101
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Capturing the third dimension in drug discovery: Spatially-resolved tools for interrogation of complex 3D cell models. Biotechnol Adv 2021; 55:107883. [PMID: 34875362 DOI: 10.1016/j.biotechadv.2021.107883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Advanced three-dimensional (3D) cell models have proven to be capable of depicting architectural and microenvironmental features of several tissues. By providing data of higher physiological and pathophysiological relevance, 3D cell models have been contributing to a better understanding of human development, pathology onset and progression mechanisms, as well as for 3D cell-based assays for drug discovery. Nonetheless, the characterization and interrogation of these tissue-like structures pose major challenges on the conventional analytical methods, pushing the development of spatially-resolved technologies. Herein, we review recent advances and pioneering technologies suitable for the interrogation of multicellular 3D models, while capable of retaining biological spatial information. We focused on imaging technologies and omics tools, namely transcriptomics, proteomics and metabolomics. The advantages and shortcomings of these novel methodologies are discussed, alongside the opportunities to intertwine data from the different tools.
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102
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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103
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Bharathan SP, Ferrario A, Stepanian K, Fernandez GE, Reid MW, Kim JS, Hutchens C, Harutyunyan N, Marks C, Thornton ME, Grubbs BH, Cobrinik D, Aparicio JG, Nagiel A. Characterization and staging of outer plexiform layer development in human retina and retinal organoids. Development 2021; 148:272710. [PMID: 34738615 DOI: 10.1242/dev.199551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/26/2021] [Indexed: 11/20/2022]
Abstract
The development of the first synapse of the visual system between photoreceptors and bipolar cells in the outer plexiform layer (OPL) of the human retina is critical for visual processing but poorly understood. By studying the maturation state and spatial organization of photoreceptors, depolarizing bipolar cells, and horizontal cells in the human fetal retina, we establish a pseudo-temporal staging system for OPL development that we term OPL-Stages 0 to 4. This was validated through quantification of increasingly precise subcellular localization of Bassoon to the OPL with each stage (p<0.0001). By applying these OPL staging criteria to human retinal organoids (HROs) derived from human embryonic and induced pluripotent stem cells, we observed comparable maturation from OPL-Stage 0 at day 100 in culture up to OPL-Stage 3 by day 160. Quantification of presynaptic protein localization confirmed progression from OPL-Stage 0 to 3 (p<0.0001). Overall, this study defines stages of human OPL development through mid-gestation and establishes HROs as a model system that recapitulates key aspects of human photoreceptor-bipolar cell synaptogenesis in vitro.
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Affiliation(s)
- Sumitha Prameela Bharathan
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Angela Ferrario
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Kayla Stepanian
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - G Esteban Fernandez
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Mark W Reid
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Justin S Kim
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Chloe Hutchens
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Narine Harutyunyan
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Carolyn Marks
- Core Center of Excellence in Nano Imaging, University of Southern California, Los Angeles, CA, USA
| | - Matthew E Thornton
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brendan H Grubbs
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Cobrinik
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jennifer G Aparicio
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Aaron Nagiel
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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104
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Yi SA, Zhang Y, Rathnam C, Pongkulapa T, Lee KB. Bioengineering Approaches for the Advanced Organoid Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007949. [PMID: 34561899 PMCID: PMC8682947 DOI: 10.1002/adma.202007949] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/09/2021] [Indexed: 05/09/2023]
Abstract
Recent advances in 3D cell culture technology have enabled scientists to generate stem cell derived organoids that recapitulate the structural and functional characteristics of native organs. Current organoid technologies have been striding toward identifying the essential factors for controlling the processes involved in organoid development, including physical cues and biochemical signaling. There is a growing demand for engineering dynamic niches characterized by conditions that resemble in vivo organogenesis to generate reproducible and reliable organoids for various applications. Innovative biomaterial-based and advanced engineering-based approaches have been incorporated into conventional organoid culture methods to facilitate the development of organoid research. The recent advances in organoid engineering, including extracellular matrices and genetic modulation, are comprehensively summarized to pinpoint the parameters critical for organ-specific patterning. Moreover, perspective trends in developing tunable organoids in response to exogenous and endogenous cues are discussed for next-generation developmental studies, disease modeling, and therapeutics.
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Affiliation(s)
- Sang Ah Yi
- Epigenome Dynamics Control Research Center, School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Yixiao Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Christopher Rathnam
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
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105
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Zhang X, Wang W, Jin ZB. Retinal organoids as models for development and diseases. CELL REGENERATION (LONDON, ENGLAND) 2021; 10:33. [PMID: 34719743 PMCID: PMC8557999 DOI: 10.1186/s13619-021-00097-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022]
Abstract
The evolution of pluripotent stem cell-derived retinal organoids (ROs) has brought remarkable opportunities for developmental studies while also presenting new therapeutic avenues for retinal diseases. With a clear understanding of how well these models mimic native retinas, such preclinical models may be crucial tools that are widely used for the more efficient translation of studies into novel treatment strategies for retinal diseases. Genetic modifications or patient-derived ROs can allow these models to simulate the physical microenvironments of the actual disease process. However, we are currently at the beginning of the three-dimensional (3D) RO era, and a general quantitative technology for analyzing ROs derived from numerous differentiation protocols is still missing. Continued efforts to improve the efficiency and stability of differentiation, as well as understanding the disparity between the artificial retina and the native retina and advancing the current treatment strategies, will be essential in ensuring that these scientific advances can benefit patients with retinal disease. Herein, we briefly discuss RO differentiation protocols, the current applications of RO as a disease model and the treatments for retinal diseases by using RO modeling, to have a clear view of the role of current ROs in retinal development and diseases.
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Affiliation(s)
- Xiao Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Wen Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China.
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106
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Swamy VS, Fufa TD, Hufnagel RB, McGaughey DM. Building the mega single-cell transcriptome ocular meta-atlas. Gigascience 2021; 10:giab061. [PMID: 34651173 PMCID: PMC8514335 DOI: 10.1093/gigascience/giab061] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/27/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The development of highly scalable single-cell transcriptome technology has resulted in the creation of thousands of datasets, >30 in the retina alone. Analyzing the transcriptomes between different projects is highly desirable because this would allow for better assessment of which biological effects are consistent across independent studies. However it is difficult to compare and contrast data across different projects because there are substantial batch effects from computational processing, single-cell technology utilized, and the natural biological variation. While many single-cell transcriptome-specific batch correction methods purport to remove the technical noise, it is difficult to ascertain which method functions best. RESULTS We developed a lightweight R package (scPOP, single-cell Pick Optimal Parameters) that brings in batch integration methods and uses a simple heuristic to balance batch merging and cell type/cluster purity. We use this package along with a Snakefile-based workflow system to demonstrate how to optimally merge 766,615 cells from 33 retina datsets and 3 species to create a massive ocular single-cell transcriptome meta-atlas. CONCLUSIONS This provides a model for how to efficiently create meta-atlases for tissues and cells of interest.
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Affiliation(s)
- Vinay S Swamy
- Bioinformatics Group, Ophthalmic Genetics & Visual Function Branch, National Eye Institute, National Institutes of Health, 20892, Bethesda, Maryland, USA
| | - Temesgen D Fufa
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, 20892, Bethesda, Maryland, USA
| | - Robert B Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, 20892, Bethesda, Maryland, USA
| | - David M McGaughey
- Bioinformatics Group, Ophthalmic Genetics & Visual Function Branch, National Eye Institute, National Institutes of Health, 20892, Bethesda, Maryland, USA
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107
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Gabriel E, Albanna W, Pasquini G, Ramani A, Josipovic N, Mariappan A, Schinzel F, Karch CM, Bao G, Gottardo M, Suren AA, Hescheler J, Nagel-Wolfrum K, Persico V, Rizzoli SO, Altmüller J, Riparbelli MG, Callaini G, Goureau O, Papantonis A, Busskamp V, Schneider T, Gopalakrishnan J. Human brain organoids assemble functionally integrated bilateral optic vesicles. Cell Stem Cell 2021; 28:1740-1757.e8. [PMID: 34407456 DOI: 10.1016/j.stem.2021.07.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/23/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
During embryogenesis, optic vesicles develop from the diencephalon via a multistep process of organogenesis. Using induced pluripotent stem cell (iPSC)-derived human brain organoids, we attempted to simplify the complexities and demonstrate formation of forebrain-associated bilateral optic vesicles, cellular diversity, and functionality. Around day 30, brain organoids attempt to assemble optic vesicles, which develop progressively as visible structures within 60 days. These optic vesicle-containing brain organoids (OVB-organoids) constitute a developing optic vesicle's cellular components, including primitive corneal epithelial and lens-like cells, retinal pigment epithelia, retinal progenitor cells, axon-like projections, and electrically active neuronal networks. OVB-organoids also display synapsin-1, CTIP-positive myelinated cortical neurons, and microglia. Interestingly, various light intensities could trigger photosensitive activity of OVB-organoids, and light sensitivities could be reset after transient photobleaching. Thus, brain organoids have the intrinsic ability to self-organize forebrain-associated primitive sensory structures in a topographically restricted manner and can allow interorgan interaction studies within a single organoid.
