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Identification of key regulatory pathways in response to long-term zinc supplementation in human primary retinal pigment epithelium: a multi-omics approach

ABSTRACT: Purpose: In age-related macular degeneration (AMD), both systemic and local zinc concentrations are decreased. Elevating zinc levels by nutrition or oral supplementation has a positive impact on delaying the progression to end-stage AMD in clinical studies. Here we set out to identify key regulatory pathways involved in this beneficial effect in retinal pigment epithelial cells. Methods: Transcriptome profiles of 5 weeks old primary human fetal retinal pigment epithelial cells from 3 different donors were generated by RNA sequencing using Illumina NextSeq 5000. The samples from the 3 donors represent replicates of each conditions. The sequence reads that passed quality filters were analyzed further for differentially expressed genes (DEG) performing quasi-likelihood F-test in edgeR package (Robinson, McCarthy et al. 2010). Lowly expressed genes were filtered out using the following script was used: > keep <- rowSums(cpm(y)> 0.05) >= 1. To be considered as differentislly expressed gene, the Benjamini-Hochberg–adjusted P value was less than 0.05. Results: Using our data analysis workflow, we were able to identify over 32,000 transcripts. 826 of these were significantly changed in the three independent samples after apical and 218 after basal zinc supplementation when compared to untreated controls. Apical zinc supplementation upregulated 415 and down-regulated 411 transcripts. Basal zinc supplementation upregulated 157 and down-regulated 59 transcripts. 163 transcripts changed similarly after both apical and basal treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE156452 | GEO | 2021/08/19

REPOSITORIES: GEO

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