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Single-cell RNA sequencing in human retinal degeneration reveals distinct glial cell populations.

ABSTRACT: Purpose: The goals of this study were to identify cell specific expression patterns from a donor with a presumed diagnosis of autoimmune retinopathy (AIR). A particular focus of this study was to identify expression signatures of Müller glia and astrocytes in AIR. Methods: Independent libraries were prepared for foveal and peripheral retina from five human donors in two experiments. Foveal and peripheral samples in donors 1-3 were acquired, analyzed, and uploaded in a previous experiment (GSE130636). In donors 4-5, new reads were acquired from a 2-mm fovea-centered punch and an 8-mm peripheral punch from the inferotemporal region in each donor. Donor 4 had no documented history of retinal disease. Donor 5 was followed for 19 years at the University of Iowa Hospitals and Clinics for progressive visual field loss and pigmentary changes and was given a presumptive diagnosis of autoimmune retinopathy. Foveal and peripheral retinal tissue were gently dissociated in papain for 1.25 hours before cryopreservation. In both experiments, libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from all five donors were aggregated to the same effective sequencing depth, and log-normalization of aggregated reads was performed with Seurat (v2.3.4) using a scale factor of 10,000. Results: A total of 23,429 cells were recovered after filtering with 117,885,744 corresponding reads. A total of 9,801 cells were recovered from the fovea while 13,628 cells were recovered from the periphery. A total of 7,189 cells were recovered from the donor with presumed AIR. In total, 23 clusters were identified and corresponded to all retinal cell types. The proportion of recovered cells was compared between the control (donors 1-4) and AIR (donor 5) patients. In addition, differential expression analysis identified genes enriched in each population of cells originating from the AIR donor. Particular emphasis was given to the expression profiles of glial cells (Müller cells and astrocytes) that originated from the AIR donor. Conclusions: This study provides a complementary clinical and molecular interrogation of the retina in a blinding inflammatory condition. Glial cells from the AIR donor were enriched in genes implicated in reactive gliosis, including ANXA1. Clinical, histologic, and transcriptomic evidence identify the loss of cone and rod photoreceptor cells with relative preservation of inner retinal cell types.

ORGANISM(S): Homo sapiens

PROVIDER: GSE142449 | GEO | 2020/02/17

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study were to identify cell specific expression patterns of the retinal pigment epithelium (RPE) and a variety of choroidal cell types originating from the macula and the periphery of human donor eyes, with a particular emphasis on identifying expression signatures of choroidal endothelial cells. Methods: Independent libraries were prepared for macular and peripheral samples of combined RPE/choroid from seven donors in two single cell sequencing experiments. In the first experiment, 8-mm macular and peripheral punches of RPE/choroid from Donors 1-3 were digested in papain prior to cryopreservation and subsequent GEM barcoding/library construction. Donors 1-2 had no noted ophthalmologic disease documented, while Donor 3 was diagnosed with age-related macular degeneration. In the second experiment, 12-mm macular and peripheral punches of RPE/choroid from Donors 4-7 were digested in collagenase II prior to cryopreservation, CD31-magentic bead enrichment and subsequent GEM barcoding/library construction. Donors 5-7 had no noted ophthalmologic disease documented, while Donor 4 was diagnosed with age-related macular degeneration. In both experiments, libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 will CellRanger(v3.0.1) and filters removed cells likely to be doublets or cells with a high proportion of mitochondrial reads. Clustering of cells with similar expression profiles was performed with Seurat (v3.0.2). Results: In the first experiment with unenriched RPE/choroid from donors 1-3, we recovered 4,355 cells post filtering with 40,177,477 corresponding reads. A total of 2,167 cells originated from the macula and 2,168 cells originated from the periphery. A total of 11 clusters were identified, and highly enriched genes in each cluster were used to classify clusters into their presumed dominant cell type. Differential expression analysis was performed between cells of macular and peripheral origin in each cluster and between donors with and without a history of age-related macular degeneration. Results: In the second experiment with CD31-enriched RPE/choroid from donors 4-7, we recovered 14,234 cells post filtering with 135,742,297 corresponding reads. A total of 7,647 cells originated from the macula and 6,587 cells originated from the periphery. A total of 8,521 of these cells were presumed endothelial cells. A total of 13 clusters were identified, and highly enriched genes in each cluster were used to classify clusters into their presumed dominant cell type(s). Differential expression analysis was performed between cells of macular and peripheral origin in each cluster and between donors with and without a history of age-related macular degeneration. Within each of the endothelial clusters (Clusters 5-8), differential expression analysis was performed between each cluster and the remaining endothelial cells. Conclusions: This study provides a large atlas of single-cell level gene expression patterns of the human retinal pigment epithelium and choroidal cell types. We identify expression patterns of most expected choroidal cell populations and describe macular versus peripheral regional differences. We additionally identify enriched transcripts in specific cell populations in age-related macular degeneration. We characterize gene expression patterns along the choroidal vascular tree, and identify populations of arterial, capillary, and venous endothelial cells. Our results show that single-cell sequencing can be performed on human RPE/choroid after cryopreservation, and that CD31 magnetic bead enrichment can be employed to enrich for endothelial cells for single-cell sequencing.

Project description:Purpose: The goals of this study were to identify cell specific expression patterns from infant and aged choroid, with a particular emphasis on how endothelial gene expression changes with age. Methods: Independent libraries were prepared for infant and adult choroidal cells from four human donors. Macular and peripheral samples from single-cell donors 18-21 were acquired, analyzed, and uploaded in a previous experiment (GSE135922). In single-cell donors 22-25, new reads were acquired from a 12-mm macula-centered punch. Choroidal punches gently dissociated in collagenase II for 1 hours before cryopreservation. Thawed cells were enriched endothelial cells by incubating with anti-CD31-microbeads. Both CD31-positive and CD31-negative libraries from single-cell donors 22-25 were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build hg19 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from single-cell donors 22-25 were aggregated with donors 18-21 using canonical correlation analysis. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1). Results: A total of 37,070 cells were recovered after filtering with 415,740,738 corresponding reads. A total of 17,229 cells were recovered from infant libraries while 19,841 cells were recovered from the adult libraries. Clusters were assigned to known choroidal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from infant versus adult libraries. Particular emphasis was given to genes enriched in infant choriocapillaris endothelial cells. Conclusions: This study provides a transcriptomic comparison of infant and aged human donor choroid at the bulk and single-cell levels. The aged choroid, in particular the aged vasculature, is enriched in pro-inflammatory genes.

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Single-cell RNA sequencing in human retinal degeneration reveals distinct glial cell populations.

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