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Affiliation(s)
- Elke Gabriel
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Walid Albanna
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; Department of Neurosurgery, RWTH Aachen University, 52074 Aachen, Germany
| | - Giovanni Pasquini
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Anand Ramani
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, 37075 Göttingen, Germany; Center for molecular medicine, Cologne, Universität zu Köln, 50931 Köln, Germany
| | - Aruljothi Mariappan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Friedrich Schinzel
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO 63116, USA
| | - Guobin Bao
- Institute of Neurophysiology and Cellular Biophysics, University Medicine Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Marco Gottardo
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Ata Alp Suren
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Veronica Persico
- Department of Life Sciences and Medical Biotechnology University of Siena, Siena 53100, Italy
| | - Silvio O Rizzoli
- Institute of Neurophysiology and Cellular Biophysics, University Medicine Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Universität zu Köln, Köln, Germany; Center for molecular medicine, Cologne, Universität zu Köln, 50931 Köln, Germany
| | | | - Giuliano Callaini
- Department of Life Sciences and Medical Biotechnology University of Siena, Siena 53100, Italy
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Argyris Papantonis
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, 37075 Göttingen, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Toni Schneider
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany.
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108
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Afanasyeva TAV, Corral-Serrano JC, Garanto A, Roepman R, Cheetham ME, Collin RWJ. A look into retinal organoids: methods, analytical techniques, and applications. Cell Mol Life Sci 2021; 78:6505-6532. [PMID: 34420069 PMCID: PMC8558279 DOI: 10.1007/s00018-021-03917-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
Inherited retinal diseases (IRDs) cause progressive loss of light-sensitive photoreceptors in the eye and can lead to blindness. Gene-based therapies for IRDs have shown remarkable progress in the past decade, but the vast majority of forms remain untreatable. In the era of personalised medicine, induced pluripotent stem cells (iPSCs) emerge as a valuable system for cell replacement and to model IRD because they retain the specific patient genome and can differentiate into any adult cell type. Three-dimensional (3D) iPSCs-derived retina-like tissue called retinal organoid contains all major retina-specific cell types: amacrine, bipolar, horizontal, retinal ganglion cells, Müller glia, as well as rod and cone photoreceptors. Here, we describe the main applications of retinal organoids and provide a comprehensive overview of the state-of-art analysis methods that apply to this model system. Finally, we will discuss the outlook for improvements that would bring the cellular model a step closer to become an established system in research and treatment development of IRDs.
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Affiliation(s)
- Tess A V Afanasyeva
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | | | - Alejandro Garanto
- Department of Pediatrics, Amalia Children's Hospital and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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109
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Shiau F, Ruzycki PA, Clark BS. A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq. Dev Biol 2021; 478:41-58. [PMID: 34146533 PMCID: PMC8386138 DOI: 10.1016/j.ydbio.2021.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
Recent advances in high throughput single-cell RNA sequencing (scRNA-seq) technology have enabled the simultaneous transcriptomic profiling of thousands of individual cells in a single experiment. To investigate the intrinsic process of retinal development, researchers have leveraged this technology to quantify gene expression in retinal cells across development, in multiple species, and from numerous important models of human disease. In this review, we summarize recent applications of scRNA-seq and discuss how these datasets have complemented and advanced our understanding of retinal progenitor cell competence, cell fate specification, and differentiation. Finally, we also highlight the outstanding questions in the field that advances in single-cell data generation and analysis will soon be able to answer.
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Affiliation(s)
- Fion Shiau
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A Ruzycki
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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110
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Guy B, Zhang JS, Duncan LH, Johnston RJ. Human neural organoids: Models for developmental neurobiology and disease. Dev Biol 2021; 478:102-121. [PMID: 34181916 PMCID: PMC8364509 DOI: 10.1016/j.ydbio.2021.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 12/25/2022]
Abstract
Human organoids stand at the forefront of basic and translational research, providing experimentally tractable systems to study human development and disease. These stem cell-derived, in vitro cultures can generate a multitude of tissue and organ types, including distinct brain regions and sensory systems. Neural organoid systems have provided fundamental insights into molecular mechanisms governing cell fate specification and neural circuit assembly and serve as promising tools for drug discovery and understanding disease pathogenesis. In this review, we discuss several human neural organoid systems, how they are generated, advances in 3D imaging and bioengineering, and the impact of organoid studies on our understanding of the human nervous system.
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Affiliation(s)
- Brian Guy
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Jingliang Simon Zhang
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Leighton H Duncan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA.
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111
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Retinal Organoid Technology: Where Are We Now? Int J Mol Sci 2021; 22:ijms221910244. [PMID: 34638582 PMCID: PMC8549701 DOI: 10.3390/ijms221910244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022] Open
Abstract
It is difficult to regenerate mammalian retinal cells once the adult retina is damaged, and current clinical approaches to retinal damages are very limited. The introduction of the retinal organoid technique empowers researchers to study the molecular mechanisms controlling retinal development, explore the pathogenesis of retinal diseases, develop novel treatment options, and pursue cell/tissue transplantation under a certain genetic background. Here, we revisit the historical background of retinal organoid technology, categorize current methods of organoid induction, and outline the obstacles and potential solutions to next-generation retinal organoids. Meanwhile, we recapitulate recent research progress in cell/tissue transplantation to treat retinal diseases, and discuss the pros and cons of transplanting single-cell suspension versus retinal organoid sheet for cell therapies.
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112
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Eldred KC, Reh TA. Human retinal model systems: Strengths, weaknesses, and future directions. Dev Biol 2021; 480:114-122. [PMID: 34529997 DOI: 10.1016/j.ydbio.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The retina is a complex neuronal structure that converts light energy into visual perception. Many specialized aspects of the primate retina, including a cone rich macula for high acuity vision, ocular size, and cell type diversity are not found in other animal models. In addition, the unique morphologies and distinct laminar positions of cell types found in the retina make this model system ideal for the study of neuronal cell fate specification. Many key early events of human retinal development are inaccessible to investigation as they occur during gestation. For these reasons, it has been necessary to develop retinal model systems to gain insight into human-specific retinal development and disease. Recent advances in culturing retinal tissue have generated new systems for retinal research and have moved us closer to generating effective regenerative therapies for vision loss. Here, we describe the strengths, weaknesses, and future directions for different human retinal model systems including dissociated primary tissue, explanted primary tissue, retinospheres, and stem cell-derived retinal organoids.
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Affiliation(s)
- Kiara C Eldred
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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113
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Xue Y, Seiler MJ, Tang WC, Wang JY, Delgado J, McLelland BT, Nistor G, Keirstead HS, Browne AW. Retinal organoids on-a-chip: a micro-millifluidic bioreactor for long-term organoid maintenance. LAB ON A CHIP 2021; 21:3361-3377. [PMID: 34236056 PMCID: PMC8387452 DOI: 10.1039/d1lc00011j] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Retinal degeneration is a leading cause of vision impairment and blindness worldwide and medical care for advanced disease does not exist. Stem cell-derived retinal organoids (RtOgs) became an emerging tool for tissue replacement therapy. However, existing RtOg production methods are highly heterogeneous. Controlled and predictable methodology and tools are needed to standardize RtOg production and maintenance. In this study, we designed a shear stress-free micro-millifluidic bioreactor for nearly labor-free retinal organoid maintenance. We used a stereolithography (SLA) 3D printer to fabricate a mold from which Polydimethylsiloxane (PDMS) was cast. We optimized the chip design using in silico simulations and in vitro evaluation to optimize mass transfer efficiency and concentration uniformity in each culture chamber. We successfully cultured RtOgs at three different differentiation stages (day 41, 88, and 128) on an optimized bioreactor chip for more than 1 month. We used different quantitative and qualitative techniques to fully characterize the RtOgs produced by static dish culture and bioreactor culture methods. By analyzing the results from phase contrast microscopy, single-cell RNA sequencing (scRNA seq), quantitative polymerase chain reaction (qPCR), immunohistology, and electron microscopy, we found that bioreactor-cultured RtOgs developed cell types and morphology comparable to static cultured ones and exhibited similar retinal genes expression levels. We also evaluated the metabolic activity of RtOgs in both groups using fluorescence lifetime imaging (FLIM), and found that the outer surface region of bioreactor cultured RtOgs had a comparable free/bound NADH ratio and overall lower long lifetime species (LLS) ratio than static cultured RtOgs during imaging. To summarize, we validated an automated micro-millifluidic device with significantly reduced shear stress to produce RtOgs of comparable quality to those maintained in conventional static culture.
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Affiliation(s)
- Yuntian Xue
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
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114
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Belote RL, Le D, Maynard A, Lang UE, Sinclair A, Lohman BK, Planells-Palop V, Baskin L, Tward AD, Darmanis S, Judson-Torres RL. Human melanocyte development and melanoma dedifferentiation at single-cell resolution. Nat Cell Biol 2021; 23:1035-1047. [PMID: 34475532 DOI: 10.1038/s41556-021-00740-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/18/2021] [Indexed: 12/13/2022]
Abstract
In humans, epidermal melanocytes are responsible for skin pigmentation, defence against ultraviolet radiation and the deadliest common skin cancer, melanoma. Although there is substantial overlap in melanocyte development pathways between different model organisms, species-dependent differences are frequent and the conservation of these processes in human skin remains unresolved. Here, we used a single-cell enrichment and RNA-sequencing pipeline to study human epidermal melanocytes directly from the skin, capturing transcriptomes across different anatomical sites, developmental age, sexes and multiple skin tones. We uncovered subpopulations of melanocytes that exhibit anatomical site-specific enrichment that occurs during gestation and persists through adulthood. The transcriptional signature of the volar-enriched subpopulation is retained in acral melanomas. Furthermore, we identified human melanocyte differentiation transcriptional programs that are distinct from gene signatures generated from model systems. Finally, we used these programs to define patterns of dedifferentiation that are predictive of melanoma prognosis and response to immune checkpoint inhibitor therapy.
