropic benzodiazepine delorazepam. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 102:104235. [PMID: 37481049 DOI: 10.1016/j.etap.2023.104235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/03/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Benzodiazepines, psychotropic drugs, are among the most frequently found pharmaceuticals in aquatic matrices. An increasing number of studies are reporting their harmful effects on adults' behaviour and physiology, while little information is available regarding developing organisms exposed since early stages. Improper activation of GABA receptors during embryonic development is likely to induce relevant consequences on the morphogenesis and, at later stages, on behaviour. This study investigated the negative effects of three increasing concentrations of delorazepam on Xenopus laevis retinal and skeletal muscle morphogenesis. Morphological and ultrastructural investigations were correlated with gene expression, while Raman spectroscopy highlighted the main biochemical components affected. Conventional phototactic response and orientation in the magnetic field were assessed as indicators of proper interaction between sensory organs and the nervous system. Results confirm the profound impact of delorazepam on development and return an alarming picture of the amphibians' survival potentialities in a benzodiazepine-contaminated environment.
Collapse
Affiliation(s)
- Chiara Fogliano
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Rosa Carotenuto
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Giulia Rusciano
- Department of Physics, University of Naples Federico II, Naples, Italy
| | - Antonio Sasso
- Department of Physics, University of Naples Federico II, Naples, Italy
| | | | - Claudio Agnisola
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Bice Avallone
- Department of Biology, University of Naples Federico II, Naples, Italy
| |
Collapse
|
20
|
Rocha-Martins M, Nerli E, Kretzschmar J, Weigert M, Icha J, Myers EW, Norden C. Neuronal migration prevents spatial competition in retinal morphogenesis. Nature 2023; 620:615-624. [PMID: 37558872 DOI: 10.1038/s41586-023-06392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/30/2023] [Indexed: 08/11/2023]
Abstract
The concomitant occurrence of tissue growth and organization is a hallmark of organismal development1-3. This often means that proliferating and differentiating cells are found at the same time in a continuously changing tissue environment. How cells adapt to architectural changes to prevent spatial interference remains unclear. Here, to understand how cell movements that are key for growth and organization are orchestrated, we study the emergence of photoreceptor neurons that occur during the peak of retinal growth, using zebrafish, human tissue and human organoids. Quantitative imaging reveals that successful retinal morphogenesis depends on the active bidirectional translocation of photoreceptors, leading to a transient transfer of the entire cell population away from the apical proliferative zone. This pattern of migration is driven by cytoskeletal machineries that differ depending on the direction: microtubules are exclusively required for basal translocation, whereas actomyosin is involved in apical movement. Blocking the basal translocation of photoreceptors induces apical congestion, which hampers the apical divisions of progenitor cells and leads to secondary defects in lamination. Thus, photoreceptor migration is crucial to prevent competition for space, and to allow concurrent tissue growth and lamination. This shows that neuronal migration, in addition to its canonical role in cell positioning4, can be involved in coordinating morphogenesis.
Collapse
Affiliation(s)
- Mauricio Rocha-Martins
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden (CSBD), Dresden, Germany.
| | - Elisa Nerli
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Jenny Kretzschmar
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
- Institute of Bioengineering, School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jaroslav Icha
- 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 (CSBD), Dresden, Germany
| | - Caren Norden
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Lu CF, Zhou YN, Zhang J, Su S, Liu Y, Peng GH, Zang W, Cao J. The role of epigenetic methylation/demethylation in the regulation of retinal photoreceptors. Front Cell Dev Biol 2023; 11:1149132. [PMID: 37305686 PMCID: PMC10251769 DOI: 10.3389/fcell.2023.1149132] [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: 01/21/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Photoreceptors are integral and crucial for the retina, as they convert light into electrical signals. Epigenetics plays a vital role in determining the precise expression of genetic information in space and time during the development and maturation of photoreceptors, cell differentiation, degeneration, death, and various pathological processes. Epigenetic regulation has three main manifestations: histone modification, DNA methylation, and RNA-based mechanisms, where methylation is involved in two regulatory mechanisms-histone methylation and DNA methylation. DNA methylation is the most studied form of epigenetic modification, while histone methylation is a relatively stable regulatory mechanism. Evidence suggests that normal methylation regulation is essential for the growth and development of photoreceptors and the maintenance of their functions, while abnormal methylation can lead to many pathological forms of photoreceptors. However, the role of methylation/demethylation in regulating retinal photoreceptors remains unclear. Therefore, this study aims to review the role of methylation/demethylation in regulating photoreceptors in various physiological and pathological situations and discuss the underlying mechanisms involved. Given the critical role of epigenetic regulation in gene expression and cellular differentiation, investigating the specific molecular mechanisms underlying these processes in photoreceptors may provide valuable insights into the pathogenesis of retinal diseases. Moreover, understanding these mechanisms could lead to the development of novel therapies that target the epigenetic machinery, thereby promoting the maintenance of retinal function throughout an individual's lifespan.
