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

Anne Senabouth, Maciej Daniszewski, Grace E. Lidgerwood, Helena H. Liang, Damián Hernández, Mehdi Mirzaei, Stacey N. Keenan, Ran Zhang, Xikun Han, Drew Neavin, Louise Rooney, Maria Isabel G. Lopez Sanchez, Lerna Gulluyan, Joao A. Paulo, Linda Clarke, Lisa S. Kearns, Vikkitharan Gnanasambandapillai, Chia Ling Chan, Uyen Nguyen, Angela M. SteinmannRachael A. McCloy, Nona Farbehi, Vivek K. Gupta, David A. Mackey, Guy Bylsma, Nitin Verma, Stuart MacGregor, Matthew J. Watt, Robyn H. Guymer, Joseph E. Powell*, Alex W. Hewitt, Alice Pébay

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)
61 Downloads (Pure)


There are currently no treatments for geographic atrophy, the advanced form of age-related macular degeneration. Hence, innovative studies are needed to model this condition and prevent or delay its progression. Induced pluripotent stem cells generated from patients with geographic atrophy and healthy individuals were differentiated to retinal pigment epithelium. Integrating transcriptional profiles of 127,659 retinal pigment epithelium cells generated from 43 individuals with geographic atrophy and 36 controls with genotype data, we identify 445 expression quantitative trait loci in cis that are asssociated with disease status and specific to retinal pigment epithelium subpopulations. Transcriptomics and proteomics approaches identify molecular pathways significantly upregulated in geographic atrophy, including in mitochondrial functions, metabolic pathways and extracellular cellular matrix reorganization. Five significant protein quantitative trait loci that regulate protein expression in the retinal pigment epithelium and in geographic atrophy are identified - two of which share variants with cis- expression quantitative trait loci, including proteins involved in mitochondrial biology and neurodegeneration. Investigation of mitochondrial metabolism confirms mitochondrial dysfunction as a core constitutive difference of the retinal pigment epithelium from patients with geographic atrophy. This study uncovers important differences in retinal pigment epithelium homeostasis associated with geographic atrophy.

Original languageEnglish
Article number4233
Pages (from-to)1-18
Number of pages18
JournalNature Communications
Issue number1
Publication statusPublished - 26 Jul 2022

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