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Affiliation(s)
- Rachel L Belote
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Daniel Le
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech Inc, South San Francisco, CA, USA
| | - Ashley Maynard
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ursula E Lang
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Adriane Sinclair
- Department of Urology and Division of Pediatric Urology, University of California, San Francisco, CA, USA
| | - Brian K Lohman
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Vicente Planells-Palop
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Laurence Baskin
- Department of Urology and Division of Pediatric Urology, University of California, San Francisco, CA, USA
| | - Aaron D Tward
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, CA, USA
| | - Spyros Darmanis
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech Inc, South San Francisco, CA, USA.
| | - Robert L Judson-Torres
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA.
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA.
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115
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Plössl K, Milenkovic A, Weber BHF. Challenges and opportunities for modeling monogenic and complex disorders of the human retina via induced pluripotent stem cell technology. MED GENET-BERLIN 2021; 33:221-227. [PMID: 38835692 PMCID: PMC11007631 DOI: 10.1515/medgen-2021-2092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 06/06/2024]
Abstract
The human retina is a highly structured and complex neurosensory tissue central to perceiving and processing visual signals. In a healthy individual, the close interplay between the neuronal retina, the adjacent retinal pigment epithelium and the underlying blood supply, the choriocapillaris, is critical for maintaining eyesight over a lifetime. An impairment of this delicate and metabolically highly active system, caused by genetic alteration, environmental impact or both, results in a multitude of pathological phenotypes of the retina. Understanding and treating these disease processes are motivated by a marked medical need in young as well as in older patients. While naturally occurring or gene-manipulated animal models have been used successfully in ophthalmological research for many years, recent advances in induced pluripotent stem cell technology have opened up new avenues to generate patient-derived retinal model systems. Here, we explore to what extent these cellular models can be useful to mirror human pathologies in vitro ultimately allowing to analyze disease mechanisms and testing treatment options in the cell type of interest on an individual patient-specific genetic background.
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Affiliation(s)
- Karolina Plössl
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Milenkovic
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
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116
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Regulatory Mechanisms of Retinal Photoreceptors Development at Single Cell Resolution. Int J Mol Sci 2021; 22:ijms22168357. [PMID: 34445064 PMCID: PMC8395061 DOI: 10.3390/ijms22168357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/18/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Photoreceptors are critical components of the retina and play a role in the first step of the conversion of light to electric signals. With the discovery of the intrinsically photosensitive retinal ganglion cells, which regulate non-image-forming visual processes, our knowledge of the photosensitive cell family in the retina has deepened. Photoreceptor development is regulated by specific genes and proteins and involves a series of molecular processes including DNA transcription, post-transcriptional modification, protein translation, and post-translational modification. Single-cell sequencing is a promising technology for the study of photoreceptor development. This review presents an overview of the types of human photoreceptors, summarizes recent discoveries in the regulatory mechanisms underlying their development at single-cell resolution, and outlines the prospects in this field.
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117
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Abstract
It has been known for over a century that the basic organization of the retina is conserved across vertebrates. It has been equally clear that retinal cells can be classified into numerous types, but only recently have methods been devised to explore this diversity in unbiased, scalable, and comprehensive ways. Advances in high-throughput single-cell RNA-sequencing (scRNA-seq) have played a pivotal role in this effort. In this article, we outline the experimental and computational components of scRNA-seq and review studies that have used them to generate retinal atlases of cell types in several vertebrate species. These atlases have enabled studies of retinal development, responses of retinal cells to injury, expression patterns of genes implicated in retinal disease, and the evolution of cell types. Recently, the inquiry has expanded to include the entire eye and visual centers in the brain. These studies have enhanced our understanding of retinal function and dysfunction and provided tools and insights for exploring neural diversity throughout the brain. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; and California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, USA;
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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118
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Mullin NK, Voigt AP, Cooke JA, Bohrer LR, Burnight ER, Stone EM, Mullins RF, Tucker BA. Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease. Prog Retin Eye Res 2021; 83:100918. [PMID: 33130253 PMCID: PMC8559964 DOI: 10.1016/j.preteyeres.2020.100918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of inherited retinal disease has benefited immensely from molecular genetic analysis over the past several decades. New technologies that allow for increasingly detailed examination of a patient's DNA have expanded the catalog of genes and specific variants that cause retinal disease. In turn, the identification of pathogenic variants has allowed the development of gene therapies and low-cost, clinically focused genetic testing. Despite this progress, a relatively large fraction (at least 20%) of patients with clinical features suggestive of an inherited retinal disease still do not have a molecular diagnosis today. Variants that are not obviously disruptive to the codon sequence of exons can be difficult to distinguish from the background of benign human genetic variations. Some of these variants exert their pathogenic effect not by altering the primary amino acid sequence, but by modulating gene expression, isoform splicing, or other transcript-level mechanisms. While not discoverable by DNA sequencing methods alone, these variants are excellent targets for studies of the retinal transcriptome. In this review, we present an overview of the current state of pathogenic variant discovery in retinal disease and identify some of the remaining barriers. We also explore the utility of new technologies, specifically patient-derived induced pluripotent stem cell (iPSC)-based modeling, in further expanding the catalog of disease-causing variants using transcriptome-focused methods. Finally, we outline bioinformatic analysis techniques that will allow this new method of variant discovery in retinal disease. As the knowledge gleaned from previous technologies is informing targets for therapies today, we believe that integrating new technologies, such as iPSC-based modeling, into the molecular diagnosis pipeline will enable a new wave of variant discovery and expanded treatment of inherited retinal disease.
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Affiliation(s)
- Nathaniel K Mullin
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Andrew P Voigt
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jessica A Cooke
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Laura R Bohrer
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Erin R Burnight
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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119
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Wagstaff EL, Heredero Berzal A, Boon CJF, Quinn PMJ, ten Asbroek ALMA, Bergen AA. The Role of Small Molecules and Their Effect on the Molecular Mechanisms of Early Retinal Organoid Development. Int J Mol Sci 2021; 22:7081. [PMID: 34209272 PMCID: PMC8268497 DOI: 10.3390/ijms22137081] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 12/12/2022] Open
Abstract
Early in vivo embryonic retinal development is a well-documented and evolutionary conserved process. The specification towards eye development is temporally controlled by consecutive activation or inhibition of multiple key signaling pathways, such as the Wnt and hedgehog signaling pathways. Recently, with the use of retinal organoids, researchers aim to manipulate these pathways to achieve better human representative models for retinal development and disease. To achieve this, a plethora of different small molecules and signaling factors have been used at various time points and concentrations in retinal organoid differentiations, with varying success. Additions differ from protocol to protocol, but their usefulness or efficiency has not yet been systematically reviewed. Interestingly, many of these small molecules affect the same and/or multiple pathways, leading to reduced reproducibility and high variability between studies. In this review, we make an inventory of the key signaling pathways involved in early retinogenesis and their effect on the development of the early retina in vitro. Further, we provide a comprehensive overview of the small molecules and signaling factors that are added to retinal organoid differentiation protocols, documenting the molecular and functional effects of these additions. Lastly, we comparatively evaluate several of these factors using our established retinal organoid methodology.
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Affiliation(s)
- Ellie L. Wagstaff
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands;
| | - Andrea Heredero Berzal
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands; (A.H.B.); (C.J.F.B.)
| | - Camiel J. F. Boon
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands; (A.H.B.); (C.J.F.B.)
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Peter M. J. Quinn
- Jonas Children’s Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology & Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center—New York-Presbyterian Hospital, New York, NY 10032, USA;
| | | | - Arthur A. Bergen
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands;
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam (UvA), 1105 AZ Amsterdam, The Netherlands; (A.H.B.); (C.J.F.B.)
- Netherlands Institute for Neuroscience (NIN-KNAW), 1105 BA Amsterdam, The Netherlands
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120
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Louey A, Hernández D, Pébay A, Daniszewski M. Automation of Organoid Cultures: Current Protocols and Applications. SLAS DISCOVERY 2021; 26:1138-1147. [PMID: 34167363 DOI: 10.1177/24725552211024547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GRAPHICAL ABSTRACT [Formula: see text].
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Affiliation(s)
- Alexandra Louey
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia.,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
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121
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Retinal Ganglion Cell Transplantation: Approaches for Overcoming Challenges to Functional Integration. Cells 2021; 10:cells10061426. [PMID: 34200991 PMCID: PMC8228580 DOI: 10.3390/cells10061426] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
As part of the central nervous system, mammalian retinal ganglion cells (RGCs) lack significant regenerative capacity. Glaucoma causes progressive and irreversible vision loss by damaging RGCs and their axons, which compose the optic nerve. To functionally restore vision, lost RGCs must be replaced. Despite tremendous advancements in experimental models of optic neuropathy that have elucidated pathways to induce endogenous RGC neuroprotection and axon regeneration, obstacles to achieving functional visual recovery through exogenous RGC transplantation remain. Key challenges include poor graft survival, low donor neuron localization to the host retina, and inadequate dendritogenesis and synaptogenesis with afferent amacrine and bipolar cells. In this review, we summarize the current state of experimental RGC transplantation, and we propose a set of standard approaches to quantifying and reporting experimental outcomes in order to guide a collective effort to advance the field toward functional RGC replacement and optic nerve regeneration.