Collapse
Affiliation(s)
- Chao-Fan Lu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Ya-Nan Zhou
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jingjing Zhang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Songxue Su
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Yupeng Liu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Guang-Hua Peng
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou, China
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Weidong Zang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cao
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
23
|
Choudhary M, Malek G. Potential therapeutic targets for age-related macular degeneration: The nuclear option. Prog Retin Eye Res 2023; 94:101130. [PMID: 36220751 PMCID: PMC10082136 DOI: 10.1016/j.preteyeres.2022.101130] [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: 05/01/2022] [Revised: 09/18/2022] [Accepted: 09/18/2022] [Indexed: 02/07/2023]
Abstract
The functions and activities of nuclear receptors, the largest family of transcription factors in the human genome, have classically focused on their ability to act as steroid and hormone sensors in endocrine organs. However, they are responsible for a diverse array of physiological functions, including cellular homeostasis and metabolism, during development and aging. Though the eye is not a traditional endocrine organ, recent studies have revealed high expression levels of nuclear receptors in cells throughout the posterior pole. These findings have precipitated an interest in investigating the role of these transcription factors in the eye as a function of age and ocular disease, in particular age-related macular degeneration (AMD). As the leading cause of vision impairment in the elderly, identifying signaling pathways that may be targeted for AMD therapy is of great importance, given the lack of therapeutic options for over 85% of patients with this disease. Herein we review this relatively new field and recent findings supporting the hypothesis that the eye is a secondary endocrine organ, in which nuclear receptors serve as the bedrock for biological processes in cells vulnerable in AMD, including retinal pigment epithelial and choroidal endothelial cells, and discuss the therapeutic potential of targeting these receptors for AMD.
Collapse
Affiliation(s)
- Mayur Choudhary
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Goldis Malek
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA; Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
24
|
Hagiwara A, Mizutani A, Kawamura S, Abe M, Hida Y, Sakimura K, Ohtsuka T. Critical Role of the Presynaptic Protein CAST in Maintaining the Photoreceptor Ribbon Synapse Triad. Int J Mol Sci 2023; 24:ijms24087251. [PMID: 37108413 PMCID: PMC10138387 DOI: 10.3390/ijms24087251] [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: 03/05/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The cytomatrix at the active zone-associated structural protein (CAST) and its homologue, named ELKS, being rich in glutamate (E), leucine (L), lysine (K), and serine (S), belong to a family of proteins that organize presynaptic active zones at nerve terminals. These proteins interact with other active zone proteins, including RIMs, Munc13s, Bassoon, and the β subunit of Ca2+ channels, and have various roles in neurotransmitter release. A previous study showed that depletion of CAST/ELKS in the retina causes morphological changes and functional impairment of this structure. In this study, we investigated the roles of CAST and ELKS in ectopic synapse localization. We found that the involvement of these proteins in ribbon synapse distribution is complex. Unexpectedly, CAST and ELKS, in photoreceptors or in horizontal cells, did not play a major role in ribbon synapse ectopic localization. However, depletion of CAST and ELKS in the mature retina resulted in degeneration of the photoreceptors. These findings suggest that CAST and ELKS play critical roles in maintaining neural signal transduction in the retina, but the regulation of photoreceptor triad synapse distribution is not solely dependent on their actions within photoreceptors and horizontal cells.
Collapse
Affiliation(s)
- Akari Hagiwara
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Ayako Mizutani
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Saki Kawamura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Yamato Hida
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Toshihisa Ohtsuka
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| |
Collapse
|
25
|
Kuzelova A, Dupacova N, Antosova B, Sunny SS, Kozmik Z, Paces J, Skoultchi AI, Stopka T, Kozmik Z. Chromatin Remodeling Enzyme Snf2h Is Essential for Retinal Cell Proliferation and Photoreceptor Maintenance. Cells 2023; 12:1035. [PMID: 37048108 PMCID: PMC10093269 DOI: 10.3390/cells12071035] [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: 02/14/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Chromatin remodeling complexes are required for many distinct nuclear processes such as transcription, DNA replication, and DNA repair. However, the contribution of these complexes to the development of complex tissues within an organism is poorly characterized. Imitation switch (ISWI) proteins are among the most evolutionarily conserved ATP-dependent chromatin remodeling factors and are represented by yeast Isw1/Isw2, and their vertebrate counterparts Snf2h (Smarca5) and Snf2l (Smarca1). In this study, we focused on the role of the Snf2h gene during the development of the mammalian retina. We show that Snf2h is expressed in both retinal progenitors and post-mitotic retinal cells. Using Snf2h conditional knockout mice (Snf2h cKO), we found that when Snf2h is deleted, the laminar structure of the adult retina is not retained, the overall thickness of the retina is significantly reduced compared with controls, and the outer nuclear layer (ONL) is completely missing. The depletion of Snf2h did not influence the ability of retinal progenitors to generate all the differentiated retinal cell types. Instead, the Snf2h function is critical for the proliferation of retinal progenitor cells. Cells lacking Snf2h have a defective S-phase, leading to the entire cell division process impairments. Although all retinal cell types appear to be specified in the absence of the Snf2h function, cell-cycle defects and concomitantly increased apoptosis in Snf2h cKO result in abnormal retina lamination, complete destruction of the photoreceptor layer, and consequently, a physiologically non-functional retina.
Collapse
Affiliation(s)
- Andrea Kuzelova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Naoko Dupacova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Barbora Antosova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Sweetu Susan Sunny
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Jan Paces
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Arthur I. Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Tomas Stopka
- Biocev, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
- Research Unit for Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| |
Collapse
|
26
|
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).
Collapse
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;
| |
Collapse
|
27
|
Frederick CE, Zenisek D. Ribbon Synapses and Retinal Disease: Review. Int J Mol Sci 2023; 24:ijms24065090. [PMID: 36982165 PMCID: PMC10049380 DOI: 10.3390/ijms24065090] [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: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Synaptic ribbons are presynaptic protein complexes that are believed to be important for the transmission of sensory information in the visual system. Ribbons are selectively associated with those synapses where graded changes in membrane potential drive continuous neurotransmitter release. Defective synaptic transmission can arise as a result of the mutagenesis of a single ribbon component. Visual diseases that stem from malfunctions in the presynaptic molecular machinery of ribbon synapses in the retina are rare. In this review, we provide an overview of synaptopathies that give rise to retinal malfunction and our present understanding of the mechanisms that underlie their pathogenesis and discuss muscular dystrophies that exhibit ribbon synapse involvement in the pathology.
