{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE307nnn/GSE307355/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Homo sapiens"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307355"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"3D epigenomic landscape of human retinal pigment epithelium [RNA-seq]","description":"Retinal pigment epithelium (RPE) serves as a vital guardian of visual function, with its dysfunction driving pathogenesis in various retinal diseases, including age-related macular degeneration and inherited retinal disorders. While ongoing RPE cells transplantation clinical trials worldwide, the absence of standardized quality metrics for stem cell-derived RPE represents a significant gap. In this study, we aim to systematically dissect epigenomic divergence among human primary RPE (hRPE), induced pluripotent stem cell-derived RPE (iPSC-RPE), and immortalized ARPE-19 cells through multi-omic analyses. Our study elucidated the distinct functional characteristics of the three types of RPE and their underlying epigenetic regulatory mechanisms, with a particular focus on the development and functional maturation of iPSC-RPE. We further revealed cell-type-specific regulatory blueprints: hRPE exhibits strong extracellular matrix (ECM) organization capacity through 3D-epigenomic (3D genome folding and epigenomic state) regulation, as exemplified by the enrichment of the RUNX1 motif, whereas iPSC-RPE retains signatures of RPE development and weak ECM function, marked by transcription factors such as Hand1, OTX2, PAX6, and ECM-associated genes. On the other hand, ARPE-19 exhibits greater cell proliferation ability and specifically regulated by transcription factors such as KLF5. Together, our data greatly advance our understanding of RPE biology and provide a robust foundation for optimizing iPSC-RPE differentiation protocols and developing innovative therapeutic strategies for retinal diseases.","dates":{"publication":"2026/07/26"},"accession":"GSE307355","cross_references":{"GSM":["GSM9222709","GSM9883377","GSM9222708","GSM9222712","GSM9222713","GSM9222710","GSM9222711","GSM9883376"],"GPL":["24676"],"GSE":["307355"],"taxon":["Homo sapiens"]}}