Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells

• Published in: Molecular vision 2017, Vol.23, p.60-89
• Main Authors: Samuel, William, Jaworski, Cynthia, Postnikova, Olga A, Kutty, R Krishnan, Duncan, Todd, Tan, Li Xuan, Poliakov, Eugenia, Lakkaraju, Aparna, Redmond, T Michael
• Format: Article
• Language: English
• Subjects: Animal models; Cell culture; Cell cycle; Cell Differentiation - genetics; Cell Line; Cell proliferation; Data processing; Down-Regulation - genetics; Epithelial Cells - metabolism; Gene expression; Gene Expression Profiling; Gene Ontology; Genotype & phenotype; Humans; Immunocytochemistry; Melanins - metabolism; MicroRNAs - genetics; MicroRNAs - metabolism; Ontology; Phagocytosis; Phagocytosis - genetics; Phenotype; Phenotypes; Photopigments; Pigmentation; Proteins; Pyruvic acid; Retinal Pigment Epithelium - cytology; Retinal Pigment Epithelium - metabolism; Retinoids - metabolism; Ribonucleic acid; RNA; Stem cells; Transcription factors; Up-Regulation - genetics; Western blotting
• ISSN: 1090-0535; 1090-0535

The RPE cell line ARPE-19 provides a dependable and widely used alternative to native RPE. However, replication of the native RPE phenotype becomes more difficult because these cells lose their specialized phenotype after multiple passages. Compounding this problem is the widespread use of ARPE-19 cells in an undifferentiated state to attempt to model RPE functions. We wished to determine whether suitable culture conditions and differentiation could restore the RPE-appropriate expression of genes and proteins to ARPE-19, along with a functional and morphological phenotype resembling native RPE. We compared the transcriptome of ARPE-19 cells kept in long-term culture with those of primary and other human RPE cells to assess the former's inherent plasticity relative to the latter. ARPE-19 cells at passages 9 to 12 grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum were differentiated for up to 4 months. Immunocytochemistry was performed on ARPE-19 cells grown on filters. Total RNA extracted from ARPE-19 cells cultured for either 4 days or 4 months was used for RNA sequencing (RNA-Seq) analysis using a 2 × 50 bp paired end protocol. The RNA-Seq data were analyzed to identify the affected pathways and recognize shared ontological classification among differentially expressed genes. RPE-specific mRNAs and miRNAs were assessed with quantitative real-time (RT)-PCR, and proteins with western blotting. ARPE-19 cells grown for 4 months developed the classic native RPE phenotype with heavy pigmentation. RPE-expressed genes, including , , and , as well as miR-204/211, were greatly increased in the ARPE-19 cells maintained at confluence for 4 months. The RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of the genes in the differentiated ARPE-19 cells. Of the 16,757 genes with detectable signals, nearly 1,681 genes were upregulated, and 1,629 genes were downregulated with a fold change of 2.5 or more differences between 4 months and 4 days of culture. Gene Ontology analysis showed that the upregulated genes were associated with visual cycle, phagocytosis, pigment synthesis, cell differentiation, and RPE-related transcription factors. The majority of the downregulated genes play a role in cell cycle and proliferation. The ARPE-19 cells cultured for 4 months developed a phenotype characteristic of native RPE and expressed proteins, mRNAs, and miRNAs characteristic of the RPE. Comparison of the