Collapse
Affiliation(s)
- Courtney E Frederick
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208026, New Haven, CT 06510, USA
| | - David Zenisek
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208026, New Haven, CT 06510, USA
| |
Collapse
|
28
|
Towards a New Biomarker for Diabetic Retinopathy: Exploring RBP3 Structure and Retinoids Binding for Functional Imaging of Eyes In Vivo. Int J Mol Sci 2023; 24:ijms24054408. [PMID: 36901838 PMCID: PMC10002987 DOI: 10.3390/ijms24054408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Diabetic retinopathy (DR) is a severe disease with a growing number of afflicted patients, which places a heavy burden on society, both socially and financially. While there are treatments available, they are not always effective and are usually administered when the disease is already at a developed stage with visible clinical manifestation. However, homeostasis at a molecular level is disrupted before visible signs of the disease are evident. Thus, there has been a constant search for effective biomarkers that could signal the onset of DR. There is evidence that early detection and prompt disease control are effective in preventing or slowing DR progression. Here, we review some of the molecular changes that occur before clinical manifestations are observable. As a possible new biomarker, we focus on retinol binding protein 3 (RBP3). We argue that it displays unique features that make it a very good biomarker for non-invasive, early-stage DR detection. Linking chemistry to biological function and focusing on new developments in eye imaging and two-photon technology, we describe a new potential diagnostic tool that would allow rapid and effective quantification of RBP3 in the retina. Moreover, this tool would also be useful in the future to monitor therapeutic effectiveness if levels of RBP3 are elevated by DR treatments.
Collapse
|
29
|
Kuzelova A, Dupacova N, Antosova B, Sunny SS, Kozmik Z, Paces J, Skoultchi AI, Stopka T, Kozmik Z. Chromatin remodeling enzyme Snf2h is essential for retinal cell proliferation and photoreceptor maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528323. [PMID: 36824843 PMCID: PMC9948993 DOI: 10.1101/2023.02.13.528323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Chromatin remodeling complexes are required for many distinct nuclear processes such as transcription, DNA replication and DNA repair. However, how these complexes contribute to the development of complex tissues within an organism is poorly characterized. Imitation switch (ISWI) proteins are among the most evolutionarily conserved ATP-dependent chromatin remodeling factors and are represented by yeast Isw1/Isw2, and their vertebrate counterparts Snf2h (Smarca5) and Snf2l (Smarca1). In this study, we focused on the role of the Snf2h gene during development of the mammalian retina. We show that Snf2h is expressed in both retinal progenitors and post-mitotic retinal cells. Using Snf2h conditional knockout mice ( Snf2h cKO), we found that when Snf2h is deleted the laminar structure of the adult retina is not retained, the overall thickness of the retina is significantly reduced compared with controls, and the outer nuclear layer (ONL) is completely missing. Depletion of Snf2h did not influence the ability of retinal progenitors to generate all of the differentiated retinal cell types. Instead, Snf2h function is critical for proliferation of retinal progenitor cells. Cells lacking Snf2h have a defective S-phase, leading to the entire cell division process impairments. Although, all retinal cell types appear to be specified in the absence of Snf2h function, cell cycle defects and concomitantly increased apoptosis in Snf2h cKO result in abnormal retina lamination, complete destruction of the photoreceptor layer and, consequently, in a physiologically non-functional retina.
Collapse
|
30
|
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.
Collapse
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)
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Mueller-Buehl C, Wegrzyn D, Bauch J, Faissner A. Regulation of the E/I-balance by the neural matrisome. Front Mol Neurosci 2023; 16:1102334. [PMID: 37143468 PMCID: PMC10151766 DOI: 10.3389/fnmol.2023.1102334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
In the mammalian cortex a proper excitatory/inhibitory (E/I) balance is fundamental for cognitive functions. Especially γ-aminobutyric acid (GABA)-releasing interneurons regulate the activity of excitatory projection neurons which form the second main class of neurons in the cortex. During development, the maturation of fast-spiking parvalbumin-expressing interneurons goes along with the formation of net-like structures covering their soma and proximal dendrites. These so-called perineuronal nets (PNNs) represent a specialized form of the extracellular matrix (ECM, also designated as matrisome) that stabilize structural synapses but prevent the formation of new connections. Consequently, PNNs are highly involved in the regulation of the synaptic balance. Previous studies revealed that the formation of perineuronal nets is accompanied by an establishment of mature neuronal circuits and by a closure of critical windows of synaptic plasticity. Furthermore, it has been shown that PNNs differentially impinge the integrity of excitatory and inhibitory synapses. In various neurological and neuropsychiatric disorders alterations of PNNs were described and aroused more attention in the last years. The following review gives an update about the role of PNNs for the maturation of parvalbumin-expressing interneurons and summarizes recent findings about the impact of PNNs in different neurological and neuropsychiatric disorders like schizophrenia or epilepsy. A targeted manipulation of PNNs might provide an interesting new possibility to indirectly modulate the synaptic balance and the E/I ratio in pathological conditions.
