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Series GSE236197 Query DataSets for GSE236197
Status Public on Apr 01, 2024
Title NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary While dysfunction and/or death of light-detecting photoreceptor cells underlies most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids using induced pluripotent stem cells (iPSC) derived from a patient with genetic photoreceptor disease, an isogenic control, and an unrelated control. Organoids were sampled using single-cell RNA sequencing across the developmental window encompassing photoreceptor specification, emergence, and maturation; up to 260 days of in vitro differentiation. Using single-cell transcriptomics data, we reconstruct the rod photoreceptor developmental lineage and identify a branchpoint in development unique to the disease state that gives rise to a divergent rod photoreceptor cell population. We show that the rod-specific transcription factor NR2E3 is required for the proper expression of genes involved in phototransduction, including expression of the light-sensitive protein rhodopsin, which is absent in divergent rods. NR2E3-null rods additionally misexpress several cone-specific phototransduction genes at both the transcript and protein level. Using joint multimodal single-cell sequencing on late-stage retinal organoids, we further identify the specific putative regulatory sites where rod-specific factors act to steer rod and cone photoreceptor cell development. Importantly, these findings are strikingly different than that observed in rodent models of disease. Together, these data provide a roadmap of human photoreceptor development and leverage patient iPSCs to define the specific roles of rod transcription factors in photoreceptor cell emergence and maturation.
 
Overall design Three iPSC lines (ND [no disease] Control, NR2E3-null, and Isogenic Control) were differentiated to retinal organoids for 260 days. Samples were assayed by 3' scRNAseq at D40, D80, D120, D160 and D260 from all three lines. In a separate differentiation batch, NR2E3-null and Isogenic Control organoids were assayed by joint (RNA & ATAC) single-nucleus multimodal sequencing at D160 and D280. Multimodal runs yield paired scRNAseq and scATACseq libraries.
For AAV experiments, NR2E3-null organoids were cultured for 120 days. Organoids were treated with AAV carrying NR2E3-T2A-GFP or GFP or left untransduced as described. Organoids were harvested at D120 or following treatment at D160 and assayed by 3' scRNAseq. For ESCS Patient 2 experiment, an iPSC line from ESCS Patient 2 was differentiated to retinal organoids and assayed at D80 and D160 by 3' scRNAseq.
>>>Raw data were not provided for ATAC-seq Samples due to patient privacy concerns<<<
 
Contributor(s) Mullin NK, Bohrer LR, Tucker BA
Citation(s) 38652563
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 EY033308 Molecular Studies of the Choriocapillaris in AMD THE UNIVERSITY OF IOWA Budd A Tucker
R01 EY033331 A Next Generation Outer Retinal Microphysiological System THE UNIVERSITY OF IOWA Budd A Tucker
T32 GM008629 Predoctoral Training Program in Genetics THE UNIVERSITY OF IOWA Daniel F Eberl
T32 GM139776 Medical Scientist Training Program THE UNIVERSITY OF IOWA Steven R Lentz
F30 EY034009 Pathogenesis of Mitochondrial Retina Disease THE UNIVERSITY OF IOWA Nathaniel Kevin Mullin
F30 EY031923 The Membrane Attack Complex and the Choriocapillaris in Health and Age-Related Macular Degeneration THE UNIVERSITY OF IOWA Andrew P Voigt
P30 EY025585 NEI Center Core Grant for Vision Research CLEVELAND CLINIC LERNER COLLEGE OF MEDICINE - CWRU Bela Anand-Apte
Submission date Jun 29, 2023
Last update date Apr 25, 2024
Contact name Nathaniel Kevin Mullin
Organization name University of Iowa
Street address 375 Newton Road
City Iowa City
State/province IA
ZIP/Postal code 52246
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (29)
GSM8181635 retinal organoid, NR2E3-null, D130, untransduced, scRNAseq
GSM8181636 retinal organoid, NR2E3-null, D160, aav-gfp, scRNAseq
GSM8181637 retinal organoid, NR2E3-null, D160, aav-nr2e3-gfp, scRNAseq
Relations
BioProject PRJNA989235

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Supplementary file Size Download File type/resource
GSE236197_RAW.tar 1.8 Gb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data not provided for this record
Processed data provided as supplementary file

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