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      Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis

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          Abstract

          The developmental pathway of the neural retina (NR) and retinal pigment epithelium (RPE) has been revealed by extensive research in mice. However, the molecular mechanisms underlying the development of the human NR and RPE, as well as the interactions between these two tissues, have not been well defined. Here, we analyzed 2,421 individual cells from human fetal NR and RPE using single-cell RNA sequencing (RNA-seq) technique and revealed the tightly regulated spatiotemporal gene expression network of human retinal cells. We identified major cell classes of human fetal retina and potential crucial transcription factors for each cell class. We dissected the dynamic expression patterns of visual cycle– and ligand-receptor interaction–related genes in the RPE and NR. Moreover, we provided a map of disease-related genes for human fetal retinal cells and highlighted the importance of retinal progenitor cells as potential targets of inherited retinal diseases. Our findings captured the key in vivo features of the development of the human NR and RPE and offered insightful clues for further functional studies.

          Abstract

          Single-cell RNA sequencing allows dissection of the transcriptomic landscape of the human fetal neural retina (NR) and retinal pigment epithelium (RPE), revealing a tightly regulated spatiotemporal gene expression network of human retinal cells, as well as dynamic and functional interactions between the NR and RPE.

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          Most cited references44

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          Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.

          Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constituent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data were projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves-all without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the transcriptomes of 85 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology, and disease.
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            Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.

            Human fetal germ cells (FGCs) are precursors to sperm and eggs and are crucial for maintenance of the species. However, the developmental trajectories and heterogeneity of human FGCs remain largely unknown. Here we performed single-cell RNA-seq analysis of over 2,000 FGCs and their gonadal niche cells in female and male human embryos spanning several developmental stages. We found that female FGCs undergo four distinct sequential phases characterized by mitosis, retinoic acid signaling, meiotic prophase, and oogenesis. Male FGCs develop through stages of migration, mitosis, and cell-cycle arrest. Individual embryos of both sexes simultaneously contain several subpopulations, highlighting the asynchronous and heterogeneous nature of FGC development. Moreover, we observed reciprocal signaling interactions between FGCs and their gonadal niche cells, including activation of the bone morphogenic protein (BMP) and Notch signaling pathways. Our work provides key insights into the crucial features of human FGCs during their highly ordered mitotic, meiotic, and gametogenetic processes in vivo.
              • Record: found
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              • Article: not found

              Next-generation regenerative medicine: organogenesis from stem cells in 3D culture.

              The behavior of stem cells, when they work collectively, can be much more sophisticated than one might expect from their individual programming. This Perspective covers recent discoveries about the dynamic patterning and structural self-formation of complex organ buds in 3D stem cell culture, including the generation of various neuroectodermal and endodermal tissues. For some tissues, epithelial-mesenchymal interactions can also be manipulated in coculture to guide organogenesis. This new area of stem cell research-the spatiotemporal control of dynamic cellular interactions-will open a new avenue for next-generation regenerative medicine. Copyright © 2013 Elsevier Inc. All rights reserved.

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Formal analysisRole: MethodologyRole: SupervisionRole: Validation
                Role: Data curationRole: Formal analysisRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Formal analysisRole: MethodologyRole: ValidationRole: Visualization
                Role: Data curationRole: Formal analysisRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Funding acquisitionRole: Investigation
                Role: Investigation
                Role: InvestigationRole: Methodology
                Role: Investigation
                Role: Investigation
                Role: InvestigationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Academic Editor
                Journal
                PLoS Biol
                PLoS Biol
                plos
                plosbiol
                PLoS Biology
                Public Library of Science (San Francisco, CA USA )
                1544-9173
                1545-7885
                3 July 2019
                July 2019
                3 July 2019
                : 17
                : 7
                : e3000365
                Affiliations
                [1 ] Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, Third Hospital, College of Life Sciences, Peking University, Beijing, China
                [2 ] Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Biomedical Pioneering Innovation Center, Peking University, Beijing, China
                [3 ] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China
                [4 ] Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
                [5 ] Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
                University of Michigan, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-3515-3333
                Article
                PBIOLOGY-D-19-00043
                10.1371/journal.pbio.3000365
                6634428
                31269016
                798067f5-7cdd-4a4e-989d-fde01d780735
                © 2019 Hu et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 7 January 2019
                : 25 June 2019
                Page count
                Figures: 8, Tables: 1, Pages: 26
                Funding
                Funded by: National Basic Research Program of China
                Award ID: 2018YFA0107601
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31625018
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81521002
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31522034
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31571544
                Award Recipient :
                JQ and FT were supported by grants from the National Basic Research Program of China (2018YFA0107601) and the National Natural Science Foundation of China (31625018, 31522034, 31571544, and 81521002); YH was supported in part by the Postdoctoral Fellowship of Peking-Tsinghua Center for Life Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Methods and Resources
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Neurons
                Afferent Neurons
                Retinal Ganglion Cells
                Biology and Life Sciences
                Neuroscience
                Cellular Neuroscience
                Neurons
                Afferent Neurons
                Retinal Ganglion Cells
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Neurons
                Ganglion Cells
                Retinal Ganglion Cells
                Biology and Life Sciences
                Neuroscience
                Cellular Neuroscience
                Neurons
                Ganglion Cells
                Retinal Ganglion Cells
                Biology and Life Sciences
                Anatomy
                Ocular System
                Ocular Anatomy
                Retina
                Medicine and Health Sciences
                Anatomy
                Ocular System
                Ocular Anatomy
                Retina
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Transcription Factors
                Biology and Life Sciences
                Genetics
                Gene Expression
                Gene Regulation
                Transcription Factors
                Biology and Life Sciences
                Biochemistry
                Proteins
                Regulatory Proteins
                Transcription Factors
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cell Cycle and Cell Division
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Gene Ontologies
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Gene Ontologies
                Biology and Life Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Medicine and Health Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Custom metadata
                vor-update-to-uncorrected-proof
                2019-07-16
                The expression pattern of single-cell RNA-seq data in the present study is available at http://49.4.93.68:30004/. All sequencing data and the table of normalized expression (TPM) reported in this paper have been deposited in NCBI GEO under accession code GEO: GSE107618, and its secure token is khihsockldczdip to allow review.

                Life sciences
                Life sciences

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