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122
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Human Pluripotent Stem-Cell-Derived Models as a Missing Link in Drug Discovery and Development. Pharmaceuticals (Basel) 2021; 14:ph14060525. [PMID: 34070895 PMCID: PMC8230131 DOI: 10.3390/ph14060525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs), have the potential to accelerate the drug discovery and development process. In this review, by analyzing each stage of the drug discovery and development process, we identified the active role of hPSC-derived in vitro models in phenotypic screening, target-based screening, target validation, toxicology evaluation, precision medicine, clinical trial in a dish, and post-clinical studies. Patient-derived or genome-edited PSCs can generate valid in vitro models for dissecting disease mechanisms, discovering novel drug targets, screening drug candidates, and preclinically and post-clinically evaluating drug safety and efficacy. With the advances in modern biotechnologies and developmental biology, hPSC-derived in vitro models will hopefully improve the cost-effectiveness and the success rate of drug discovery and development.
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123
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Fligor CM, Lavekar SS, Harkin J, Shields PK, VanderWall KB, Huang KC, Gomes C, Meyer JS. Extension of retinofugal projections in an assembled model of human pluripotent stem cell-derived organoids. Stem Cell Reports 2021; 16:2228-2241. [PMID: 34115986 PMCID: PMC8452489 DOI: 10.1016/j.stemcr.2021.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 01/31/2023] Open
Abstract
The development of the visual system involves the coordination of spatial and temporal events to specify the organization of varied cell types, including the elongation of axons from retinal ganglion cells (RGCs) to post-synaptic targets in the brain. Retinal organoids recapitulate many features of retinal development, yet have lacked downstream targets into which RGC axons extend, limiting the ability to model projections of the human visual system. To address these issues, retinal organoids were generated and organized into an in vitro assembloid model of the visual system with cortical and thalamic organoids. RGCs responded to environmental cues and extended axons deep into assembloids, modeling the projections of the visual system. In addition, RGC survival was enhanced in long-term assembloids, overcoming prior limitations of retinal organoids in which RGCs are lost. Overall, these approaches will facilitate studies of human visual system development, as well as diseases or injuries to this critical pathway. Human stem cell-derived RGC axons respond to target-derived cues Assembloids were generated between retinal, thalamic, and cortical organoids Retinofugal projections robustly extend toward thalamic targets
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Affiliation(s)
- Clarisse M Fligor
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Sailee S Lavekar
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Jade Harkin
- Interdisciplinary Biomedical Research Gateway Program, Indiana University School of Medicine, Indianapolis IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis IN, USA
| | - Priya K Shields
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Kirstin B VanderWall
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Kang-Chieh Huang
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis IN, USA
| | - Cátia Gomes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis IN, USA
| | - Jason S Meyer
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis IN, USA; Department of Ophthalmology, Indiana University School of Medicine, Indianapolis IN, USA.
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124
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Voigt AP, Mullin NK, Whitmore SS, DeLuca AP, Burnight ER, Liu X, Tucker BA, Scheetz TE, Stone EM, Mullins RF. Human photoreceptor cells from different macular subregions have distinct transcriptional profiles. Hum Mol Genet 2021; 30:1543-1558. [PMID: 34014299 PMCID: PMC8330894 DOI: 10.1093/hmg/ddab140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022] Open
Abstract
The human neural retina is a light sensitive tissue with remarkable spatial and cellular organization. Compared with the periphery, the central retina contains more densely packed cone photoreceptor cells with unique morphologies and synaptic wiring. Some regions of the central retina exhibit selective degeneration or preservation in response to retinal disease and the basis for this variation is unknown. In this study, we used both bulk and single-cell RNA sequencing to compare gene expression within concentric regions of the central retina. We identified unique gene expression patterns of foveal cone photoreceptor cells, including many foveal-enriched transcription factors. In addition, we found that the genes RORB1, PPFIA1 and KCNAB2 are differentially spliced in the foveal, parafoveal and macular regions. These results provide a highly detailed spatial characterization of the retinal transcriptome and highlight unique molecular features of different retinal regions.
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Affiliation(s)
- Andrew P Voigt
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Nathaniel K Mullin
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Adam P DeLuca
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Erin R Burnight
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Xiuying Liu
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, the University of Iowa, Iowa City, IA 52242, USA
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125
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Cowan CS, Renner M, De Gennaro M, Gross-Scherf B, Goldblum D, Hou Y, Munz M, Rodrigues TM, Krol J, Szikra T, Cuttat R, Waldt A, Papasaikas P, Diggelmann R, Patino-Alvarez CP, Galliker P, Spirig SE, Pavlinic D, Gerber-Hollbach N, Schuierer S, Srdanovic A, Balogh M, Panero R, Kusnyerik A, Szabo A, Stadler MB, Orgül S, Picelli S, Hasler PW, Hierlemann A, Scholl HPN, Roma G, Nigsch F, Roska B. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution. Cell 2021; 182:1623-1640.e34. [PMID: 32946783 PMCID: PMC7505495 DOI: 10.1016/j.cell.2020.08.013] [Citation(s) in RCA: 309] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/14/2020] [Accepted: 08/06/2020] [Indexed: 01/05/2023]
Abstract
Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable "developed" state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas.
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Affiliation(s)
- Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Martina De Gennaro
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Brigitte Gross-Scherf
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - David Goldblum
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Yanyan Hou
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Martin Munz
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tiago M Rodrigues
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Jacek Krol
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tamas Szikra
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Rachel Cuttat
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Annick Waldt
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Roland Diggelmann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, 4058 Basel, Switzerland
| | - Claudia P Patino-Alvarez
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Patricia Galliker
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Stefan E Spirig
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Dinko Pavlinic
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | | | - Sven Schuierer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Aldin Srdanovic
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marton Balogh
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Riccardo Panero
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Akos Kusnyerik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, Semmelweis University, 1085 Budapest, Hungary
| | - Arnold Szabo
- Department of Anatomy, Histology and Embryology, Semmelweis University, 1085 Budapest, Hungary
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Selim Orgül
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Pascal W Hasler
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, 4058 Basel, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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126
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Zhang X, Mandric I, Nguyen KH, Nguyen TTT, Pellegrini M, Grove JCR, Barnes S, Yang XJ. Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development. Front Cell Dev Biol 2021; 9:653305. [PMID: 34055784 PMCID: PMC8155690 DOI: 10.3389/fcell.2021.653305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES cell-derived retinal organoids. Single cell transcriptome analyses identify three states of proliferating retinal progenitors: pre-neurogenic, neurogenic, and cell cycle-exiting progenitors. Each shows different expression profile of bHLH factors. The cell cycle-exiting progenitors feed into a postmitotic heterozygous neuroblast pool that gives rise to early born neuronal lineages. Elevating ATOH7 or Neurog2 expression accelerates the transition from the pre-neurogenic to the neurogenic state, and expands the exiting progenitor and neuroblast populations. In addition, ATOH7 and Neurog2 significantly, yet differentially, enhance retinal ganglion cell and cone photoreceptor production. Moreover, single cell transcriptome analyses reveal that ATOH7 and Neurog2 each assert positive autoregulation, and both suppress key bHLH factors associated with the pre-neurogenic and states and elevate bHLH factors expressed by exiting progenitors and differentiating neuroblasts. This study thus provides novel insight regarding how ATOH7 and Neurog2 impact human retinal progenitor behaviors and neuroblast fate choices.
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Affiliation(s)
- Xiangmei Zhang
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Igor Mandric
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin H Nguyen
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thao T T Nguyen
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - James C R Grove
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Steven Barnes
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Doheny Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xian-Jie Yang
- Department of Ophthalmology, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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127
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Collin J, Queen R, Zerti D, Steel DH, Bowen C, Parulekar M, Lako M. Dissecting the Transcriptional and Chromatin Accessibility Heterogeneity of Proliferating Cone Precursors in Human Retinoblastoma Tumors by Single Cell Sequencing-Opening Pathways to New Therapeutic Strategies? Invest Ophthalmol Vis Sci 2021; 62:18. [PMID: 34003213 PMCID: PMC8132003 DOI: 10.1167/iovs.62.6.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/18/2021] [Indexed: 01/03/2023] Open
Abstract
Purpose Retinoblastoma (Rb) is a malignant neoplasm arising during retinal development from mutations in the RB1 gene. Loss or inactivation of both copies of RB1 results in initiation of retinoblastoma tumors; however, additional genetic changes are needed for the continued growth and spread of the tumor. Ex vivo research has shown that in humans, retinoblastoma may initiate from RB1-depleted cone precursors. Notwithstanding, it has not been possible to assess the full spectrum of clonal types within the tumor itself in vivo and the molecular changes occurring at the cells of origin, enabling their malignant conversion. To overcome these challenges, we have performed the first single cell (sc) RNA- and ATAC-Seq analyses of primary tumor tissues, enabling us to dissect the transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human Rb tumors. Methods Two Rb tumors each characterized by two pathogenic RB1 mutations were dissociated to single cells and subjected to scRNA-Seq and scATAC-Seq using the 10× Genomics platform. In addition, nine human embryonic and fetal retina samples were dissociated to single cells and subjected to scRNA- and ATAC-Seq analyses. The scRNA- and ATAC-Seq data were embedded using Uniform Manifold Approximation and Projection and clustered with Seurat graph-based clustering. Integrated scATAC-Seq analysis of Rb tumors and human embryonic/fetal retina samples was performed to identify Rb cone enriched subclusters. Pseudo time analysis of proliferating cones in the Rb samples was performed with Monocle. Ingenuity Pathway Analysis was used to identify the signaling pathway and upstream regulators in the Rb cone-enriched subclusters. Results Our single cell analyses revealed the predominant presence of cone precursors at different stages of the cell cycle in the Rb tumors and among those identified the G2/M subset as the cell type of origin. scATAC-Seq analysis identified two Rb enriched cone subclusters, each characterized by activation of different upstream regulators and signaling pathways, enabling proliferating cone precursors to escape cell cycle arrest and/or apoptosis. Conclusions Our study provides evidence of Rb tumor heterogeneity and defines molecular pathways that can be targeted to define new treatment strategies.
