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Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [bulk RNA-seq]

ABSTRACT: Purpose: The goals of this study were to identify cell specific expression patterns from the fovea, perifovea, and macular neural retina. Methods: Independent libraries were prepared for human foveal (1mm), perifoveal (4mm), and macular (8mm) regions of neural retina. Poly-A selected RNA transcripts underwent 150 base-pair paired-end sequencing with an Illumina HiSeq 4000. Reads were mapped to the human genome hg19 with STAR (version = 020201) and quantified with the featureCounts function from the Rsubread package (version = 1.28.1). Differential expression analysis was performed with edgeR (version = 3.26.8). Results: Differential expression analysis identified genes enriched in each retinal region. Conclusions: This study provides a transcriptomic comparison of foveal, perifoveal, and macular human neural retina at the bulk and single-cell levels.

ORGANISM(S): Homo sapiens

PROVIDER: GSE169046 | GEO | 2021/05/13

REPOSITORIES: GEO

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Human photoreceptor cells from different macular subregions have distinct transcriptional profiles [single-cell RNA-seq]

Project description:Purpose: The goals of this study were to identify expression patterns in foveal versus parafoveal cells isolated from the human retina. Methods: Independent libraries were prepared for foveal and parafoveal cells isolated from four human donors (donors 5-8). A foveal (1 mm) and parafoveal (4 mm) punch of neural retina was acquired from each donor. Each punch of neural retina was gently dissociated in papain (Worthington biochemical) for 1.25 hours before cryopreservation. Thawed cells were barcoded with the 10X chromium and resulting libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build GRCh38 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 5-8 were aggregated 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 34,493 cells were recovered after filtering with 139,962,070 corresponding reads. A total of 5,856 cells were recovered from foveal libraries while 28,637 cells were recovered from the parafoveal libraries. Clusters were assigned to known retinal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from the fovea versus the parafovea. Particular emphasis was given to regionally expressed genes in cone photoreceptor cells and Muller cells. Conclusions: This study provides a transcriptomic comparison of the foveal and parafoveal human retina at the bulk and single-cell levels. The foveal retina is transcriptomically distinct from the directly surrounding parafovea.

2021-05-13 | GSE169047 | GEO

Human Retina Proteomics - Dissection of Human Retina and RPE-Choroid for Proteomic Analysis

Project description:Differences in regional protein expression within the human retina may explain molecular predisposition of specific regions to ophthalmic diseases like age-related macular degeneration, cystoid macular edema, retinitis pigmentosa, and diabetic retinopathy. To quantify protein levels in the human retina and identify patterns of differentially-expressed proteins, we collected foveal, macular, and peripheral retina punch biopsies from healthy donor eyes and analyzed protein content by liquid chromatography-tandem mass spectrometry (LC-MS/MS).

2018-02-26 | PXD008462 | Pride

Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset

Project description:In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the degree of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing (scRNA-seq) to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults.

2023-12-26 | GSE249004 | GEO

Transcriptome analysis of human maturing macula

Project description:The macula is an essential region of the retina responsible for visual acuity. Abnormalities in development of the fovea at the center of the macula lead to severe diseases. To identify macula-specific differentially expressed genes in maturing stage of macular development, we compared the gene expression profiles of the macular and peripheral region of the pediatric retina.

2023-03-31 | GSE144300 | GEO

Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina

Project description:Purpose: Single-cell RNA sequencing has revolutionized cell-type specific gene expression analysis. The goals of this study are to compare cell specific gene expression patterns between retinal cell types originating from the fovea and the periphery of human eyes. Methods: Independent libraries were prepared for foveal and peripheral samples of neural retina from three donors using the 10x Chromium system. 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 (v2.3.4). Results: Independent libraries were prepared for foveal and peripheral samples of neural retina from three donors using the 10x Chromium system. 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 (v2.3.4). Conclusions: Our study generates a large atlas of human retinal transcriptomes at the single cell level. We identified the majority of expected neural and supportive cell types, and describe regional differences in gene expression between the fovea and the periphery. Our results show that that single-cell RNA sequencing can be performed on human retina after cryopreservation, and that cone photoreceptors and Muller cells demonstrate region-specific patterns of gene expression.

