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Updated: Jul 29, 2025
Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells
Published on: May 22, 2017
Single-cell RNA sequencing reveals a unique pericyte type associated with capillary dysfunction
Min Xia1,2, Lyu Jiao3, Xiao-Han Wang3
1The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing 210000, China.
Insights
Collagen type 1 alpha 1 (Col1a1) is a key marker for vulnerable pericytes in retinal capillary dysfunction. Targeting Col1a1 shows promise for treating proliferative retinopathies.
Area of Science:
- Vascular biology
- Retinal cell biology
- Molecular ophthalmology
Background:
- Capillary dysfunction, marked by pericyte and endothelial cell (EC) degeneration, underlies severe vascular diseases.
- The molecular mechanisms driving pericyte heterogeneity and their role in capillary dysfunction remain incompletely understood.
Purpose of the Study:
- To elucidate the molecular profiles governing pericyte heterogeneity in the context of retinal capillary dysfunction.
- To identify specific pericyte subpopulations and molecular targets for therapeutic intervention in conditions like oxygen-induced proliferative retinopathy (OIR).
Main Methods:
- Single-cell RNA sequencing of mouse retinas to create a comprehensive cellular atlas.
- Bioinformatics analysis, including sub-clustering, Gene Ontology (GO), and KEGG pathway analysis, to identify vulnerable pericyte populations.
- Quantitative reverse transcription PCR (qRT-PCR), Western blotting, and in vitro assays (Matrigel co-culture, PI, JC-1 staining) to validate the role of Collagen type 1 alpha 1 (Col1a1).
Main Results:
- A single-cell atlas revealed 10 distinct retinal cell types, with pericytes sub-clustered into three subpopulations.
- Pericyte sub-population 2 was identified as vulnerable to capillary dysfunction, with Col1a1 identified as its marker gene.
- Col1a1 expression was upregulated in OIR retinas and in patients with proliferative diabetic retinopathy (PDR) and retinopathy of prematurity (ROP); Col1a1 silencing ameliorated OIR pathology in vitro and in vivo.
Conclusions:
- Col1a1 is a critical marker for a vulnerable pericyte subpopulation and a potential therapeutic target for retinal capillary dysfunction.
- Targeting Col1a1 may offer a novel strategy for treating sight-threatening proliferative retinopathies by mitigating pericyte loss and neovascularization.
Abstract:
Background: Capillary dysfunction has been implicated in a series of life- threatening vascular diseases characterized by pericyte and endothelial cell (EC) degeneration. However, the molecular profiles that govern the heterogeneity of pericytes have not been fully elucidated. Methods: Single-cell RNA sequencing was conducted on oxygen-induced proliferative retinopathy (OIR) model. Bioinformatics analysis was conducted to identify specific pericytes involved in capillary dysfunction. qRT-PCRs and western blots were conducted to detect Col1a1 expression pattern during capillary dysfunction. Matrigel co-culture assays, PI staining, and JC-1 staining was conducted to determine the role of Col1a1 in pericyte biology. IB4 and NG2 staining was conducted to determine the role of Col1a1 in capillary dysfunction. Results: We constructed an atlas of > 76,000 single-cell transcriptomes from 4 mouse retinas, which could be annotated to 10 distinct retinal cell types. Using the sub-clustering analysis, we further characterized retinal pericytes into 3 different subpopulations. Notably, GO and KEGG pathway analysis demonstrated that pericyte sub-population 2 was identified to be vulnerable to retinal capillary dysfunction. Based on the single-cell sequencing results, Col1a1 was identified as a marker gene of pericyte sub-population 2 and a promising therapeutic target for capillary dysfunction. Col1a1 was abundantly expressed in pericytes and its expression was obviously upregulated in OIR retinas. Col1a1 silencing could retard the recruitment of pericytes toward endothelial cells and aggravated hypoxia-induced pericyte apoptosis in vitro. Col1a1 silencing could reduce the size of neovascular area and avascular area in OIR retinas and suppressed pericyte-myofibroblast transition and endothelial-mesenchymal transition. Moreover, Col1a1 expression was up-regulated in the aqueous humor of the patients with proliferative diabetic retinopathy (PDR) or retinopathy of prematurity (ROP) and up-regulated in the proliferative membranes of PDR patients. Conclusions: These findings enhance the understanding of the complexity and heterogeneity of retinal cells and have important implications for future treatment of capillary dysfunction.