Collapse
|
33
|
Bunker J, Bashir M, Bailey S, Boodram P, Perry A, Delaney R, Tsachaki M, Sprecher SG, Nelson E, Call GB, Rister J. Blimp-1/PRDM1 and Hr3/RORβ specify the blue-sensitive photoreceptor subtype in Drosophila by repressing the hippo pathway. Front Cell Dev Biol 2023; 11:1058961. [PMID: 36960411 PMCID: PMC10027706 DOI: 10.3389/fcell.2023.1058961] [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: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
During terminal differentiation of the mammalian retina, transcription factors control binary cell fate decisions that generate functionally distinct subtypes of photoreceptor neurons. For instance, Otx2 and RORβ activate the expression of the transcriptional repressor Blimp-1/PRDM1 that represses bipolar interneuron fate and promotes rod photoreceptor fate. Moreover, Otx2 and Crx promote expression of the nuclear receptor Nrl that promotes rod photoreceptor fate and represses cone photoreceptor fate. Mutations in these four transcription factors cause severe eye diseases such as retinitis pigmentosa. Here, we show that a post-mitotic binary fate decision in Drosophila color photoreceptor subtype specification requires ecdysone signaling and involves orthologs of these transcription factors: Drosophila Blimp-1/PRDM1 and Hr3/RORβ promote blue-sensitive (Rh5) photoreceptor fate and repress green-sensitive (Rh6) photoreceptor fate through the transcriptional repression of warts/LATS, the nexus of the phylogenetically conserved Hippo tumor suppressor pathway. Moreover, we identify a novel interaction between Blimp-1 and warts, whereby Blimp-1 represses a warts intronic enhancer in blue-sensitive photoreceptors and thereby gives rise to specific expression of warts in green-sensitive photoreceptors. Together, these results reveal that conserved transcriptional regulators play key roles in terminal cell fate decisions in both the Drosophila and the mammalian retina, and the mechanistic insights further deepen our understanding of how Hippo pathway signaling is repurposed to control photoreceptor fates for Drosophila color vision.
Collapse
Affiliation(s)
- Joseph Bunker
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Mhamed Bashir
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Sydney Bailey
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Pamela Boodram
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
- NYU Langone Medical Center, New York, NY, United States
| | - Alexis Perry
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Rory Delaney
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Maria Tsachaki
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Erik Nelson
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, United States
| | - Gerald B. Call
- Department of Pharmacology, College of Graduate Studies, Midwestern University, Glendale, AZ, United States
| | - Jens Rister
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
- *Correspondence: Jens Rister,
| |
Collapse
|
34
|
Sun C, Chen S. Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development. Front Mol Neurosci 2023; 16:1134839. [PMID: 37181651 PMCID: PMC10172487 DOI: 10.3389/fnmol.2023.1134839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Photoreceptor development of the vertebrate visual system is controlled by a complex transcription regulatory network. OTX2 is expressed in the mitotic retinal progenitor cells (RPCs) and controls photoreceptor genesis. CRX that is activated by OTX2 is expressed in photoreceptor precursors after cell cycle exit. NEUROD1 is also present in photoreceptor precursors that are ready to specify into rod and cone photoreceptor subtypes. NRL is required for the rod fate and regulates downstream rod-specific genes including the orphan nuclear receptor NR2E3 which further activates rod-specific genes and simultaneously represses cone-specific genes. Cone subtype specification is also regulated by the interplay of several transcription factors such as THRB and RXRG. Mutations in these key transcription factors are responsible for ocular defects at birth such as microphthalmia and inherited photoreceptor diseases such as Leber congenital amaurosis (LCA), retinitis pigmentosa (RP) and allied dystrophies. In particular, many mutations are inherited in an autosomal dominant fashion, including the majority of missense mutations in CRX and NRL. In this review, we describe the spectrum of photoreceptor defects that are associated with mutations in the above-mentioned transcription factors, and summarize the current knowledge of molecular mechanisms underlying the pathogenic mutations. At last, we deliberate the outstanding gaps in our understanding of the genotype-phenotype correlations and outline avenues for future research of the treatment strategies.
Collapse
Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- *Correspondence: Chi Sun,
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
| |
Collapse
|
35
|
Kandoi S, Martinez C, Merriman DK, Lamba DA. Characterization of Retinal Development in 13-Lined Ground Squirrels. Transl Vis Sci Technol 2022; 11:17. [DOI: 10.1167/tvst.11.11.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Sangeetha Kandoi
- Department of Ophthalmology, UCSF Medical Center, 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
| | - Cassandra Martinez
- Department of Ophthalmology, UCSF Medical Center, 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
| | - Dana K. Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Deepak A. Lamba
- Department of Ophthalmology, UCSF Medical Center, 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
| |
Collapse
|
36
|
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.
Collapse
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.
| |
Collapse
|
37
|
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.
Collapse
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;,
| |
Collapse
|
38
|
Langouët M, Jolicoeur C, Javed A, Mattar P, Gearhart MD, Daiger SP, Bertelsen M, Tranebjærg L, Rendtorff ND, Grønskov K, Jespersgaard C, Chen R, Sun Z, Li H, Alirezaie N, Majewski J, Bardwell VJ, Sui R, Koenekoop RK, Cayouette M. Mutations in BCOR, a co-repressor of CRX/OTX2, are associated with early-onset retinal degeneration. SCIENCE ADVANCES 2022; 8:eabh2868. [PMID: 36070393 PMCID: PMC9451151 DOI: 10.1126/sciadv.abh2868] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/21/2022] [Indexed: 06/10/2023]
Abstract
Many transcription factors regulating the production, survival, and function of photoreceptor cells have been identified, but little is known about transcriptional co-regulators in retinal health and disease. Here, we show that BCL6 co-repressor (BCOR), a Polycomb repressive complex 1 factor mutated in various cancers, is involved in photoreceptor degenerative diseases. Using proteomics and transcription assays, we report that BCOR interacts with the transcription factors CRX and OTX2 and reduces their ability to activate the promoters of photoreceptor-specific genes. CUT&RUN sequencing further shows that BCOR shares genome-wide binding profiles with CRX/OTX2, consistent with a general co-repression activity. We also identify missense mutations in human BCOR in five families that have no evidence of cancer but present severe early-onset X-linked retinal degeneration. Last, we show that the human BCOR mutants cause degeneration when expressed in the mouse retina and have enhanced repressive activity on OTX2. These results uncover a role for BCOR in photoreceptors in both health and disease.
