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

Author

Listed:
  • Anne Senabouth

    (Garvan Institute of Medical Research)

  • Maciej Daniszewski

    (The University of Melbourne
    Royal Victorian Eye and Ear Hospital)

  • Grace E. Lidgerwood

    (The University of Melbourne
    Royal Victorian Eye and Ear Hospital)

  • Helena H. Liang

    (Royal Victorian Eye and Ear Hospital)

  • Damián Hernández

    (The University of Melbourne
    Royal Victorian Eye and Ear Hospital)

  • Mehdi Mirzaei

    (Macquarie University)

  • Stacey N. Keenan

    (The University of Melbourne)

  • Ran Zhang

    (Garvan Institute of Medical Research)

  • Xikun Han

    (QIMR Berghofer Medical Research Institute)

  • Drew Neavin

    (Garvan Institute of Medical Research)

  • Louise Rooney

    (The University of Melbourne)

  • Maria Isabel G. Lopez Sanchez

    (Royal Victorian Eye and Ear Hospital)

  • Lerna Gulluyan

    (The University of Melbourne)

  • Joao A. Paulo

    (Harvard Medical School)

  • Linda Clarke

    (Royal Victorian Eye and Ear Hospital)

  • Lisa S. Kearns

    (Royal Victorian Eye and Ear Hospital)

  • Vikkitharan Gnanasambandapillai

    (Garvan Institute of Medical Research)

  • Chia-Ling Chan

    (Garvan Institute of Medical Research)

  • Uyen Nguyen

    (Garvan Institute of Medical Research)

  • Angela M. Steinmann

    (Garvan Institute of Medical Research)

  • Rachael A. McCloy

    (Garvan Institute of Medical Research)

  • Nona Farbehi

    (Garvan Institute of Medical Research)

  • Vivek K. Gupta

    (Macquarie University)

  • David A. Mackey

    (University of Western Australia
    University of Tasmania)

  • Guy Bylsma

    (University of Western Australia)

  • Nitin Verma

    (University of Tasmania)

  • Stuart MacGregor

    (QIMR Berghofer Medical Research Institute)

  • Matthew J. Watt

    (The University of Melbourne)

  • Robyn H. Guymer

    (Royal Victorian Eye and Ear Hospital
    The University of Melbourne)

  • Joseph E. Powell

    (Garvan Institute of Medical Research
    University of New South Wales)

  • Alex W. Hewitt

    (Royal Victorian Eye and Ear Hospital
    University of Tasmania
    The University of Melbourne
    University of Tasmania)

  • Alice Pébay

    (The University of Melbourne
    Royal Victorian Eye and Ear Hospital
    The University of Melbourne)

Abstract

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.

Suggested Citation

  • 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, 2022. "Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31707-4
    DOI: 10.1038/s41467-022-31707-4
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    References listed on IDEAS

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    1. Olivier Delaneau & Halit Ongen & Andrew A. Brown & Alexandre Fort & Nikolaos I. Panousis & Emmanouil T. Dermitzakis, 2017. "A complete tool set for molecular QTL discovery and analysis," Nature Communications, Nature, vol. 8(1), pages 1-7, August.
    2. Ryan Lister & Mattia Pelizzola & Yasuyuki S. Kida & R. David Hawkins & Joseph R. Nery & Gary Hon & Jessica Antosiewicz-Bourget & Ronan O’Malley & Rosa Castanon & Sarit Klugman & Michael Downes & Ruth , 2011. "Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells," Nature, Nature, vol. 471(7336), pages 68-73, March.
    3. Yibo Yu & Yu Weng & Jing Guo & Guangdi Chen & Ke Yao, 2013. "Association of Glutathione S transferases Polymorphisms with Glaucoma: A Meta-Analysis," PLOS ONE, Public Library of Science, vol. 8(1), pages 1-7, January.
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