Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

Emily Welby; Jorn Lakowski; Valentina Di Foggia; Dimitri Budinger; Anai Gonzalez-Cordero; Aaron T.L. Lun; Michael Epstein; Aara Patel; Elisa Cuevas; Kamil Kruczek; Arifa Naeem; Federico Minneci; Mike Hubank; David T. Jones; John C. Marioni; Robin R. Ali; Jane C. Sowden

Stem Cell Reports (Dec 2017)

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

Emily Welby,
Jorn Lakowski,
Valentina Di Foggia,
Dimitri Budinger,
Anai Gonzalez-Cordero,
Aaron T.L. Lun,
Michael Epstein,
Aara Patel,
Elisa Cuevas,
Kamil Kruczek,
Arifa Naeem,
Federico Minneci,
Mike Hubank,
David T. Jones,
John C. Marioni,
Robin R. Ali,
Jane C. Sowden

Affiliations

Emily Welby: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
Jorn Lakowski: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
Valentina Di Foggia: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
Dimitri Budinger: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
Anai Gonzalez-Cordero: Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
Aaron T.L. Lun: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
Michael Epstein: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
Aara Patel: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
Elisa Cuevas: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
Kamil Kruczek: Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
Arifa Naeem: Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
Federico Minneci: Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
Mike Hubank: UCL Genomics, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
David T. Jones: Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
John C. Marioni: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Robin R. Ali: Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
Jane C. Sowden: Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; Corresponding author

Journal volume & issue: Vol. 9, no. 6
pp. 1898 – 1915

Abstract

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Summary: Loss of cone photoreceptors, crucial for daylight vision, has the greatest impact on sight in retinal degeneration. Transplantation of stem cell-derived L/M-opsin cones, which form 90% of the human cone population, could provide a feasible therapy to restore vision. However, transcriptomic similarities between fetal and stem cell-derived cones remain to be defined, in addition to development of cone cell purification strategies. Here, we report an analysis of the human L/M-opsin cone photoreceptor transcriptome using an AAV2/9.pR2.1:GFP reporter. This led to the identification of a cone-enriched gene signature, which we used to demonstrate similar gene expression between fetal and stem cell-derived cones. We then defined a cluster of differentiation marker combination that, when used for cell sorting, significantly enriches for cone photoreceptors from the fetal retina and stem cell-derived retinal organoids, respectively. These data may facilitate more efficient isolation of human stem cell-derived cones for use in clinical transplantation studies. : Welby et al. define a cone-enriched gene signature within a human fetal L/M-opsin cone population, which is used as a baseline reference to demonstrate similar cone gene expression between bona fide and stem cell-derived L/M-opsin cone cells. Furthermore, profiling of cell surface molecules in human fetal cones led to the generation of a cluster of differentiation marker panel, which provides enrichment of fetal and stem cell-derived cones. Keywords: retinal dystrophies, cone photoreceptor cells, transcriptome, human pluripotent stem cells, retinal organoids, cell surface markers, cell transplantation therapy

Published in Stem Cell Reports

ISSN: 2213-6711 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Medicine (General); Science: Biology (General)
Website: http://www.cell.com/stem-cell-reports/home

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