Collapse
Affiliation(s)
- Maéva Langouët
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Awais Javed
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Micah D. Gearhart
- Department of Genetics, Cell Biology and Development, Development Biology Center, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen P. Daiger
- EHGED Department, Human Genetics Center, School of Public Health, University of Texas HSC, Houston, TX 77030, USA
| | - Mette Bertelsen
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
- Department of Ophthalmology, Rigshospitalet, The Kennedy Centre, Glostrup, Denmark
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Denmark
| | - Nanna D. Rendtorff
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Catherine Jespersgaard
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Zixi Sun
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hui Li
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Najmeh Alirezaie
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vivian J. Bardwell
- Department of Genetics, Cell Biology and Development, Development Biology Center, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ruifang Sui
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Robert K. Koenekoop
- Departments of Pediatric Surgery, Human Genetics, Adult Ophthalmology and the McGill Ocular Genetics Laboratory, McGill University Health Center Research Institute, Montreal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Anatomy and Cell Biology, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| |
Collapse
|
39
|
Krueger LA, Morris AC. Eyes on CHARGE syndrome: Roles of CHD7 in ocular development. Front Cell Dev Biol 2022; 10:994412. [PMID: 36172288 PMCID: PMC9512043 DOI: 10.3389/fcell.2022.994412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
The development of the vertebrate visual system involves complex morphogenetic interactions of cells derived from multiple embryonic lineages. Disruptions in this process are associated with structural birth defects such as microphthalmia, anophthalmia, and coloboma (collectively referred to as MAC), and inherited retinal degenerative diseases such as retinitis pigmentosa and allied dystrophies. MAC and retinal degeneration are also observed in systemic congenital malformation syndromes. One important example is CHARGE syndrome, a genetic disorder characterized by coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear abnormalities. Mutations in the gene encoding Chromodomain helicase DNA binding protein 7 (CHD7) cause the majority of CHARGE syndrome cases. However, the pathogenetic mechanisms that connect loss of CHD7 to the ocular complications observed in CHARGE syndrome have not been identified. In this review, we provide a general overview of ocular development and congenital disorders affecting the eye. This is followed by a comprehensive description of CHARGE syndrome, including discussion of the spectrum of ocular defects that have been described in this disorder. In addition, we discuss the current knowledge of CHD7 function and focus on its contributions to the development of ocular structures. Finally, we discuss outstanding gaps in our knowledge of the role of CHD7 in eye formation, and propose avenues of investigation to further our understanding of how CHD7 activity regulates ocular and retinal development.
Collapse
Affiliation(s)
| | - Ann C. Morris
- Department of Biology, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
40
|
Fogg LG, Cortesi F, Lecchini D, Gache C, Marshall NJ, de Busserolles F. Development of dim-light vision in the nocturnal reef fish family Holocentridae I: retinal gene expression. J Exp Biol 2022; 225:276222. [PMID: 35929500 PMCID: PMC9482368 DOI: 10.1242/jeb.244513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/24/2022] [Indexed: 11/20/2022]
Abstract
Developmental changes to the visual systems of animals are often associated with ecological shifts. Reef fishes experience a change in habitat between larval life in the shallow open ocean to juvenile and adult life on the reef. Some species also change their lifestyle over this period and become nocturnal. While these ecological transitions are well documented, little is known about the ontogeny of nocturnal reef fish vision. Here, we used transcriptomics to investigate visual development in 12 representative species from both subfamilies, Holocentrinae (squirrelfishes) and Myripristinae (soldierfishes), in the nocturnal coral reef fish family, Holocentridae. Results revealed that the visual systems of holocentrids are initially well adapted to photopic conditions with pre-settlement larvae having high levels of cone opsin gene expression and a broad cone opsin gene repertoire (8 genes). At reef settlement, holocentrids started to invest more in their scotopic visual system, and compared with adults, showed upregulation of genes involved in cell differentiation/proliferation. By adulthood, holocentrids had well developed scotopic vision with high levels of rod opsin gene expression, reduced cone opsin gene expression and repertoire (1–4 genes) and upregulated phototransduction genes. Finally, although the two subfamilies shared similar ecologies across development, their visual systems diverged after settlement, with Myripristinae investing more in scotopic vision than Holocentrinae. Hence, both ecology and phylogeny are likely to determine the development of the holocentrid visual system. Summary: Coral reef fishes in the family Holocentridae remodel their retina at the molecular level to adapt to a nocturnal lifestyle during development.
