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EMBO J. 2019 Sep 16;38(18):e100811. doi: 10.15252/embj.2018100811. Epub 2019 Aug 22.

A single-cell transcriptome atlas of the adult human retina.

Author information

1
Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia.
2
Monash University, Melbourne, Vic., Australia.
3
National Institute for Aging, National Institutes of Health, Baltimore, MD, USA.
4
Centre for Eye Research Australia, Melbourne, Vic., Australia.
5
Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic., Australia.
6
Jinan University, Guangzhou, China.
7
The University of Sydney, Faculty of Medicine, Save Sight Institute, Sydney, NSW, Australia.
8
Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.
9
Australian Genome Research Facility, Melbourne, Vic., Australia.
10
Stem Cells and Regenerative Medicine Section, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, London, UK.
11
Lions Eye Donation Services, Melbourne, Vic., Australia.
12
John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
13
Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Vic., Australia.
14
Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, China.
15
Menzies Institute for Medical Research, University of Tasmania, Hobart, Tas., Australia.
16
UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia.
17
Shenzhen Eye Hospital, Shenzhen University School of Medicine, Shenzhen, China.

Abstract

The retina is a specialized neural tissue that senses light and initiates image processing. Although the functional organization of specific retina cells has been well studied, the molecular profile of many cell types remains unclear in humans. To comprehensively profile the human retina, we performed single-cell RNA sequencing on 20,009 cells from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct cell populations representing all known neural retinal cells: rod photoreceptors, cone photoreceptors, Müller glia, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, astrocytes, and microglia. Our data captured molecular profiles for healthy and putative early degenerating rod photoreceptors, and revealed the loss of MALAT1 expression with longer post-mortem time, which potentially suggested a novel role of MALAT1 in rod photoreceptor degeneration. We have demonstrated the use of this retina transcriptome atlas to benchmark pluripotent stem cell-derived cone photoreceptors and an adult Müller glia cell line. This work provides an important reference with unprecedented insights into the transcriptional landscape of human retinal cells, which is fundamental to understanding retinal biology and disease.

KEYWORDS:

photoreceptor subtypes; retina; single-cell RNA sequencing; transcriptome

PMID:
31436334
DOI:
10.15252/embj.2018100811

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