Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution (original) (raw)
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2019
SummaryHow closely human organoids recapitulate cell-type diversity and cell-type maturation of their target organs is not well understood. We developed human retinal organoids with multiple nuclear and synaptic layers. We sequenced the RNA of 158,844 single cells from these organoids at six 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 and the transcriptomes of organoid cell types converged towards the transcriptomes of adult peripheral retinal cell types. The expression of disease-associated genes was significantly 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 mechanis...
Retinal organoids: a window into human retinal development
Development
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 enab...
The advent of single-cell RNA-sequencing (scRNA-seq) has enabled high resolution studies of cell type diversity and transcriptional networks governing cell fate specification. In order to examine the transcriptional networks governing human retinal development, we performed scRNA-seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene use across retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we examined gene expression differences between developing macula and periphery and between two distinct populations of horizontal cells. We also highlight both shared and unique gene usage during human and mouse retinal development. Finally, we identify an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. Together, these studies present a comprehensive atlas of gene expr...
Transcriptome analysis of the retina
Genome Biology - GENOME BIOL, 2002
The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in visual transduction and the availability of mutants. These investigations are being greatly facilitated by the ongoing identification of genes expressed in the retina using high-throughput methods.
Transcriptome of the human retina, retinal pigmented epithelium and choroid
Genomics, 2015
The retina and its adjacent supporting tissues - retinal pigmented epithelium (RPE) and choroid - are critical structures in human eyes required for normal visual perception. Abnormal changes in these layers have been implicated in diseases such as age-related macular degeneration and glaucoma. With the advent of high-throughput methods, such as serial analysis of gene expression, cDNA microarray, and RNA sequencing, there is unprecedented opportunity to facilitate our understanding of the normal retina, RPE, and choroid. This information can be used to identify dysfunction in age-related macular degeneration and glaucoma. In this review, we describe the current status in our understanding of these transcriptomes through the use of high-throughput techniques.
Cell, 2001
S1 at http://www.cell.com/cgi/content/full/107/5/579/ DC1). This feature appears to be a common property of photoreceptor disorders, also holding true for rd mutations in Drosophila (Ranganathan et al., 1995) and other organisms (Semple-Rowland et al., 1998; Suber et al., ), although the reason for this selective vulnerability is poorly understood. Even in retinal diseases where an Boston, Massachusetts 02115 2 Center of Developmental Biology inner retinal phenotype is observed, such as X-linked retinoschisis, a rod-specific expression pattern of the The University of Texas Southwestern Medical Center at Dallas disease gene is seen (Reid et al., 1999). So high is this correlation between tissue specificity of expression and 5323 Harry Hines Boulevard Dallas, Texas 75235 clinical phenotype that gene expression profiles could in principle be an important tool for identification of retinal disease genes. Thus, a major limiting factor in cloning additional retinal disease genes has been the Summary lack of a full catalog of genes that are selectively expressed in photoreceptors. While approaches such as To identify the full set of genes expressed by mammasubtractive hybridization (Bascom et al., 1993; Guillonlian rods, we conducted serial analysis of gene expresneau et al., 1999) and examination of EST databases sion (SAGE) by using libraries generated from mature (Sohocki et al., 2000)
Proceedings of the National Academy of Sciences, 2002
We used the serial analysis of gene expression (SAGE) technique to catalogue and measure the relative levels of expression of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium (RPE) from one or both of two humans, aged 88 and 44 years. The cone photoreceptor contribution to all transcription in the retina was found to be similar in the macula versus the retinal periphery, whereas the rod contribution was greater in the periphery versus the macula. Genes encoding structural proteins for axons were found to be expressed at higher levels in the macula versus the retinal periphery, probably reflecting the large proportion of ganglion cells in the central retina. In comparison with the younger eye, the peripheral retina of the older eye had a substantially higher proportion of mRNAs from genes encoding proteins involved in iron metabolism or protection against oxidative damage and a substantially lower proportion of mRNAs from genes encoding proteins involved in rod phototransduction. These differences may reflect the difference in age between the two donors or merely interindividual variation. The RPE library had numerous previously unencountered tags, suggesting that this cell type has a large, idiosyncratic repertoire of expressed genes. Comparison of these libraries with 100 reported nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a retinal disease and 53 are RPE-specific genes. We expect that these libraries will serve as a resource for understanding the relative expression levels of genes in the retina and the RPE and for identifying additional disease genes.
Transcriptional code and disease map for adult retinal cell types
Nature Neuroscience, 2012
Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of an individual adult brain region differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes in one brain region, the mouse retina. We found that each adult cell type expressed a specific set of genes, including a unique set of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes carried enough information to categorize cells into morphological classes and types. Several genes that were specifically expressed in particular retinal circuit elements, such as inhibitory neuron types, are associated with eye diseases. The resource described here allows gene expression to be compared across adult retinal cell types, experimenting with specific transcription factors to differentiate stem or somatic cells to retinal cell types, and predicting cellular targets of newly discovered disease-associated genes.
Generation of human neural retina transcriptome atlas by single cell RNA sequencing
The retina is a highly specialized neural tissue that senses light and initiates image processing. Although the functional organisation of specific cells within the retina has been well-studied, the molecular profile of many cell types remains unclear in humans. To comprehensively profile cell types in the human retina, we performed single cell RNA-sequencing on 20,009 cells obtained post-mortem from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct clusters representing all known retinal cells: rod photoreceptors, cone photoreceptors, Muller glia cells, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, retinal astrocytes and microglia. Notably, our data reveal novel subpopulations of rod photoreceptors that can be distinguished by MALAT1 expression levels. We also demonstrated the use of this retina transcriptome atlas to benchmark pluripotent stem cell-derived cone p...