Collapse
Affiliation(s)
- Lily G Fogg
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David Lecchini
- PSL Research University, EPHE-UPVD-CNRS, UAR3278 CRIOBE, 98729 Papetoai, Moorea, French Polynesia, France.,Laboratoire d'Excellence "CORAIL", Paris, France
| | - Camille Gache
- PSL Research University, EPHE-UPVD-CNRS, UAR3278 CRIOBE, 98729 Papetoai, Moorea, French Polynesia, France.,Laboratoire d'Excellence "CORAIL", Paris, France
| | - N Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Fanny de Busserolles
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, 4072, Australia
| |
Collapse
|
41
|
Sharma P, Ramachandran R. Retina regeneration: lessons from vertebrates. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac012. [PMID: 38596712 PMCID: PMC10913848 DOI: 10.1093/oons/kvac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/24/2022] [Accepted: 06/25/2022] [Indexed: 04/11/2024]
Abstract
Unlike mammals, vertebrates such as fishes and frogs exhibit remarkable tissue regeneration including the central nervous system. Retina being part of the central nervous system has attracted the interest of several research groups to explore its regenerative ability in different vertebrate models including mice. Fishes and frogs completely restore the size, shape and tissue structure of an injured retina. Several studies have unraveled molecular mechanisms underlying retina regeneration. In teleosts, soon after injury, the Müller glial cells of the retina reprogram to form a proliferating population of Müller glia-derived progenitor cells capable of differentiating into various neural cell types and Müller glia. In amphibians, the transdifferentiation of retinal pigment epithelium and differentiation of ciliary marginal zone cells contribute to retina regeneration. In chicks and mice, supplementation with external growth factors or genetic modifications cause a partial regenerative response in the damaged retina. The initiation of retina regeneration is achieved through sequential orchestration of gene expression through controlled modulations in the genetic and epigenetic landscape of the progenitor cells. Several developmental biology pathways are turned on during the Müller glia reprogramming, retinal pigment epithelium transdifferentiation and ciliary marginal zone differentiation. Further, several tumorigenic pathways and gene expression events also contribute to the complete regeneration cascade of events. In this review, we address the various retinal injury paradigms and subsequent gene expression events governed in different vertebrate species. Further, we compared how vertebrates such as teleost fishes and amphibians can achieve excellent regenerative responses in the retina compared with their mammalian counterparts.
Collapse
Affiliation(s)
- Poonam Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO, 140306 Mohali, Punjab, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Knowledge City, SAS Nagar, Sector 81, Manauli PO, 140306 Mohali, Punjab, India
| |
Collapse
|
42
|
Daniele LL, Han JYS, Samuels IS, Komirisetty R, Mehta N, McCord JL, Yu M, Wang Y, Boesze-Battaglia K, Bell BA, Du J, Peachey NS, Philp NJ. Glucose uptake by GLUT1 in photoreceptors is essential for outer segment renewal and rod photoreceptor survival. FASEB J 2022; 36:e22428. [PMID: 35766190 PMCID: PMC9438481 DOI: 10.1096/fj.202200369r] [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: 03/22/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 02/07/2023]
Abstract
Photoreceptors consume glucose supplied by the choriocapillaris to support phototransduction and outer segment (OS) renewal. Reduced glucose supply underlies photoreceptor cell death in inherited retinal degeneration and age-related retinal disease. We have previously shown that restricting glucose transport into the outer retina by conditional deletion of Slc2a1 encoding GLUT1 resulted in photoreceptor loss and impaired OS renewal. However, retinal neurons, glia, and the retinal pigment epithelium play specialized, synergistic roles in metabolite supply and exchange, and the cell-specific map of glucose uptake and utilization in the retina is incomplete. In these studies, we conditionally deleted Slc2a1 in a pan-retinal or rod-specific manner to better understand how glucose is utilized in the retina. Using non-invasive ocular imaging, electroretinography, and histochemical and biochemical analyses we show that genetic deletion of Slc2a1 from retinal neurons and Müller glia results in reduced OS growth and progressive rod but not cone photoreceptor cell death. Rhodopsin levels were severely decreased even at postnatal day 20 when OS length was relatively normal. Arrestin levels were not changed suggesting that glucose uptake is required to synthesize membrane glycoproteins. Rod-specific deletion of Slc2a1 resulted in similar changes in OS length and rod photoreceptor cell death. These studies demonstrate that glucose is an essential carbon source for rod photoreceptor cell OS maintenance and viability.
Collapse
Affiliation(s)
- Lauren L Daniele
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - John Y S Han
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ivy S Samuels
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Ravikiran Komirisetty
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Nikhil Mehta
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Jessica L McCord
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Minzhong Yu
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Yekai Wang
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brent A Bell
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Neal S Peachey
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Nancy J Philp
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
43
|
Bian F, Daghsni M, Lu F, Liu S, Gross JM, Aldiri I. Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis. Development 2022; 149:dev200642. [PMID: 35831950 PMCID: PMC9440754 DOI: 10.1242/dev.200642] [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: 02/14/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
Abstract
Vsx2 is a transcription factor essential for retinal proliferation and bipolar cell differentiation, but the molecular mechanisms underlying its developmental roles are unclear. Here, we have profiled VSX2 genomic occupancy during mouse retinogenesis, revealing extensive retinal genetic programs associated with VSX2 during development. VSX2 binds and transactivates its enhancer in association with the transcription factor PAX6. Mice harboring deletions in the Vsx2 regulatory landscape exhibit specific abnormalities in retinal proliferation and in bipolar cell differentiation. In one of those deletions, a complete loss of bipolar cells is associated with a bias towards photoreceptor production. VSX2 occupies cis-regulatory elements nearby genes associated with photoreceptor differentiation and homeostasis in the adult mouse and human retina, including a conserved region nearby Prdm1, a factor implicated in the specification of rod photoreceptors and suppression of bipolar cell fate. VSX2 interacts with the transcription factor OTX2 and can act to suppress OTX2-dependent enhancer transactivation of the Prdm1 enhancer. Taken together, our analyses indicate that Vsx2 expression can be temporally and spatially uncoupled at the enhancer level, and they illuminate important mechanistic insights into how VSX2 is engaged with gene regulatory networks that are essential for retinal proliferation and cell fate acquisition.
Collapse
Affiliation(s)
- Fuyun Bian
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marwa Daghsni
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Fangfang Lu
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M Gross
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Issam Aldiri
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| |
Collapse
|
44
|
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.
