Comparative Analysis of Single-cell and Single-nucleus RNA-sequencing in a Rabbit Model of Retinal Detachment-related Proliferative Vitreoretinopathy.

Autor:	Santiago CP; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland., Gimmen MY; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland., Lu Y; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland., McNally MM; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland., Duncan LH; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland., Creamer TJ; Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, Maryland., Orzolek LD; Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, Maryland., Blackshaw S; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland.; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland.; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.; Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland.; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland., Singh MS; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Jazyk:	angličtina
Zdroj:	Ophthalmology science [Ophthalmol Sci] 2023 May 23; Vol. 3 (4), pp. 100335. Date of Electronic Publication: 2023 May 23 (Print Publication: 2023).
DOI:	10.1016/j.xops.2023.100335
Abstrakt:	Purpose: Proliferative vitreoretinopathy (PVR) is the most common cause of failure of retinal reattachment surgery, and the molecular changes leading to this aberrant wound healing process are currently unknown. Our ultimate goal is to study PVR pathogenesis by employing single-cell transcriptomics to dissect cellular heterogeneity. Design: Here we aimed to compare single-cell RNA sequencing (scRNA-seq)  and single-nucleus RNA-sequencing (snRNA-seq) of retinal PVR samples in the rabbit model. Participants: Unilateral induction of PVR lesions in rabbit eyes with contralateral eyes serving as controls. Methods: Proliferative vitreoretinopathy was induced unilaterally in Dutch Belted rabbits. At different timepoints after PVR induction, retinas were dissociated into either cells or nuclei suspension and processed for scRNA-seq or snRNA-seq. Main Outcome Measures: Single cell and nuclei transcriptomic profiles of retinas after PVR induction. Results: Single-cell RNA sequencing and snRNA-seq were conducted on retinas at 4 hours and 14 days after disease induction. Although the capture rate of unique molecular identifiers and genes were greater in scRNA-seq samples, overall gene expression profiles of individual cell types were highly correlated between scRNA-seq and snRNA-seq. A major disparity between the 2 sequencing modalities was the cell type capture rate, however, with glial cell types overrepresented in scRNA-seq, and inner retinal neurons were enriched by snRNA-seq. Furthermore, fibrotic Müller glia were overrepresented in snRNA-seq samples, whereas reactive Müller glia were overrepresented in scRNA-seq samples. Trajectory analyses were similar between the 2 methods, allowing for the combined analysis of the scRNA-seq and snRNA-seq data sets. Conclusions: These findings highlight limitations of both scRNA-seq and snRNA-seq analysis and imply that use of both techniques together can more accurately identify transcriptional networks critical for aberrant fibrogenesis in PVR than using either in isolation. Financial Disclosures: Proprietary or commercial disclosure may be found after the references. (© 2023 by the American Academy of Ophthalmology.)
Databáze:	MEDLINE
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