Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci.

Erin N Smith,William W Greenwald,Agnieszka D'Antonio-Chronowska,Robert Pogue,Matteo D'Antonio,Lana R Aguiar,Radha Ayyagari,Paola Benaglio,Victor Borja,Kelly A Frazer,Hiroko Matsui,Shyamanga Borooah

doi:10.1016/j.stemcr.2019.04.012

Abstract

SummaryWe evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to those of native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observed high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal RPE. We performed fine mapping of AMD risk loci by integrating molecular data from the iPSC-RPE, adult retina, and adult RPE, which identified rs943080 as the probable causal variant at VEGFA. We show that rs943080 is associated with altered chromatin accessibility of a distal ATAC-seq peak, decreased overall gene expression of VEGFA, and allele-specific expression of a non-coding transcript. Our study thus provides a potential mechanism underlying the association of the VEGFA locus with AMD.

Highlights

Age-related macular degeneration (AMD) is a leading cause of vision loss that affects 1.6 million people over the age of 50 years in the United States (CDC, 2018) and has limited therapeutic options (Al-Zamil and Yassin, 2017)
We show that the iPSC-retinal pigment epithelium (RPE) shows morphological and molecular characteristics that are similar to those of native RPE including a characteristic polygonal shape, strong melanin pigmentation and expression, and strong zonula occludens 1 (ZO-1), bestrofin 1 (BEST1), and microphthalmia-associated transcription factor (MITF) immunostaining
We show that iPSC-RPE gene expression profiles are highly similar to that of human fetal RPE, and that their ATAC-seq peaks are enriched for relevant transcription factor motifs

Summary

Introduction

Age-related macular degeneration (AMD) is a leading cause of vision loss that affects 1.6 million people over the age of 50 years in the United States (CDC, 2018) and has limited therapeutic options (Al-Zamil and Yassin, 2017). AMD has a strong genetic component (Seddon et al, 2005), and through a large international study of 16,144 AMD cases and 17,832 controls, 52 independent AMD risk variants mapping to 34 AMD-associated loci have been identified (Fritsche et al, 2016). Regulatory variants that affect human disease, such as the variant that affects IRX3 expression in obesity (Smemo et al, 2014), can have strong effects, but it can be challenging to identify causal distal regulatory variants and link them with their target genes. For AMD, while some candidate target genes have been identified (Fritsche et al, 2016), the causal variants and the downstream processes by which they mediate their effects are generally unknown

Results

Discussion

Conclusion