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Affiliation(s)
- Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Darin Zerti
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
| | - David H Steel
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Claire Bowen
- Birmingham Women's and Children NHS Foundation Trust, Birmingham, United Kingdom
| | - Manoj Parulekar
- Birmingham Women's and Children NHS Foundation Trust, Birmingham, United Kingdom
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
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128
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Fathi M, Ross CT, Hosseinzadeh Z. Functional 3-Dimensional Retinal Organoids: Technological Progress and Existing Challenges. Front Neurosci 2021; 15:668857. [PMID: 33958988 PMCID: PMC8095320 DOI: 10.3389/fnins.2021.668857] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Stem cell scientists have developed methods for the self-formation of artificial organs, often referred to as organoids. Organoids can be used as model systems for research in multiple biological disciplines. Yoshiki Sasai’s innovation for deriving mammalian retinal tissue from in vitro stem cells has had a large impact on the study of the biology of vision. New developments in retinal organoid technology provide avenues for in vitro models of human retinal diseases, studies of pathological mechanisms, and development of therapies for retinal degeneration, including electronic retinal implants and gene therapy. Moreover, these innovations have played key roles in establishing models for large-scale drug screening, studying the stages of retinal development, and providing a human model for personalized therapeutic approaches, like cell transplants to replace degenerated retinal cells. Here, we first discuss the importance of human retinal organoids to the biomedical sciences. Then, we review various functional features of retinal organoids that have been developed. Finally, we highlight the current limitations of retinal organoid technologies.
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Affiliation(s)
- Meimanat Fathi
- Department of Cell Techniques and Applied Stem Cell Biology, Faculty of Medicine, Center for Biotechnology and Biomedicine (BBZ), University of Leipzig, Leipzig, Germany.,Physiology and Pathophysiology of the Retina Group, Department of Molecular and Cellular Mechanisms of Neurodegeneration, Paul Flechsig Institute of Brain Research, University of Leipzig, Leipzig, Germany
| | - Cody T Ross
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Zohreh Hosseinzadeh
- Physiology and Pathophysiology of the Retina Group, Department of Molecular and Cellular Mechanisms of Neurodegeneration, Paul Flechsig Institute of Brain Research, University of Leipzig, Leipzig, Germany
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129
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Fishman ES, Louie M, Miltner AM, Cheema SK, Wong J, Schlaeger NM, Moshiri A, Simó S, Tarantal AF, La Torre A. MicroRNA Signatures of the Developing Primate Fovea. Front Cell Dev Biol 2021; 9:654385. [PMID: 33898453 PMCID: PMC8060505 DOI: 10.3389/fcell.2021.654385] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/16/2021] [Indexed: 11/22/2022] Open
Abstract
Rod and cone photoreceptors differ in their shape, photopigment expression, synaptic connection patterns, light sensitivity, and distribution across the retina. Although rods greatly outnumber cones, human vision is mostly dependent on cone photoreceptors since cones are essential for our sharp visual acuity and color discrimination. In humans and other primates, the fovea centralis (fovea), a specialized region of the central retina, contains the highest density of cones. Despite the vast importance of the fovea for human vision, the molecular mechanisms guiding the development of this region are largely unknown. MicroRNAs (miRNAs) are small post-transcriptional regulators known to orchestrate developmental transitions and cell fate specification in the retina. Here, we have characterized the transcriptional landscape of the developing rhesus monkey retina. Our data indicates that non-human primate fovea development is significantly accelerated compared to the equivalent retinal region at the other side of the optic nerve head, as described previously. Notably, we also identify several miRNAs differentially expressed in the presumptive fovea, including miR-15b-5p, miR-342-5p, miR-30b-5p, miR-103-3p, miR-93-5p as well as the miRNA cluster miR-183/-96/-182. Interestingly, miR-342-5p is enriched in the nasal primate retina and in the peripheral developing mouse retina, while miR-15b is enriched in the temporal primate retina and increases over time in the mouse retina in a central-to-periphery gradient. Together our data constitutes the first characterization of the developing rhesus monkey retinal miRNome and provides novel datasets to attain a more comprehensive understanding of foveal development.
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Affiliation(s)
- Elizabeth S Fishman
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Mikaela Louie
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Adam M Miltner
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Simranjeet K Cheema
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Joanna Wong
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Nicholas M Schlaeger
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Ala Moshiri
- Department of Ophthalmology, University of California, Davis, Davis, CA, United States
| | - Sergi Simó
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Alice F Tarantal
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States.,Department of Pediatrics, University of California, Davis, Davis, CA, United States.,California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
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130
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Frum T, Spence JR. hPSC-derived organoids: models of human development and disease. J Mol Med (Berl) 2021; 99:463-473. [PMID: 32857169 PMCID: PMC7914270 DOI: 10.1007/s00109-020-01969-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/30/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022]
Abstract
Organoids derived from human pluripotent stem cells (hPSCs) have emerged as important models for investigating human-specific aspects of development and disease. Here we discuss hPSC-derived organoids through the lens of development-highlighting how stages of human development align with the development of hPSC-derived organoids in the tissue culture dish. Using hPSC-derived lung and intestinal organoids as examples, we discuss the value and application of such systems for understanding human biology, as well as strategies for enhancing organoid complexity and maturity.
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Affiliation(s)
- Tristan Frum
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA.
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131
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Zerti D, Molina MM, Dorgau B, Mearns S, Bauer R, Al-Aama J, Lako M. IGFBPs mediate IGF-1's functions in retinal lamination and photoreceptor development during pluripotent stem cell differentiation to retinal organoids. Stem Cells 2021; 39:458-466. [PMID: 33442906 DOI: 10.1002/stem.3331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/06/2020] [Accepted: 12/10/2020] [Indexed: 02/02/2023]
Abstract
Development of the retina is regulated by growth factors, such as insulin-like growth factors 1 and 2 (IGF-1/2), which coordinate proliferation, differentiation, and maturation of the neuroepithelial precursors cells. In the circulation, IGF-1/2 are transported by the insulin growth factor binding proteins (IGFBPs) family members. IGFBPs can impact positively and negatively on IGF-1, by making it available or sequestering IGF-1 to or from its receptor. In this study, we investigated the expression of IGFBPs and their role in the generation of human retinal organoids from human pluripotent stem cells, showing a dynamic expression pattern suggestive of different IGFBPs being used in a stage-specific manner to mediate IGF-1 functions. Our data show that IGF-1 addition to culture media facilitated the generation of retinal organoids displaying the typical laminated structure and photoreceptor maturation. The organoids cultured in the absence of IGF-1, lacked the typical laminated structure at the early stages of differentiation and contained significantly less photoreceptors and more retinal ganglion cells at the later stages of differentiation, confirming the positive effects of IGF-1 on retinal lamination and photoreceptor development. The organoids cultured with the IGFBP inhibitor (NBI-31772) and IGF-1 showed lack of retinal lamination at the early stages of differentiation, an increased propensity to generate horizontal cells at mid-stages of differentiation and reduced photoreceptor development at the later stages of differentiation. Together these data suggest that IGFBPs enable IGF-1's role in retinal lamination and photoreceptor development in a stage-specific manner.
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Affiliation(s)
- Darin Zerti
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Microscopy Centre and Department of Applied Clinical Sciences and Biotechnology, University of L'Aquila, L'Aquila, Italy
| | - Marina Moya Molina
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Birthe Dorgau
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah Mearns
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Roman Bauer
- Department of Computer Science, University of Surrey, Guildford, UK
| | - Jumana Al-Aama
- Department of Genetic Medicine and Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majlinda Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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132
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Singh RK, Binette F, Seiler M, Petersen-Jones SM, Nasonkin IO. Pluripotent Stem Cell-Based Organoid Technologies for Developing Next-Generation Vision Restoration Therapies of Blindness. J Ocul Pharmacol Ther 2021; 37:147-156. [PMID: 33052761 PMCID: PMC8060716 DOI: 10.1089/jop.2020.0016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/28/2020] [Indexed: 12/25/2022] Open
Abstract
Blindness, associated with death of retinal cells at the back of the eye, is caused by a number of conditions with high prevalence such as glaucoma, age-related macular degeneration, and diabetic retinopathy. In addition, a large number of orphan inherited (mostly monogenic) conditions, such as retinitis pigmentosa and Leber Congenital Amaurosis, add to the overall number of patients with blinding retinal degenerative diseases. Blindness caused by deterioration and loss of retina is so far incurable. Modern biomedical research leveraging molecular and regenerative medicine approaches had a number of groundbreaking discoveries and proof-of-principle treatments of blindness in animals. However, these methods are slow to be standardized and commercialized as therapies to benefit people losing their eyesight due to retinal degenerative conditions. In this review, we will outline major regenerative medicine approaches, which are emerging as promising for preserving or/and restoring vision. We discuss the potential of each of these approaches to reach commercialization step and be converted to treatments, which could at least ameliorate blindness caused by retinal cell death.
