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Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Author

Listed:
  • Madhvi Menon

    (Broad Institute of MIT and Harvard
    Harvard Medical School
    Evergrande Center for Immunologic Diseases, Harvard Medical School)

  • Shahin Mohammadi

    (Broad Institute of MIT and Harvard
    MIT Computer Science and Artificial Intelligence Laboratory)

  • Jose Davila-Velderrain

    (Broad Institute of MIT and Harvard
    MIT Computer Science and Artificial Intelligence Laboratory)

  • Brittany A. Goods

    (Broad Institute of MIT and Harvard
    Institute for Medical Engineering and Science and Department of Chemistry, MIT
    Koch Institute for Integrative Cancer Research, MIT
    Ragon Institute of MGH, MIT and Harvard)

  • Tanina D. Cadwell

    (Evergrande Center for Immunologic Diseases, Harvard Medical School)

  • Yu Xing

    (Evergrande Center for Immunologic Diseases, Harvard Medical School)

  • Anat Stemmer-Rachamimov

    (Massachusetts General Hospital)

  • Alex K. Shalek

    (Broad Institute of MIT and Harvard
    Institute for Medical Engineering and Science and Department of Chemistry, MIT
    Koch Institute for Integrative Cancer Research, MIT
    Ragon Institute of MGH, MIT and Harvard)

  • John Christopher Love

    (Broad Institute of MIT and Harvard
    Koch Institute for Integrative Cancer Research, MIT)

  • Manolis Kellis

    (Broad Institute of MIT and Harvard
    Evergrande Center for Immunologic Diseases, Harvard Medical School
    MIT Computer Science and Artificial Intelligence Laboratory)

  • Brian P. Hafler

    (Broad Institute of MIT and Harvard
    Harvard Medical School
    Evergrande Center for Immunologic Diseases, Harvard Medical School
    Yale School of Medicine)

Abstract

Genome-wide association studies (GWAS) have identified genetic variants associated with age-related macular degeneration (AMD), one of the leading causes of blindness in the elderly. However, it has been challenging to identify the cell types associated with AMD given the genetic complexity of the disease. Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the first single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures. Heterogeneity is observed within macroglia, suggesting that human retinal glia are more diverse than previously thought. Finally, GWAS-based enrichment analysis identifies glia, vascular cells, and cone photoreceptors to be associated with the risk of AMD. These data provide a detailed analysis of the human retina, and show how scRNA-seq can provide insight into cell types involved in complex, inflammatory genetic diseases.

Suggested Citation

  • Madhvi Menon & Shahin Mohammadi & Jose Davila-Velderrain & Brittany A. Goods & Tanina D. Cadwell & Yu Xing & Anat Stemmer-Rachamimov & Alex K. Shalek & John Christopher Love & Manolis Kellis & Brian P, 2019. "Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12780-8
    DOI: 10.1038/s41467-019-12780-8
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    Cited by:

    1. Manuela Völkner & Felix Wagner & Lisa Maria Steinheuer & Madalena Carido & Thomas Kurth & Ali Yazbeck & Jana Schor & Stephanie Wieneke & Lynn J. A. Ebner & Claudia Toro Runzer & David Taborsky & Katja, 2022. "HBEGF-TNF induce a complex outer retinal pathology with photoreceptor cell extrusion in human organoids," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    2. Manik Kuchroo & Marcello DiStasio & Eric Song & Eda Calapkulu & Le Zhang & Maryam Ige & Amar H. Sheth & Abdelilah Majdoubi & Madhvi Menon & Alexander Tong & Abhinav Godavarthi & Yu Xing & Scott Gigant, 2023. "Single-cell analysis reveals inflammatory interactions driving macular degeneration," Nature Communications, Nature, vol. 14(1), pages 1-22, December.

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