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

Exp Eye Res. 2019 Jul;184:234-242. doi: 10.1016/j.exer.2019.05.001. Epub 2019 May 8.


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.

Keywords: Cones; Fovea; Retina; Single-cell; Transferrin.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged, 80 and over
  • Dioxygenases / genetics
  • Female
  • Fovea Centralis / cytology*
  • Fovea Centralis / metabolism
  • Gene Expression Profiling*
  • Humans
  • Male
  • Middle Aged
  • RNA, Messenger / genetics
  • Retina / cytology*
  • Retina / metabolism
  • Retinal Cone Photoreceptor Cells / cytology*
  • Retinal Cone Photoreceptor Cells / metabolism
  • Sequence Analysis, RNA*
  • Tissue Donors
  • Transferrin / genetics


  • RNA, Messenger
  • Transferrin
  • Dioxygenases
  • BCO2 protein, human