Document Type


Publication Date


Publication Title

Int J Mol Sci


JGM, JMG, Animals, Gene Expression Profiling, Male, Mammals, Mice, Mice, Inbred C57BL, Retinal Pigment Epithelium, Sequence Analysis, RNA, Transcriptome

JAX Source

Int J Mol Sci. 2022;23(18):10419.











The research presented in this publication was supported by the National Eye Institute of the National Institutes of Health under award numbers R01EY011996 to P. M. N., R01EY027305 to P. M. N. and M.P.K., R01EY027860 to P. M. N. and G. W. C., and R01EY028561 to J. K. N., and by The Jackson Laboratory, Director’s Innovation Fund (DIF), award number 19000-16-13. The authors also wish to acknowledge the support of the JAX Cancer Center Single Cell Biology, Genome Technologies, and Flow Cytometry Shared Resources, supported by the National Cancer Institute of the National Institutes of Health under award number P30CA034196.


Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity within native tissue, which adds complexity to global transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2667 and 2846 RPE cells. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell populations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1-2% of total cells) exhibited the hallmarks of stem and/or progenitor (SP) cells. Placing C1-6 along a pseudotime axis suggested a relative decrease in melanogenesis and SP gene expression and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means clustering of all detected transcripts identified additional expression patterns that may advance the understanding of RPE SP cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.


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