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Affiliation(s)
| | | | - Magdalene Seiler
- Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
- Department of Physical Medicine & Rehabilitation, University of California, Irvine, Irvine, California, USA
- Department of Ophthalmology, University of California, Irvine, Irvine, California, USA
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, California, USA
| | - Simon M. Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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133
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Lyu J, Mu X. Genetic control of retinal ganglion cell genesis. Cell Mol Life Sci 2021; 78:4417-4433. [PMID: 33782712 DOI: 10.1007/s00018-021-03814-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/27/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
Retinal ganglion cells (RGCs) are the only projection neurons in the neural retina. They receive and integrate visual signals from upstream retinal neurons in the visual circuitry and transmit them to the brain. The function of RGCs is performed by the approximately 40 RGC types projecting to various central brain targets. RGCs are the first cell type to form during retinogenesis. The specification and differentiation of the RGC lineage is a stepwise process; a hierarchical gene regulatory network controlling the RGC lineage has been identified and continues to be elaborated. Recent studies with single-cell transcriptomics have led to unprecedented new insights into their types and developmental trajectory. In this review, we summarize our current understanding of the functions and relationships of the many regulators of the specification and differentiation of the RGC lineage. We emphasize the roles of these key transcription factors and pathways in different developmental steps, including the transition from retinal progenitor cells (RPCs) to RGCs, RGC differentiation, generation of diverse RGC types, and central projection of the RGC axons. We discuss critical issues that remain to be addressed for a comprehensive understanding of these different aspects of RGC genesis and emerging technologies, including single-cell techniques, novel genetic tools and resources, and high-throughput genome editing and screening assays, which can be leveraged in future studies.
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Affiliation(s)
- Jianyi Lyu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA.
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134
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You M, Rong R, Zeng Z, Li H, Xia X, Ji D. Single-cell RNA sequencing: A new opportunity for retinal research. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1652. [PMID: 33754496 DOI: 10.1002/wrna.1652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/08/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a technology for single-cell transcriptome analysis that can be used to characterize complex dynamics of various retinal cell types. It provides deep scrutiny into the gene expression character of diverse cell types, lending insight into all the biological processes being carried out. The scRNA-seq is an alternative to regular RNA-seq, which does not achieve cellular heterogeneity. The retina, is a part of the central nervous system (CNS) and consists of six types of neurons and several types of glial cells. Studying retinal cell heterogeneity is important for understanding retinal diseases. Currently, scRNA-seq is employed to assess retina development and retinal disease pathogenesis and has improved our understanding of the relationship between the retina, its visual pathways, and the brain. Moreover, this technology provides new ideas on the sensitivity and molecular mechanisms of cell subtypes involved in retinal-related diseases. The application of scRNA-seq technology has given us a deeper understanding of the latest advancements and challenges in retinal development and diseases. We advocate scRNA-seq as one of the important tools for developing novel therapies for retinal diseases. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Development RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Mengling You
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Rong Rong
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Zhou Zeng
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Haibo Li
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Xiaobo Xia
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
| | - Dan Ji
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, China
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135
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McNerney C, Johnston RJ. Thyroid hormone signaling specifies cone photoreceptor subtypes during eye development: Insights from model organisms and human stem cell-derived retinal organoids. VITAMINS AND HORMONES 2021; 116:51-90. [PMID: 33752828 DOI: 10.1016/bs.vh.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Cones are the color-detecting photoreceptors of the vertebrate eye. Cones are specialized into subtypes whose functions are determined by the expression of color-sensitive opsin proteins. Organisms differ greatly in the number and patterning of cone subtypes. Despite these differences, thyroid hormone is an important regulator of opsin expression in most vertebrates. In this chapter, we outline how the timing of thyroid hormone signaling controls cone subtype fates during retinal development. We first examine our current understanding of cone subtype specification in model organisms and then describe advances in human stem cell-derived organoid technology that identified mechanisms controlling development of the human retina.
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Affiliation(s)
- Christina McNerney
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States.
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136
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Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun 2021; 12:1465. [PMID: 33674582 PMCID: PMC7935890 DOI: 10.1038/s41467-021-21704-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Atoh7 has been believed to be essential for establishing the retinal ganglion cell (RGC) lineage, and Pou4f2 and Isl1 are known to regulate RGC specification and differentiation. Here we report our further study of the roles of these transcription factors. Using bulk RNA-seq, we identify genes regulated by the three transcription factors, which expand our understanding of the scope of downstream events. Using scRNA-seq on wild-type and mutant retinal cells, we reveal a transitional cell state of retinal progenitor cells (RPCs) co-marked by Atoh7 and other genes for different lineages and shared by all early retinal lineages. We further discover the unexpected emergence of the RGC lineage in the absence of Atoh7. We conclude that competence of RPCs for different retinal fates is defined by lineage-specific genes co-expressed in the transitional state and that Atoh7 defines the RGC competence and collaborates with other factors to shepherd transitional RPCs to the RGC lineage.
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Affiliation(s)
- Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jonathan E Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Julien Kann
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zihua Hu
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY, USA.
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.
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137
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Basinski BW, Balikov DA, Aksu M, Li Q, Rao RC. Ubiquitous Chromatin Modifiers in Congenital Retinal Diseases: Implications for Disease Modeling and Regenerative Medicine. Trends Mol Med 2021; 27:365-378. [PMID: 33573910 DOI: 10.1016/j.molmed.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
Retinal congenital malformations known as microphthalmia, anophthalmia, and coloboma (MAC) are associated with alterations in genes encoding epigenetic proteins that modify chromatin. We review newly discovered functions of such chromatin modifiers in retinal development and discuss the role of epigenetics in MAC in humans and animal models. Further, we highlight how advances in epigenomic technologies provide foundational and regenerative medicine-related insights into blinding disorders. Combining knowledge of epigenetics and pluripotent stem cells (PSCs) is a promising avenue because epigenetic factors cooperate with eye field transcription factors (EFTFs) to direct PSC fate - a foundation for congenital retinal disease modeling and cell therapy.
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Affiliation(s)
- Brian W Basinski
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Balikov
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Michael Aksu
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Qiang Li
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Rajesh C Rao
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI, USA; Section of Ophthalmology, Surgery Service, Veterans Administration Ann Arbor Healthsystem, Ann Arbor, MI, USA.
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138
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Harding P, Cunha DL, Moosajee M. Animal and cellular models of microphthalmia. THERAPEUTIC ADVANCES IN RARE DISEASE 2021; 2:2633004021997447. [PMID: 37181112 PMCID: PMC10032472 DOI: 10.1177/2633004021997447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
Microphthalmia is a rare developmental eye disorder affecting 1 in 7000 births. It is defined as a small (axial length ⩾2 standard deviations below the age-adjusted mean) underdeveloped eye, caused by disruption of ocular development through genetic or environmental factors in the first trimester of pregnancy. Clinical phenotypic heterogeneity exists amongst patients with varying levels of severity, and associated ocular and systemic features. Up to 11% of blind children are reported to have microphthalmia, yet currently no treatments are available. By identifying the aetiology of microphthalmia and understanding how the mechanisms of eye development are disrupted, we can gain a better understanding of the pathogenesis. Animal models, mainly mouse, zebrafish and Xenopus, have provided extensive information on the genetic regulation of oculogenesis, and how perturbation of these pathways leads to microphthalmia. However, differences exist between species, hence cellular models, such as patient-derived induced pluripotent stem cell (iPSC) optic vesicles, are now being used to provide greater insights into the human disease process. Progress in 3D cellular modelling techniques has enhanced the ability of researchers to study interactions of different cell types during eye development. Through improved molecular knowledge of microphthalmia, preventative or postnatal therapies may be developed, together with establishing genotype-phenotype correlations in order to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling. This review summarises some key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future. Plain language summary Animal and Cellular Models of the Eye Disorder, Microphthalmia (Small Eye) Microphthalmia, meaning a small, underdeveloped eye, is a rare disorder that children are born with. Genetic changes or variations in the environment during the first 3 months of pregnancy can disrupt early development of the eye, resulting in microphthalmia. Up to 11% of blind children have microphthalmia, yet currently no treatments are available. By understanding the genes necessary for eye development, we can determine how disruption by genetic changes or environmental factors can cause this condition. This helps us understand why microphthalmia occurs, and ensure patients are provided with the appropriate clinical care and genetic counselling advice. Additionally, by understanding the causes of microphthalmia, researchers can develop treatments to prevent or reduce the severity of this condition. Animal models, particularly mice, zebrafish and frogs, which can also develop small eyes due to the same genetic/environmental changes, have helped us understand the genes which are important for eye development and can cause birth eye defects when disrupted. Studying a patient's own cells grown in the laboratory can further help researchers understand how changes in genes affect their function. Both animal and cellular models can be used to develop and test new drugs, which could provide treatment options for patients living with microphthalmia. This review summarises the key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future.