Collapse
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.
| |
Collapse
|
45
|
Liang X, Brooks MJ, Swaroop A. Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina. Hum Mol Genet 2022; 31:3914-3933. [PMID: 35776116 DOI: 10.1093/hmg/ddac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022] Open
Abstract
The basic motif-leucine zipper (bZIP) transcription factor NRL determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein CRX and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. We predicted that NRL gradually establishes rod cell identity and function by temporal and dynamic regulation of stage-specific transcriptional targets. Therefore, we mapped the genomic occupancy of NRL at four stages of mouse photoreceptor differentiation by CUT&RUN analysis. Dynamics of NRL-binding revealed concordance with the corresponding changes in transcriptome of the developing rods. Notably, we identified c-Jun proto-oncogene as one of the targets of NRL, which could bind to specific cis-elements in the c-Jun promoter and modulate its activity in HEK293 cells. Coimmunoprecipitation studies showed association of NRL with c-Jun, also a bZIP protein, in transfected cells as well as in developing mouse retina. Additionally, shRNA-mediated knockdown of c-Jun in the mouse retina in vivo resulted in altered expression of almost 1000 genes, with reduced expression of phototransduction genes and many direct targets of NRL in rod photoreceptors. We propose that c-Jun-NRL heterodimers prime the NRL-directed transcriptional program in neonatal rod photoreceptors before high NRL expression suppresses c-Jun at later stages. Our study highlights a broader cooperation among cell-type restricted and widely expressed bZIP proteins, such as c-Jun, in specific spatiotemporal contexts during cellular differentiation.
Collapse
Affiliation(s)
- Xulong Liang
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Matthew J Brooks
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| |
Collapse
|
46
|
Comparison of the Response to the CXCR4 Antagonist AMD3100 during the Development of Retinal Organoids Derived from ES Cells and Zebrafish Retina. Int J Mol Sci 2022; 23:ijms23137088. [PMID: 35806093 PMCID: PMC9266567 DOI: 10.3390/ijms23137088] [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: 04/28/2022] [Revised: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Retinal organoids generated from human embryonic stem cells or iPSCs recreate the key structural and functional features of mammalian retinal tissue in vitro. However, the differences in the development of retinal organoids and normal retina in vivo are not well defined. Thus, in the present study, we analyzed the development of retinal organoids and zebrafish retina after inhibition of CXCR4, a key role in neurogenesis and optic nerve development, with the antagonist AMD3100. Our data indicated that CXCR4 was mainly expressed in ganglion cells in retinal organoids and was rarely expressed in amacrine or photoreceptor cells. AMD3100 treatment reduced the retinal organoid generation ratio, impaired differentiation, and induced morphological changes. Ganglion cells, amacrine cells, and photoreceptors were decreased and abnormal locations were observed in organoids treated with AMD3100. Neuronal axon outgrowth was also damaged in retinal organoids. Similarly, a decrease of ganglion cells, amacrine cells, and photoreceptors and the distribution of neural outgrowth was induced by AMD3100 treatment in zebrafish retina. However, abnormal photoreceptor ensembles induced by AMD3100 treatment in the organoids were not detected in zebrafish retina. Therefore, our study suggests that although retinal organoids might provide a reliable model for reproducing a retinal developmental model, there is a difference between the organoids and the retina in vivo.
Collapse
|
47
|
Hanna J, David LA, Touahri Y, Fleming T, Screaton RA, Schuurmans C. Beyond Genetics: The Role of Metabolism in Photoreceptor Survival, Development and Repair. Front Cell Dev Biol 2022; 10:887764. [PMID: 35663397 PMCID: PMC9157592 DOI: 10.3389/fcell.2022.887764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 12/11/2022] Open
Abstract
Vision commences in the retina with rod and cone photoreceptors that detect and convert light to electrical signals. The irreversible loss of photoreceptors due to neurodegenerative disease leads to visual impairment and blindness. Interventions now in development include transplanting photoreceptors, committed photoreceptor precursors, or retinal pigment epithelial (RPE) cells, with the latter protecting photoreceptors from dying. However, introducing exogenous human cells in a clinical setting faces both regulatory and supply chain hurdles. Recent work has shown that abnormalities in central cell metabolism pathways are an underlying feature of most neurodegenerative disorders, including those in the retina. Reversal of key metabolic alterations to drive retinal repair thus represents a novel strategy to treat vision loss based on cell regeneration. Here, we review the connection between photoreceptor degeneration and alterations in cell metabolism, along with new insights into how metabolic reprogramming drives both retinal development and repair following damage. The potential impact of metabolic reprogramming on retinal regeneration is also discussed, specifically in the context of how metabolic switches drive both retinal development and the activation of retinal glial cells known as Müller glia. Müller glia display latent regenerative properties in teleost fish, however, their capacity to regenerate new photoreceptors has been lost in mammals. Thus, re-activating the regenerative properties of Müller glia in mammals represents an exciting new area that integrates research into developmental cues, central metabolism, disease mechanisms, and glial cell biology. In addition, we discuss this work in relation to the latest insights gleaned from other tissues (brain, muscle) and regenerative species (zebrafish).
Collapse
Affiliation(s)
- Joseph Hanna
- Sunnybrook Research Institute, Biological Sciences, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Luke Ajay David
- Sunnybrook Research Institute, Biological Sciences, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Yacine Touahri
- Sunnybrook Research Institute, Biological Sciences, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Taylor Fleming
- Sunnybrook Research Institute, Biological Sciences, Toronto, ON, Canada
| | - Robert A. Screaton
- Sunnybrook Research Institute, Biological Sciences, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- *Correspondence: Carol Schuurmans,
| |
Collapse
|
48
|
Dou J, Liang S, Mohanty V, Miao Q, Huang Y, Liang Q, Cheng X, Kim S, Choi J, Li Y, Li L, Daher M, Basar R, Rezvani K, Chen R, Chen K. Bi-order multimodal integration of single-cell data. Genome Biol 2022; 23:112. [PMID: 35534898 PMCID: PMC9082907 DOI: 10.1186/s13059-022-02679-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 04/25/2022] [Indexed: 12/25/2022] Open
Abstract
Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provided approximate solutions. Here, we present a novel mathematical solution named bi-order canonical correlation analysis (bi-CCA), which extends the widely used CCA approach to iteratively align the rows and the columns between data matrices. Bi-CCA is generally applicable to combinations of any two single-cell modalities. Validations using co-assayed ground truth data and application to a CAR-NK study and a fetal muscle atlas demonstrate its capability in generating accurate multimodal co-embeddings and discovering cellular identity.
