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Emri E, Cappa O, Kelly C, Kortvely E, SanGiovanni JP, McKay BS, Bergen AA, Simpson DA, Lengyel I. Zinc Supplementation Induced Transcriptional Changes in Primary Human Retinal Pigment Epithelium: A Single-Cell RNA Sequencing Study to Understand Age-Related Macular Degeneration. Cells 2023; 12:773. [PMID: 36899910 PMCID: PMC10000409 DOI: 10.3390/cells12050773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Zinc supplementation has been shown to be beneficial to slow the progression of age-related macular degeneration (AMD). However, the molecular mechanism underpinning this benefit is not well understood. This study used single-cell RNA sequencing to identify transcriptomic changes induced by zinc supplementation. Human primary retinal pigment epithelial (RPE) cells could mature for up to 19 weeks. After 1 or 18 weeks in culture, we supplemented the culture medium with 125 µM added zinc for one week. RPE cells developed high transepithelial electrical resistance, extensive, but variable pigmentation, and deposited sub-RPE material similar to the hallmark lesions of AMD. Unsupervised cluster analysis of the combined transcriptome of the cells isolated after 2, 9, and 19 weeks in culture showed considerable heterogeneity. Clustering based on 234 pre-selected RPE-specific genes divided the cells into two distinct clusters, we defined as more and less differentiated cells. The proportion of more differentiated cells increased with time in culture, but appreciable numbers of cells remained less differentiated even at 19 weeks. Pseudotemporal ordering identified 537 genes that could be implicated in the dynamics of RPE cell differentiation (FDR < 0.05). Zinc treatment resulted in the differential expression of 281 of these genes (FDR < 0.05). These genes were associated with several biological pathways with modulation of ID1/ID3 transcriptional regulation. Overall, zinc had a multitude of effects on the RPE transcriptome, including several genes involved in pigmentation, complement regulation, mineralization, and cholesterol metabolism processes associated with AMD.
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Affiliation(s)
- Eszter Emri
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
- Section Ophthalmogenetics, Department of Human Genetics, Queen Emma Centre for Precision Medicine, Amsterdam UMC, Location AMC, 1105AZ Amsterdam, The Netherlands
| | - Oisin Cappa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Caoimhe Kelly
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Elod Kortvely
- Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - John Paul SanGiovanni
- Biosciences Research Laboratories, BIO5 Institute, University of Arizona, 1230 North Cherry Avenue, Tucson, AZ 85724, USA
| | - Brian S. McKay
- Department of Ophthalmology and Vision Science, University of Arizona, 1656 E. Mabel Street, Tucson, AZ 85724, USA
| | - Arthur A. Bergen
- Section Ophthalmogenetics, Department of Human Genetics, Queen Emma Centre for Precision Medicine, Amsterdam UMC, Location AMC, 1105AZ Amsterdam, The Netherlands
- The Netherlands Institute for Neuroscience (NIN-KNAW), 1105AZ Amsterdam, The Netherlands
| | - David A. Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
| | - Imre Lengyel
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University of Belfast, Belfast BT97BL, UK
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