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Affiliation(s)
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, 11-43 Bath
Street, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Foundation Trust, London, UK
- The Francis Crick Institute, London, UK
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139
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Single-cell RNA sequencing in vision research: Insights into human retinal health and disease. Prog Retin Eye Res 2020; 83:100934. [PMID: 33383180 DOI: 10.1016/j.preteyeres.2020.100934] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023]
Abstract
Gene expression provides valuable insight into cell function. As such, vision researchers have frequently employed gene expression studies to better understand retinal physiology and disease. With the advent of single-cell RNA sequencing, expression experiments provide an unparalleled resolution of information. Instead of studying aggregated gene expression across all cells in a heterogenous tissue, single-cell technology maps RNA to an individual cell, which facilitates grouping of retinal and choroidal cell types for further study. Single-cell RNA sequencing has been quickly adopted by both basic and translational vision researchers, and single-cell level gene expression has been studied in the visual systems of animal models, retinal organoids, and primary human retina, RPE, and choroid. These experiments have generated detailed atlases of gene expression and identified new retinal cell types. Likewise, single-cell RNA sequencing investigations have characterized how gene expression changes in the setting of many retinal diseases, including how choroidal endothelial cells are altered in age-related macular degeneration. In addition, this technology has allowed vision researchers to discover drivers of retinal development and model rare retinal diseases with induced pluripotent stem cells. In this review, we will overview the growing number of single-cell RNA sequencing studies in the field of vision research. We will summarize experimental considerations for designing single-cell RNA sequencing experiments and highlight important advancements in retinal, RPE, choroidal, and retinal organoid biology driven by this technology. Finally, we generalize these findings to genes involved in retinal degeneration and outline the future of single-cell expression experiments in studying retinal disease.
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140
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O'Hara-Wright M, Gonzalez-Cordero A. Retinal organoids: a window into human retinal development. Development 2020; 147:147/24/dev189746. [PMID: 33361444 PMCID: PMC7774906 DOI: 10.1242/dev.189746] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinal development and maturation are orchestrated by a series of interacting signalling networks that drive the morphogenetic transformation of the anterior developing brain. Studies in model organisms continue to elucidate these complex series of events. However, the human retina shows many differences from that of other organisms and the investigation of human eye development now benefits from stem cell-derived organoids. Retinal differentiation methods have progressed from simple 2D adherent cultures to self-organising micro-physiological systems. As models of development, these have collectively offered new insights into the previously unexplored early development of the human retina and informed our knowledge of the key cell fate decisions that govern the specification of light-sensitive photoreceptors. Although the developmental trajectories of other retinal cell types remain more elusive, the collation of omics datasets, combined with advanced culture methodology, will enable modelling of the intricate process of human retinogenesis and retinal disease in vitro. Summary: Retinal organoid systems derived from human pluripotent stem cells are micro-physiological systems that offer new insights into previously unexplored human retina development.
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Affiliation(s)
- Michelle O'Hara-Wright
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, 2145, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, 2145, NSW, Australia .,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
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141
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Lidgerwood GE, Senabouth A, Smith-Anttila CJA, Gnanasambandapillai V, Kaczorowski DC, Amann-Zalcenstein D, Fletcher EL, Naik SH, Hewitt AW, Powell JE, Pébay A. Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 19:223-242. [PMID: 33307245 PMCID: PMC8602392 DOI: 10.1016/j.gpb.2020.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 07/04/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of diseases associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate time points of retinal pigment epithelium (RPE) cultures that reflect native counterparts, we characterised the transcriptomic profiles of the hPSC-derived RPE cells from 1- and 12-month cultures. We differentiated the human embryonic stem cell line H9 into RPE cells, performed single-cell RNA-sequencing of a total of 16,576 cells to assess the molecular changes of the RPE cells across these two culture time points. Our results indicate the stability of the RPE transcriptomic signature, with no evidence of an epithelial–mesenchymal transition, and with the maturing populations of the RPE observed with time in culture. Assessment of Gene Ontology pathways revealed that as the cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions. This might reflect an increased ability to handle oxidative stress as cells mature. Comparison with native human RPE data confirms a maturing transcriptional profile of RPE cells in culture. These results suggest that long-term in vitro culture of RPE cells allows the modelling of specific phenotypes observed in native mature tissues. Our work highlights the transcriptional landscape of hPSC-derived RPE cells as they age in culture, which provides a reference for native and patient samples to be benchmarked against.
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Affiliation(s)
- Grace E Lidgerwood
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia.
| | - Anne Senabouth
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Casey J A Smith-Anttila
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Vikkitharan Gnanasambandapillai
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Dominik C Kaczorowski
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Daniela Amann-Zalcenstein
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Erica L Fletcher
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Shalin H Naik
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Alex W Hewitt
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia
| | - Joseph E Powell
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alice Pébay
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia.
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142
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Optimized culture of retinal ganglion cells and amacrine cells from adult mice. PLoS One 2020; 15:e0242426. [PMID: 33284815 PMCID: PMC7721191 DOI: 10.1371/journal.pone.0242426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/02/2020] [Indexed: 01/22/2023] Open
Abstract
Cell culture is widely utilized to study the cellular and molecular biology of different neuronal cell populations. Current techniques to study enriched neurons in vitro are primarily limited to embryonic/neonatal animals and induced pluripotent stem cells (iPSCs). Although the use of these cultures is valuable, the accessibility of purified primary adult neuronal cultures would allow for improved assessment of certain neurological diseases and pathways at the cellular level. Using a modified 7-step immunopanning technique to isolate for retinal ganglion cells (RGCs) and amacrine cells (ACs) from adult mouse retinas, we have successfully developed a model of neuronal culture that maintains for at least one week. Isolations of Thy1.2+ cells are enriched for RGCs, with the isolation cell yield being congruent to the theoretical yield of RGCs in a mouse retina. ACs of two different populations (CD15+ and CD57+) can also be isolated. The populations of these three adult neurons in culture are healthy, with neurite outgrowths in some cases greater than 500μm in length. Optimization of culture conditions for RGCs and CD15+ cells revealed that neuronal survival and the likelihood of neurite outgrowth respond inversely to different culture media. Serially diluted concentrations of puromycin decreased cultured adult RGCs in a dose-dependent manner, demonstrating the potential usefulness of these adult neuronal cultures in screening assays. This novel culture system can be used to model in vivo neuronal behaviors. Studies can now be expanded in conjunction with other methodologies to study the neurobiology of function, aging, and diseases.
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143
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Ge Y, Wu F, Cheng M, Bard J, Mu X. Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins. Dev Dyn 2020; 249:1514-1528. [PMID: 32741043 PMCID: PMC7855626 DOI: 10.1002/dvdy.233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND During development, all retinal cell types arise from retinal progenitor cells (RPCs) in a step-wise fashion. Atoh7 and Pou4f2 mark, and function in, two phases of retinal ganglion cell (RGC) genesis; Atoh7 functions in a subpopulation of RPCs to render them competent for the RGC fate, whereas Pou4f2 participates in RGC fate specification and RGC differentiation. Despite extensive research on their roles, the properties of the two phases represented by these two factors have not been well studied, likely due to the retinal cellular heterogeneity. RESULTS In this report, we describe two novel knock-in mouse alleles, Atoh7zsGreenCreERT2 and Pou4f2FlagtdTomato , which labeled retinal cells in the two phases of RGC development by fluorescent proteins. Also, the Atoh7zsGreenCreERT2 allele allowed for indirect labeling of RGCs and other cell types upon tamoxifen induction in a dose-dependent manner. Further, these alleles could be used to purify retinal cells in the different phases by fluorescence assisted cell sorting (FACS). Single cell RNA-seq analysis of purified cells from Atoh7zsGreenCreERT2 retinas further validated that this allele labeled both transitional/competent RPCs and their progenies including RGCs. CONCLUSIONS Thus, these two alleles are very useful tools for studying the molecular and genetic mechanisms underlying RGC formation.
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
| | - Mobin Cheng
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University at Buffalo, Buffalo, NY
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY
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144
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Resolving Neurodevelopmental and Vision Disorders Using Organoid Single-Cell Multi-omics. Neuron 2020; 107:1000-1013. [PMID: 32970995 DOI: 10.1016/j.neuron.2020.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
Human organoid models of the central nervous system, including the neural retina, are providing unprecedented opportunities to explore human neurodevelopment and neurodegeneration in controlled culture environments. In this Perspective, we discuss how the single-cell multi-omic toolkit has been used to identify features and limitations of brain and retina organoids and how these tools can be deployed to study congenital brain malformations and vision disorders in organoids. We also address how to improve brain and retina organoid protocols to revolutionize in vitro disease modeling.
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145
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Oliveira-Valença VM, Bosco A, Vetter ML, Silveira MS. On the Generation and Regeneration of Retinal Ganglion Cells. Front Cell Dev Biol 2020; 8:581136. [PMID: 33043015 PMCID: PMC7527462 DOI: 10.3389/fcell.2020.581136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/28/2020] [Indexed: 01/02/2023] Open
Abstract
Retinal development follows a conserved neurogenic program in vertebrates to orchestrate the generation of specific cell types from multipotent progenitors in sequential but overlapping waves. In this program, retinal ganglion cells (RGCs) are the first cell type generated. RGCs are the final output neurons of the retina and are essential for vision and circadian rhythm. Key molecular steps have been defined in multiple vertebrate species to regulate competence, specification, and terminal differentiation of this cell type. This involves neuronal-specific transcription factor networks, regulators of chromatin dynamics and miRNAs. In mammals, RGCs and their optic nerve axons undergo neurodegeneration and loss in glaucoma and other optic neuropathies, resulting in irreversible vision loss. The incapacity of RGCs and axons to regenerate reinforces the need for the design of efficient RGC replacement strategies. Here we describe the essential molecular pathways for the differentiation of RGCs in vertebrates, as well as experimental manipulations that extend the competence window for generation of this early cell type from late progenitors. We discuss recent advances in regeneration of retinal neurons in vivo in both mouse and zebrafish and discuss possible strategies and barriers to achieving RGC regeneration as a therapeutic approach for vision restoration in blinding diseases such as glaucoma.
