Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing

A.P Voigt; S.S Whitmore; M.J Flamme-Wiese; M.J Riker; L.A Wiley; B.A Tucker; E.M Stone; R.F Mullins; T.E Scheetz

doi:10.1016/j.exer.2019.05.001

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Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing

Journal article

Open access

Peer reviewed

Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing

A.P Voigt, S.S Whitmore, M.J Flamme-Wiese, M.J Riker, L.A Wiley, B.A Tucker, E.M Stone, R.F Mullins and T.E Scheetz

Experimental eye research, Vol.184, pp.234-242

07/2019

DOI: 10.1016/j.exer.2019.05.001

PMID: 31075224

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Abstract

The human retina is a complex tissue responsible for detecting photons of light and converting information from these photons into the neurochemical signals interpreted as vision. Such visual signaling not only requires sophisticated interactions between multiple classes of neurons, but also spatially-dependent molecular specialization of individual cell types. In this study, we performed single-cell RNA sequencing on neural retina isolated from both the fovea and peripheral retina in three human donors. We recovered a total of 8,217 cells, with 3,578 cells originating from the fovea and 4,639 cells originating from the periphery. Expression profiles for all major retinal cell types were compiled, and differential expression analysis was performed between cells of foveal versus peripheral origin. Globally, mRNA for the serum iron binding protein transferrin (TF), which has been associated with age-related macular degeneration pathogenesis, was enriched in peripheral samples. Cone photoreceptor cells were of particular interest and formed two predominant clusters based on gene expression. One cone cluster had 96% of cells originating from foveal samples, while the second cone cluster consisted exclusively of peripherally isolated cells. A total of 148 genes were differentially expressed between cones from the fovea versus periphery. Interestingly, peripheral cones were enriched for the gene encoding Beta-Carotene Oxygenase 2 (BCO2). A relative deficiency of this enzyme may account for the accumulation of carotenoids responsible for yellow pigment deposition within the macula. Overall, this data set provides rich expression profiles of the major human retinal cell types and highlights transcriptomic features that distinguish foveal and peripheral cells. [Display omitted] •Gene expression characterization of human retinal cell types.•Foveal and peripheral retinal cell types have distinct gene expression patterns.•Transferrin is enriched in peripheral retina cell types.

Retina

Transferrin

Cones

Single-cell

Fovea

Details

Title: Subtitle: Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing
Creators: A.P Voigt - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
S.S Whitmore - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
M.J Flamme-Wiese - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
M.J Riker - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
L.A Wiley - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
B.A Tucker - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
E.M Stone - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
R.F Mullins - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
T.E Scheetz - Departments of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
Resource Type: Journal article
Publication Details: Experimental eye research, Vol.184, pp.234-242
DOI: 10.1016/j.exer.2019.05.001
PMID: 31075224
NLM abbreviation: Exp Eye Res
ISSN: 0014-4835
eISSN: 1096-0007
Publisher: Elsevier Ltd
Grant note: DOI: 10.13039/100000002, name: National Institutes of Health, award: EY027038, EY025580; name: MSTP training, award: T32 GM007337; name: Roy J. Carver, Jr. Chair in Bioinformatics and Computational Biology
Language: English
Date published: 07/2019
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; The University of Iowa Institute for Vision Research; Iowa Neuroscience Institute; Ophthalmology and Visual Sciences
Record Identifier: 9984070822302771

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