Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration

Abstract

Induced pluripotent stem cells generated from patients with geographic atrophy as well as healthy individuals were differentiated to retinal pigment epithelium (RPE) cells. By integrating transcriptional profiles of 127,659 RPE cells generated from 43 individuals with geographic atrophy and 36 controls with genotype data, we identified 439 expression Quantitative Trait (eQTL) loci in cis that were associated with disease status and specific to subpopulations of RPE cells. We identified loci linked to two genes with known associations with geographic atrophy - PILRB and PRPH2, in addition to 43 genes with significant genotype x disease interactions that are candidates for novel genetic associations for geographic atrophy. On a transcriptome-only level, we identified molecular pathways significantly upregulated in geographic atrophy-RPE including in extracellular cellular matrix reorganisation, neurodegeneration, and mitochondrial functions. We subsequently implemented a large-scale proteomics analysis, confirming modification in proteins associated with these pathways. We also identified six significant protein (p) QTL that regulate protein expression in the RPE cells and in geographic atrophy - two of which share variants with cis-eQTL. Transcriptome-wide association analysis identified genes at loci previously associated with age-related macular degeneration. Further analysis conditional on disease status, implicated statistically significant RPE-specific eQTL. This study uncovers important differences in RPE homeostasis associated with geographic atrophy.

Human pluripotent stem cells for the modelling of retinal pigment epithelium homeostasis and disease: A review

“…74 In particular, mitochondrial pathways were identified as dysregulated in geographic atrophy RPE cells, data confirmed by mass spectrometry and by functional analysis of mitochondrial respiration. 74 Other studies using small subsets of hPSCs have also identified phenotypes associated with AMD. iPSC-RPE cells derived from patients with AMD compared to healthy controls display a reduced activity of the mitochondrial antioxidant enzyme superoxide dismutase 2 (SOD2) and have a higher susceptibility to oxidative stress.…”

“…74 The comparison of single cell RNA sequencing from iPSC-derived RPE cells of 43 patients at the phenotypic end of AMD and of 36 unaffected controls implicated genes at loci definitively associated with disease such as the CFH and ARMS2/HTRA1 loci, and also uncovered new pathogenic loci and pathways. 74 In particular, mitochondrial pathways were identified as dysregulated in geographic atrophy RPE cells, data confirmed by mass spectrometry and by functional analysis of mitochondrial respiration. 74 Other studies using small subsets of hPSCs have also identified phenotypes associated with AMD.…”

“…These loci influence distinct biological pathways, such as the complement system, lipid transport, extracellular matrix remodelling, angiogenesis and cell survival 73 . In an attempt to provide a population‐scale approach to iPSC‐disease modelling for complex disease, we recently described both transcriptomic and proteomic profiles of iPSC‐derived RPE cells from a large cohort of people with or without the advanced form of AMD geographic atrophy 74 . The comparison of single cell RNA sequencing from iPSC‐derived RPE cells of 43 patients at the phenotypic end of AMD and of 36 unaffected controls implicated genes at loci definitively associated with disease such as the CFH and ARMS2 / HTRA1 loci, and also uncovered new pathogenic loci and pathways 74 .…”

“…In an attempt to provide a population‐scale approach to iPSC‐disease modelling for complex disease, we recently described both transcriptomic and proteomic profiles of iPSC‐derived RPE cells from a large cohort of people with or without the advanced form of AMD geographic atrophy 74 . The comparison of single cell RNA sequencing from iPSC‐derived RPE cells of 43 patients at the phenotypic end of AMD and of 36 unaffected controls implicated genes at loci definitively associated with disease such as the CFH and ARMS2 / HTRA1 loci, and also uncovered new pathogenic loci and pathways 74 . In particular, mitochondrial pathways were identified as dysregulated in geographic atrophy RPE cells, data confirmed by mass spectrometry and by functional analysis of mitochondrial respiration 74 …”

Zinc supplementation induced transcriptional changes in primary human retinal pigment epithelium: a single-cell RNA sequencing study to understand age-related macular degeneration

“…Lidgerwood et al [34] used pluripotent stem cell-derived RPE to analyze transcriptomic changes after 1 month or 12 months in culture and analyzed these separately, then combined the data. In a subsequent study, the same group combined scRNA-Seq and proteomics in iPSC cells obtained from individuals with or without AMD to identify regulations in geographic atrophy [35]. Exciting opportunities are presented by scRNA-Seq studies using freshly isolated RPE from human eyes.…”