2019-05-17 | GSE130636 | GEO

Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways

Project description:The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes such as age-related macular degeneration (AMD). Unfortunately our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea. We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid.

2022-01-24 | GSE194285 | GEO

Effects of Aging and Anatomic Location on Gene Expression in Human Retina

Project description:Objective: To determine the effects of age and topographic location on gene expression in human neural retina. Methods: Macular and peripheral neural retina RNA were isolated from human donor eyes for DNA microarray and quantitative RTPCR analyses. Results: Total RNA from human donor retina preserved integrity. Hierarchic clustering analysis demonstrates the gene expression profiles of young, old, macula and peripheral retina cluster into four distinct groups. Genes which are highly expressed in macular, peripheral, young or old retina are identified, including inhibitors of Wnt Signaling Pathway (DKK1, FZD10 and SFRP2) shown preferably expressed in the periphery. Conclusions: The transcriptome of the human retina is affected by age and topographic location. Wnt pathway inhibitors in the periphery may maintain peripheral retinal cells in an undifferentiated state. Understanding the effects of age and topographic location on gene expression may lead to the development of new therapeutic interventions for age-related eye diseases. Twleve youang and older retinal macular or prepheral RNA samples are used for DNA microarray study to compare the effects of aging and anatomic location on gene expression in human retina.

2015-05-27 | E-GEOD-32614 | biostudies-arrayexpress

Multimodal single nuclei profiling of human macular and peripheral retinal pigment epithelial cells

Project description:We sought to understand how the RPE confers region-specific disease susceptibility in the retina by examining heterogeneity within human donor RPE. We profiled RPE nuclei from the macular and peripheral retina using joint single-cell RNA and ATAC sequencing.

2023-01-12 | GSE220155 | GEO

A Proteomic Approach to Understanding the Pathogenesis of Idiopathic Macular Hole Formation

Project description:Idiopathic macular holes (IMH) are full-thickness defects of retinal tissue that cause severe vision loss due to disruption of the anatomic fovea. Abnormal vitreous traction is involved in the formation of macular holes. Both glial cells and hyalocytes contribute to epiretinal membrane formation in IMH. In order to gain further insight into the pathophysiology of IMH, we conducted a discovery phase investigation of the vitreous proteome in four patients with macular holes and six controls using one-dimensional gel fractionation and liquid chromatography-tandem mass spectrometry analyses on an Orbitrap Elite mass spectrometer. Of a total of 5912 vitreous proteins, 32 proteins had increased and 39 proteins had decreased expression in IMH compared with controls, using a false discovery rate approach with p-value <0.001 and q value <0.05. IMH was associated with increased expression of proteins in the complement pathway, α-2-macroglobulin, a major inducer of Müller glial cell migration, fibrinogen, and extracellular matrix proteins, and decreased expression of proteins involved in protein folding and actin filament binding. A proteomic approach revealed proteins and biological pathways that may be involved in the pathogenesis of IMH and could be targeted for future studies.

2018-04-11 | PXD006687 | Pride

Single-cell analysis reveals inflammatory interactions driving macular degeneration

Project description:Due to commonalities in pathophysiology, age-related macular degeneration represents a uniquely accessible model to investigate therapies for neurodegenerative diseases, leading us to examine whether pathways of disease progression are shared across neurodegenerative conditions. Here we use single-nucleus RNA sequencing to profile lesions from 17 retinas with age-related macular degeneration and controls. We create a machine learning pipeline based on recent advances in data geometry and topology and identify activated glial populations enriched in the early phase of disease. Examining single-cell data from Alzheimer’s disease and progressive multiple sclerosis with our pipeline, we find a similar glial activation profile enriched in the early phase of these neurodegenerative diseases. In late-stage age-related macular degeneration, we identify a microglia-to-astrocyte signaling axis mediated by interleukin-1beta which drives angiogenesis characteristic of disease pathogenesis. Thus, due to shared glial states, the retina provides a system for investigating therapeutic approaches in neurodegenerative diseases.

2023-01-18 | GSE221042 | GEO

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