Dataset Information

Cell Atlas of The Human Fovea and Peripheral Retina.

ABSTRACT: Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral retina of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells. Nearly all types are shared between the two retinal regions, but there are notable differences in gene expression and proportions between foveal and peripheral cohorts of shared types. We then used the human retinal atlas to map expression of 636 genes implicated as causes of or risk factors for blinding diseases. Many are expressed in striking cell class-, type-, or region-specific patterns. Finally, we compared gene expression signatures of cell types between human and the cynomolgus macaque monkey, Macaca fascicularis. We show that over 90% of human types correspond transcriptomically to those previously identified in macaque, and that expression of disease-related genes is largely conserved between the two species. These results validate the use of the macaque for modeling blinding disease, and provide a foundation for investigating molecular mechanisms underlying visual processing.

SUBMITTER: Yan W

PROVIDER: S-EPMC7299956 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Cell Atlas of The Human Fovea and Peripheral Retina.

Yan Wenjun W Peng Yi-Rong YR van Zyl Tavé T Regev Aviv A Shekhar Karthik K Juric Dejan D Sanes Joshua R JR

Scientific reports 20200617 1

Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral retina of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells. Nearly all types are shared between the two retin ...[more]

PMID: 32555229

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Project description:Background We believe that our experience with patients presenting with Coats disease and macular sparing should be shared with our colleagues. We would like to show the effect of posture and prompt intervention in cases with fovea-threatening and/or fovea-involving peripheral Coats disease (FTPCD). This association has been poorly debated in our specialty and literature. We call the attention for the unexpexted scenario of observing the lost of the fovea during some types of traditional and prompt interventional treatments of these cases with previous 20/20 vision (something that we have been studying and observing for many years). In order to publish our best representative cases, we have chosen 8 Brazilian patients (age range, 7–62 years; 5 male) with FTPCD. All patients underwent multimodal imaging and different treatments (observation, sleep-posture repositioning, laser, intraocular steroids, and/or anti-vascular endothelial growth factor therapy). All patients, initially, informed to adopt a sleeping lateral-down position, favoring exudation shifting to the fovea pre-treatment. Most promptly-treated patients in this way (n = 4), developed subretinal fluid and exudates in the macula and some had irreversible central visual loss (n = 3). Patients with recent fovea-involving exudation who changed postural sleep position (to protect the foveal area) before and during treatment fared better, with some preserved central vision and an intact fovea (n = 5). The fundus status was correlated with the gravitational effects of posture before and after treatment. Despite prepared as an observational/interventional study, with a small number of cases, the most difficult part is documenting the sleep position of these patients and its influence in the outcomes as there is not good way to prove how well or poorly the positioning occurred in our cases. Finally, we also intended to call the attention to the fact that Coats disease must be studied in all its clinical stage variants and not only seen as a potential blinding and incurable ocular disease. Case presentation This study is a retrospective and/or interventional analysis of eight cases with a less severe clinical variant of classic Coats disease that we refer to as fovea-threatening and fovea-involving peripheral Coats disease (FTPCD). All cases were unilateral with no systemic disease or family history of Coats disease. The bilateral anterior segment and intraocular pressure were normal in all patients. The characteristics of all patients are shown in the Table. Conclusion The funduscopic features of FTPCD are fundamental to disease understanding and optimal management. Habitual posturing may affect the fundus morphologic features of retinal exudation as observed in all current patients with exudative peripheral Coats disease. When sleep habitual posture is not observed in patients with FTPCD, the effects of prompt invasive treatments can cause rapid visual loss because of foveal subretinal pooling of exudates post-treatment. Initial vigilant adjusting of the habitual sleep posture for several patients with FTPCD, before the indication of traditional invasive treatments (laser and/or pharmacologic medications) can result in improved vision and fundoscopic morphologic features. Supplementary Information The online version contains supplementary material available at 10.1186/s40942-022-00382-4.

Project description:This SuperSeries is composed of the SubSeries listed below. As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. In addition, to gain a better understanding of gene regulation at single cell level, it is important to include sufficient scATAC-seq data in the reference. To fill the gap, we performed snRNA-seq and snATAC-seq for the retina from healthy donors. To further increase the size of the dataset, we then collected and incorporated publicly available datasets. All data underwent a unified preprocessing pipeline and data integration. Multiple integration methods were benchmarked by scIB, and scVI was chosen. To harness the power of multiomics, snATAC-seq datasets were also preprocessed, and scGlue was used to generate co-embeddings between snRNA-seq and snATAC-seq cells. To facilitate the public use of references, we employ CELLxGENE and UCSC Cell Browser for visualization. By combining previously published and newly generated datasets, a single cell atlas of the human retina that is composed of 2.5 million single cells from 48 donors has been generated. As a result, over 90 distinct cell types are identified based on the transcriptomics profile with the rarest cell type accounting for about 0.01% of the cell population. In addition, open chromatin profiling has been generated for over 400K nuclei via single nuclei ATAC-seq, allowing systematic characterization of cis-regulatory elements for individual cell type. Integrative analysis reveals intriguing differences in the transcriptome, chromatin landscape, and gene regulatory network among cell class, subgroup, and type. In addition, changes in cell proportion, gene expression and chromatin openness have been observed between different gender and over age. Accessible through interactive browsers, this study represents the most comprehensive reference cell atlas of the human retina to date. As part of the human cell atlas project, this resource lays the foundation for further research in understanding retina biology and diseases.

Dataset Information

Cell Atlas of The Human Fovea and Peripheral Retina.

Publications

Cell Atlas of The Human Fovea and Peripheral Retina.

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