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Single-cell transcriptomes of the mouse retinal pigment epithelium response to low dose of doxorubicin

ABSTRACT: Purpose : Address heterogeneous composition in RPE cells and identify what subpopulation might be changed when cellular senescence is induced Methods: Mouse RPE cells (Control and Doxorubicin treatment) were isolated and sequenced using Chromium Next GEM Single Cell 5p RNA library v1.1. Alignment and quantification of raw data was performed through CellRanger v4.0.0 (10X Genomics) with reference to mm10 genome (FASTA). Results : As a result of mapping sequence reads to the reference genome (mm10) using the CellRanger count function, we obtained count data of 36030 filtered cells for 32285 features. R package Seurat (v 3.2.3) was used to perform additional analysis of filtered data including clustering. After classifying the clusters with the cell type marker from the clustering results of the entire cell data, the clusters showing the high expression level (log2FC >2) of RPE65, a marker gene for RPE cells, were isolated. In the isolated 3355 cells, 5 clusters and their marker genes were identified. Conclusion : In this study, we could find changes in heterogeneous composition and senescence in mouse RPE cells. RPE cells were classified into clusters according to their heterogeneity, and anti-apoptotic and senescent changes were confirmed through changes in gene expression in the Dox-treated in vivo mouse model. Some of the DEGs of Con vs Dox contained genes that have not yet been identified related to senescence. The RPE-specific transcriptome in this study enhances the understanding of the role of RPE senescence in AMD and will therefore be useful for developing treatments targeting RPE senescence and testing their effectiveness.

ORGANISM(S): Mus musculus

PROVIDER: GSE183572 | GEO | 2021/09/08

REPOSITORIES: GEO

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