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Affiliation(s)
- Viviane M Oliveira-Valença
- Laboratory of Neurogenesis, Neurobiology Program, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alejandra Bosco
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
| | - Monica L Vetter
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
| | - Mariana S Silveira
- Laboratory of Neurogenesis, Neurobiology Program, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Glial Cell Biology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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146
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Fadl BR, Brodie SA, Malasky M, Boland JF, Kelly MC, Kelley MW, Boger E, Fariss R, Swaroop A, Campello L. An optimized protocol for retina single-cell RNA sequencing. Mol Vis 2020; 26:705-717. [PMID: 33088174 PMCID: PMC7553720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/08/2020] [Indexed: 10/25/2022] Open
Abstract
Purpose Single-cell RNA sequencing (scRNA-seq) is a powerful technique used to explore gene expression at the single cell level. However, appropriate preparation of samples is essential to obtain the most information out of this transformative technology. Generating high-quality single-cell suspensions from the retina is critical to preserve the native expression profile that will ensure meaningful transcriptome data analysis. Methods We modified the conditions for rapid and optimal dissociation of retina sample preparation. We also included additional filtering steps in data analysis for retinal scRNA-seq. Results We report a gentle method for dissociation of the mouse retina that minimizes cell death and preserves cell morphology. This protocol also results in detection of higher transcriptional complexity. In addition, the modified computational pipeline leads to better-quality single-cell RNA-sequencing data in retina samples. We also demonstrate the advantages and limitations of using fresh versus frozen retinas to prepare cell or nuclei suspensions for scRNA-seq. Conclusions We provide a simple yet robust and reproducible protocol for retinal scRNA-seq analysis, especially for comparative studies.
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Affiliation(s)
- Benjamin R. Fadl
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Seth A. Brodie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health & NCI-Frederick, Leidos Biomedical Research Inc., Frederick, MD
| | - Michael Malasky
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health & NCI-Frederick, Leidos Biomedical Research Inc., Frederick, MD
| | - Joseph F. Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health & NCI-Frederick, Leidos Biomedical Research Inc., Frederick, MD
| | - Michael C. Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD
| | - Matthew W. Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Erich Boger
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Robert Fariss
- Biological Imaging Core, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Laura Campello
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
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147
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Mahalingam R, Dharmalingam P, Santhanam A, Kotla S, Davuluri G, Karmouty-Quintana H, Ashrith G, Thandavarayan RA. Single-cell RNA sequencing analysis of SARS-CoV-2 entry receptors in human organoids. J Cell Physiol 2020; 236:2950-2958. [PMID: 32944935 PMCID: PMC7537521 DOI: 10.1002/jcp.30054] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 01/05/2023]
Abstract
Coronavirus disease‐2019 (COVID‐19) is a global pandemic and caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), which has resulted in millions of deaths worldwide. Reports denote SARS‐CoV‐2 uses angiotensin‐converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2) as its primary entry point into the host cell. However, understanding the biology behind this viral replication, disease mechanism and drug discovery efforts are limited due to the lack of a suitable experimental model. Here, we used single‐cell RNA sequencing data of human organoids to analyze expressions of ACE2 and TMPRSS2, in addition to an array of RNA receptors to examine their role in SARS‐CoV‐2 pathogenesis. ACE2 is abundant in all organoids, except the prostate and brain, and TMPRSS2 is omnipresent. Innate immune pathways are upregulated in ACE2(+) cells of all organoids, except the lungs. Besides this, the expression of low‐density lipoprotein receptor is highly enriched in ACE2(+) cells in intestinal, lung, and retinal organoids, with the highest expression in lung organoids. Collectively, this study demonstrates that the organoids can be used as an experimental platform to explore this novel virus disease mechanism and for drug development.
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Affiliation(s)
- Rajasekaran Mahalingam
- Laboratory of Neuroimmunology, Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Abirami Santhanam
- Ophthalmology and Visual Science, University of Texas Health Science center, Houston, Texas, USA
| | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gangarao Davuluri
- Integrated Physiology and Molecular Metabolism, Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Guha Ashrith
- Department of Cardiology, Houston Methodist Hospital, Houston, Texas, USA
| | - Rajarajan A Thandavarayan
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Cardiology, Houston Methodist Hospital, Houston, Texas, USA
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148
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Voigt AP, Whitmore SS, Lessing ND, DeLuca AP, Tucker BA, Stone EM, Mullins RF, Scheetz TE. Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis. Exp Eye Res 2020; 200:108204. [PMID: 32910939 DOI: 10.1016/j.exer.2020.108204] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/06/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
Single-cell RNA sequencing has revolutionized ocular gene expression studies. This technology has enabled researchers to identify expression signatures for rare cell types and characterize how gene expression changes across biological conditions, such as topographic region or disease status. However, sharing single-cell RNA sequencing results remains a major obstacle, particular for individuals without a computational background. To address these limitations, we developed Spectacle, an interactive web-based resource for exploring previously published single-cell RNA sequencing data from ocular studies. Spectacle is powered by a locally developed R package, cellcuratoR, which utilizes the Shiny framework in R to generate interactive visualizations for single-cell expression data. Spectacle contains five pre-processed ocular single-cell RNA sequencing data sets and is accessible via the web at OcularGeneExpression.org/singlecell. With Spectacle, users can interactively identify which cell types express a gene of interest, detect transcriptomic subpopulations within a cell type, and perform highly flexible differential expression analyses. The freely-available Spectacle system reduces the bioinformatic barrier for interacting with rich single-cell RNA sequencing studies from ocular tissues, making it easy to quickly identify cell types that express a gene of interest.
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Affiliation(s)
- Andrew P Voigt
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - S Scott Whitmore
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas D Lessing
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Adam P DeLuca
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Budd A Tucker
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Edwin M Stone
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Robert F Mullins
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA
| | - Todd E Scheetz
- Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA.
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149
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Yi W, Lu Y, Zhong S, Zhang M, Sun L, Dong H, Wang M, Wei M, Xie H, Qu H, Peng R, Hong J, Yao Z, Tong Y, Wang W, Ma Q, Liu Z, Ma Y, Li S, Yin C, Liu J, Ma C, Wang X, Wu Q, Xue T. A single-cell transcriptome atlas of the aging human and macaque retina. Natl Sci Rev 2020; 8:nwaa179. [PMID: 34691611 PMCID: PMC8288367 DOI: 10.1093/nsr/nwaa179] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 12/23/2022] Open
Abstract
The human retina is a complex neural tissue that detects light and sends visual information to the brain. However, the molecular and cellular processes that underlie aging primate retina remain unclear. Here, we provide a comprehensive transcriptomic atlas based on 119 520 single cells of the foveal and peripheral retina of humans and macaques covering different ages. The molecular features of retinal cells differed between the two species, suggesting distinct regional and species specializations of the human and macaque retinae. In addition, human retinal aging occurred in a region- and cell-type-specific manner. Aging of human retina exhibited a foveal to peripheral gradient. MYO9A− rods and a horizontal cell subtype were greatly reduced in aging retina, indicating their vulnerability to aging. Moreover, we generated a dataset showing the cell-type- and region-specific gene expression associated with 55 types of human retinal disease, which provides a foundation to understanding of the molecular and cellular mechanisms underlying human retinal diseases. Such datasets are valuable to understanding of the molecular characteristics of primate retina, as well as molecular regulation of aging progression and related diseases.
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Affiliation(s)
- Wenyang Yi
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Mei Zhang
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Le Sun
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wei
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Haohuan Xie
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Hongqiang Qu
- Department of Ophthalmology, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China
| | - Rongmei Peng
- Department of Ophthalmology, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China
| | - Jing Hong
- Department of Ophthalmology, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China
| | - Ziqin Yao
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Yunyun Tong
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zeyuan Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuqian Ma
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Shouzhen Li
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Chonghai Yin
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwei Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Ma
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Tian Xue
- Eye Center at The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
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150
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Retinoblastoma: Etiology, Modeling, and Treatment. Cancers (Basel) 2020; 12:cancers12082304. [PMID: 32824373 PMCID: PMC7465685 DOI: 10.3390/cancers12082304] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/03/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022] Open
Abstract
Retinoblastoma is a retinal cancer that is initiated in response to biallelic loss of RB1 in almost all cases, together with other genetic/epigenetic changes culminating in the development of cancer. RB1 deficiency makes the retinoblastoma cell-of-origin extremely susceptible to cancerous transformation, and the tumor cell-of-origin appears to depend on the developmental stage and species. These are important to establish reliable preclinical models to study the disease and develop therapies. Although retinoblastoma is the most curable pediatric cancer with a high survival rate, advanced tumors limit globe salvage and are often associated with high-risk histopathological features predictive of dissemination. The advent of chemotherapy has improved treatment outcomes, which is effective for globe preservation with new routes of targeted drug delivery. However, molecularly targeted therapeutics with more effectiveness and less toxicity are needed. Here, we review the current knowledge concerning retinoblastoma genesis with particular attention to the genomic and transcriptomic landscapes with correlations to clinicopathological characteristics, as well as the retinoblastoma cell-of-origin and current disease models. We further discuss current treatments, clinicopathological correlations, which assist in guiding treatment and may facilitate globe preservation, and finally we discuss targeted therapeutics for future treatments.
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