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Transcriptome Analysis and Molecular Signature of Human Retinal Pigment Epithelium

ABSTRACT: The retinal pigment epithelium (RPE) is a polarized cell layer that is critical for photoreceptor function and survival. It’s unique relationship to the photoreceptors and its specific physiology makes the RPE a critical determinant of human vision. Therefore we performed global expression profiling of native and cultured human fetal and adult RPE and determined a unique set of highly-expressed genes (called the “signature” set) by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues.

ORGANISM(S): Homo sapiens

PROVIDER: GSE18811 | GEO | 2010/04/15

SECONDARY ACCESSION(S): PRJNA121231

REPOSITORIES: GEO

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Transcriptome Analysis and Molecular Signature of Human Retinal Pigment Epithelium

Project description:The retinal pigment epithelium (RPE) is a polarized cell layer that is critical for photoreceptor function and survival. Itâs unique relationship to the photoreceptors and its specific physiology makes the RPE a critical determinant of human vision. Therefore we performed global expression profiling of native and cultured human fetal and adult RPE and determined a unique set of highly-expressed genes (called the âsignatureâ set) by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues. A comparative analysis of transcriptomes from human fetal and adult RPE, primary cultures and commonly-used cell lines was performed. Using selection criteria of at least 10-fold higher expression in each of three RPE preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues.

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Project description:Transplantation of retinal pigment epithelial (RPE) cells holds great promise for patients with retinal degenerative diseases such as age-related macular degeneration. In-depth characterization of RPE cell product identity and critical quality attributes are needed to enhance efficacy and safety of replacement therapy strategies. Here we characterized an adult RPE stem cell-derived (RPESC-RPE) cell product using bulk and single cell RNA sequencing (sc-RNA-seq), assessing functional cell integration in vitro into a mature RPE monolayer and in vivo efficacy by vision rescue in the Royal College of Surgeons rats. scRNA-seq revealed several distinct subpopulations in the RPESC-RPE product, some with progenitor markers. We identified RPE clusters expressing genes associated with in vivo efficacy and increased cell integration capability. Gene expression analysis revealed a lncRNA (TREX) as a predictive marker of in vivo efficacy. TREX knockdown decreased cell integration while overexpression increased integration in vitro and improved vision rescue in the RCS rats.

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