Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time

Grace E. Lidgerwood; Anne Senabouth; Casey J.A. Smith-Anttila; Vikkitharan Gnanasambandapillai; Dominik C. Kaczorowski; Daniela Amann-Zalcenstein; Erica L. Fletcher; Shalin H. Naik; Alex W. Hewitt; Joseph E. Powell; Alice Pébay

Genomics, Proteomics & Bioinformatics (Apr 2021)

Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time

Grace E. Lidgerwood,
Anne Senabouth,
Casey J.A. Smith-Anttila,
Vikkitharan Gnanasambandapillai,
Dominik C. Kaczorowski,
Daniela Amann-Zalcenstein,
Erica L. Fletcher,
Shalin H. Naik,
Alex W. Hewitt,
Joseph E. Powell,
Alice Pébay

Affiliations

Grace E. Lidgerwood: Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia; Corresponding authors.
Anne Senabouth: Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
Casey J.A. Smith-Anttila: Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
Vikkitharan Gnanasambandapillai: Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
Dominik C. Kaczorowski: Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
Daniela Amann-Zalcenstein: Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
Erica L. Fletcher: Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia
Shalin H. Naik: Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
Alex W. Hewitt: Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia
Joseph E. Powell: Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia; UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
Alice Pébay: Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia; Corresponding authors.

Journal volume & issue: Vol. 19, no. 2
pp. 223 – 242

Abstract

Read online

Human pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of diseases associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate time points of retinal pigment epithelium (RPE) cultures that reflect native counterparts, we characterised the transcriptomic profiles of the hPSC-derived RPE cells from 1- and 12-month cultures. We differentiated the human embryonic stem cell line H9 into RPE cells, performed single-cell RNA-sequencing of a total of 16,576 cells to assess the molecular changes of the RPE cells across these two culture time points. Our results indicate the stability of the RPE transcriptomic signature, with no evidence of an epithelial–mesenchymal transition, and with the maturing populations of the RPE observed with time in culture. Assessment of Gene Ontology pathways revealed that as the cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions. This might reflect an increased ability to handle oxidative stress as cells mature. Comparison with native human RPE data confirms a maturing transcriptional profile of RPE cells in culture. These results suggest that long-term in vitro culture of RPE cells allows the modelling of specific phenotypes observed in native mature tissues. Our work highlights the transcriptional landscape of hPSC-derived RPE cells as they age in culture, which provides a reference for native and patient samples to be benchmarked against.

Published in Genomics, Proteomics & Bioinformatics

ISSN: 1672-0229 (Print); 2210-3244 (Online)
Publisher: Oxford University Press
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General); Medicine: Medicine (General): Computer applications to medicine. Medical informatics
Website: https://academic.oup.com/gpb

About the journal

Abstract

Keywords