June 2021
Volume 62, Issue 8
Open Access
ARVO Annual Meeting Abstract  |   June 2021
Single-cell RNA sequencing identifies unique gene expression patterns in the foveal and perifoveal human retina
Author Affiliations & Notes
  • Andrew P Voigt
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • Nathaniel Kevin Mullin
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • S Scott Whitmore
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • Todd E Scheetz
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • Edwin M Stone
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • Budd A. Tucker
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • Robert F Mullins
    The University of Iowa Department of Ophthalmology and Visual Sciences, Iowa City, Iowa, United States
  • Footnotes
    Commercial Relationships   Andrew Voigt, None; Nathaniel Mullin, None; S Whitmore, None; Todd Scheetz, None; Edwin Stone, None; Budd Tucker, None; Robert Mullins, None
  • Footnotes
    Support  NIH EY027038, NIH EY024605, NIH P30 EY025580, NIH F30 EY031923, and the MSTP training grant T32 GM007337
Investigative Ophthalmology & Visual Science June 2021, Vol.62, 463. doi:
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    • Get Citation

      Andrew P Voigt, Nathaniel Kevin Mullin, S Scott Whitmore, Todd E Scheetz, Edwin M Stone, Budd A. Tucker, Robert F Mullins; Single-cell RNA sequencing identifies unique gene expression patterns in the foveal and perifoveal human retina. Invest. Ophthalmol. Vis. Sci. 2021;62(8):463.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : In different retinal diseases, photoreceptors cells at different eccentricities can be selectively damaged or spared. Previous investigations have identified unique foveal features by comparing gene expression between the foveal versus peripheral retina. We refined these preliminary studies by focusing on differences within the macula, comparing the fovea and the directly surrounding perifoveal retina with single-cell RNA sequencing.

Methods : Paired foveal (1 mm) and perifoveal (4 mm) neural retina samples were acquired from four human donor eyes. Retinal tissue was dissociated in papain for one hour and cryopreserved so that cell suspensions could be thawed in parallel for single-cell RNA sequencing. Resulting reads were mapped to the human genome with CellRanger and analyzed with Seurat.

Results : We recovered 5,856 foveal and 28,637 perifoveal cells that corresponded to all major retinal populations (Figure 1A). Next, we compared foveal versus perifoveal gene expression across all retinal populations. Foveal cone photoreceptors demonstrated increased expression of RPGR and RP1L1, which are mutated in cone-rod dystrophy and occult macular dystrophy, respectively. In contrast, perifoveal cone photoreceptors were enriched in COL4A3, a gene with AMD-associated genetic variants. Perifoveal Müller cells showed increased expression of the visual cycle genes RDH10 and RLBP1 as well as the iron-binding protein transferrin (TF). In addition, we compared results from this study to five independent single-cell RNA sequencing investigations comparing central versus peripheral retina (Figure 1B). Foveal enriched genes from our study were increased in the central retina from these datasets. Likewise, perifoveal enriched genes from our study demonstrated increased expression in the peripheral retina of these datasets.

Conclusions : Single-cell RNA sequencing reveals regional patterns of gene expression across many different retinal cell populations. We identified foveal enrichment or depletion of several transcripts involved in inherited retinal disease.

This is a 2021 ARVO Annual Meeting abstract.

 

Figure 1. A. Single-cell RNA sequencing of foveal and perifoveal neural retina from four human donors. B. Comparison of foveal versus perifoveal expression of RP1L1 (in cones) and TF (in Muller cells) in this study (red) to five independent retinal single-cell RNA sequencing datasets (yellow, orange, blue colors).

Figure 1. A. Single-cell RNA sequencing of foveal and perifoveal neural retina from four human donors. B. Comparison of foveal versus perifoveal expression of RP1L1 (in cones) and TF (in Muller cells) in this study (red) to five independent retinal single-cell RNA sequencing datasets (yellow, orange, blue colors).

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