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Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium

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 trans...

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Autores principales: Pandey, Ravi S., Krebs, Mark P., Bolisetty, Mohan T., Charette, Jeremy R., Naggert, Jürgen K., Robson, Paul, Nishina, Patsy M., Carter, Gregory W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9499471/
https://www.ncbi.nlm.nih.gov/pubmed/36142331
http://dx.doi.org/10.3390/ijms231810419
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author Pandey, Ravi S.
Krebs, Mark P.
Bolisetty, Mohan T.
Charette, Jeremy R.
Naggert, Jürgen K.
Robson, Paul
Nishina, Patsy M.
Carter, Gregory W.
author_facet Pandey, Ravi S.
Krebs, Mark P.
Bolisetty, Mohan T.
Charette, Jeremy R.
Naggert, Jürgen K.
Robson, Paul
Nishina, Patsy M.
Carter, Gregory W.
author_sort Pandey, Ravi S.
collection PubMed
description 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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spelling pubmed-94994712022-09-23 Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium Pandey, Ravi S. Krebs, Mark P. Bolisetty, Mohan T. Charette, Jeremy R. Naggert, Jürgen K. Robson, Paul Nishina, Patsy M. Carter, Gregory W. Int J Mol Sci Article 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. MDPI 2022-09-08 /pmc/articles/PMC9499471/ /pubmed/36142331 http://dx.doi.org/10.3390/ijms231810419 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pandey, Ravi S.
Krebs, Mark P.
Bolisetty, Mohan T.
Charette, Jeremy R.
Naggert, Jürgen K.
Robson, Paul
Nishina, Patsy M.
Carter, Gregory W.
Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium
title Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium
title_full Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium
title_fullStr Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium
title_full_unstemmed Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium
title_short Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium
title_sort single-cell rna sequencing reveals molecular features of heterogeneity in the murine retinal pigment epithelium
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9499471/
https://www.ncbi.nlm.nih.gov/pubmed/36142331
http://dx.doi.org/10.3390/ijms231810419
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