Collapse
Affiliation(s)
- Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Qingnan Liang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sangbae Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jongsu Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Li Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| |
Collapse
|
49
|
Dekens MPS, Fontinha BM, Gallach M, Pflügler S, Tessmar‐Raible K. Melanopsin elevates locomotor activity during the wake state of the diurnal zebrafish. EMBO Rep 2022; 23:e51528. [PMID: 35233929 PMCID: PMC9066073 DOI: 10.15252/embr.202051528] [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: 08/16/2020] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022] Open
Abstract
Mammalian and fish pineals play a key role in adapting behaviour to the ambient light conditions through the release of melatonin. In mice, light inhibits nocturnal locomotor activity via the non‐visual photoreceptor Melanopsin. In contrast to the extensively studied function of Melanopsin in the indirect regulation of the rodent pineal, its role in the intrinsically photosensitive zebrafish pineal has not been elucidated. Therefore, it is not evident if the light signalling mechanism is conserved between distant vertebrates, and how Melanopsin could affect diurnal behaviour. A double knockout of melanopsins (opn4.1‐opn4xb) was generated in the diurnal zebrafish, which manifests attenuated locomotor activity during the wake state. Transcriptome sequencing gave insight into pathways downstream of Melanopsin, implying that sustained repression of the melatonin pathway is required to elevate locomotor activity during the diurnal wake state. Moreover, we show that light induces locomotor activity during the diurnal wake state in an intensity‐dependent manner. These observations suggest a common Melanopsin‐driven mechanism between zebrafish and mammals, while the diurnal and nocturnal chronotypes are inversely regulated downstream of melatonin.
Collapse
Affiliation(s)
- Marcus P S Dekens
- Max Perutz Laboratory Centre for Molecular Biology University of Vienna and Medical University of Vienna Vienna Austria
| | - Bruno M Fontinha
- Max Perutz Laboratory Centre for Molecular Biology University of Vienna and Medical University of Vienna Vienna Austria
| | - Miguel Gallach
- Max Perutz Laboratory Centre for Molecular Biology University of Vienna and Medical University of Vienna Vienna Austria
- Max Perutz Laboratory Centre for Integrative Bioinformatics University of Vienna and Medical University of Vienna Vienna Austria
| | - Sandra Pflügler
- Max Perutz Laboratory Centre for Molecular Biology University of Vienna and Medical University of Vienna Vienna Austria
| | - Kristin Tessmar‐Raible
- Max Perutz Laboratory Centre for Molecular Biology University of Vienna and Medical University of Vienna Vienna Austria
- Research Platform “Marine Rhythms of Life” University of Vienna Vienna Austria
| |
Collapse
|
50
|
Carstensen MB, Medvetzky A, Weinberger A, Driever W, Gothilf Y, Rath MF. Genetic ablation of the Bsx homeodomain transcription factor in zebrafish: Impact on mature pineal gland morphology and circadian behavior. J Pineal Res 2022; 72:e12795. [PMID: 35249239 PMCID: PMC9285933 DOI: 10.1111/jpi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
The pineal gland is a neuroendocrine structure in the brain, which produces and secretes the hormone melatonin at nighttime and is considered a key element in the circadian clock system. Early morphogenesis of the gland is controlled by a number of transcription factors, some of which remain active in adult life. One of these is the brain-specific homeobox (Bsx), a highly conserved homeodomain transcription factor with a developmental role in the pineal gland of several species, including zebrafish, and regulatory roles in mature pinealocytes of the rat. To determine the role of Bsx in circadian biology, we here examined the effects of a bsx loss-of-function mutation on the pineal gland in adult zebrafish and on behavioral circadian rhythms in larvae. In pineal cell type-specific Gfp/Egfp reporter zebrafish lines, we did not detect fluorescence signals in the pineal area of homozygous (bsx-/- ) mutants. Interestingly, a nonpigmented area on the dorsal surface of the head above the gland, known as the pineal window, was pigmented in the homozygous mutants. Furthermore, a structure corresponding to the pineal gland was not detectable in the midline of the adult brain in histological sections analyzed by Nissl staining and S-antigen immunohistochemistry. Moreover, the levels of pineal transcripts were greatly reduced in bsx-/- mutants, as revealed by quantitative real-time polymerase chain reaction analysis. Notably, analysis of locomotor activity at the larval stage revealed altered circadian rhythmicity in the bsx mutants with periods and phases similar to wildtype, but severely reduced amplitudes in locomotor activity patterns. Thus, Bsx is essential for full development of the pineal gland, with its absence resulting in a phenotype of morphological pineal gland ablation and disrupted circadian behavior.
Collapse
Affiliation(s)
- Mikkel Bloss Carstensen
- Department of Neuroscience, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Adar Medvetzky
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Alon Weinberger
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Wolfgang Driever
- Developmental Biology, Institute Biology, Faculty of BiologyAlbert Ludwig University of FreiburgFreiburgGermany
| | - Yoav Gothilf
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| | - Martin Fredensborg Rath
- Department of Neuroscience, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|