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Single-Cell Transcriptomic Profiling of Xenotransplanted Retinal Organoids Derived from the WA09 CRX-tdTomato Human Embryonic Stem Cell Line

ABSTRACT: Single-Cell Transcriptomic Profiling of Xenotransplanted Retinal Organoids Derived from the WA09 CRX-tdTomato Human Embryonic Stem Cell Line

PROVIDER: PRJNA1203270 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31835785.fastq.gz	Fastqsanger.gz
	SRR31835786.fastq.gz	Fastqsanger.gz
	SRR31835787.fastq.gz	Fastqsanger.gz
	SRR31835788.fastq.gz	Fastqsanger.gz
	SRR31835789.fastq.gz	Fastqsanger.gz

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Single-Cell Transcriptomic Profiling of Xenotransplanted Retinal Organoids Derived from the WA09 CRX-tdTomato Human Embryonic Stem Cell Line

Project description:Single-cell gene expression profiles were generated for human retinal organoids derived from the WA09 CRX-tdTomato human embryonic stem cell line. Fragmented organoids were transplanted into the subretinal space of normal canine retinas and analyzed three days post-transplantation. In parallel, fragmented organoids from the same batch, maintained in culture for the same duration, were used as controls. Comparative single-cell transcriptomic analysis provided insights into the early molecular changes associated with the transplanted environment versus in vitro culture conditions, shedding light on the cellular responses and adaptation of retinal organoids post-transplantation.

2025-06-01 | GSE285393 | GEO

Single-Cell Transcriptomic Profiling of Canine Neuroretina Following Transplantation of Human ESC-derived Retinal Organoids [retina]

Project description:This study aimed to identify transcriptomic changes in the host retina following subretinal xenotransplantation. Single-cell gene expression profiles were generated from the neuroretina of normal canine eyes in regions directly overlying subretinally transplanted retinal organoids, which were derived from the WA09 CRX-tdTomato human embryonic stem cell (hESC) line. For comparison, single-cell gene expression profiles were also obtained from neuroretinal regions without graft exposure.

2025-06-01 | GSE285735 | GEO

Gene therapy of dominant CRX-Leber congenital amaurosis using patient retinal organoids II

Project description:Mutations in the cone-rod homeobox (CRX) transcription factor lead to distinct retinopathy phenotypes, including early-onset vision impairment in dominant Leber congenital amaurosis (LCA). Using induced pluripotent stem cells (iPSCs) from a patient with CRX-I138fs mutation, we established an in vitro model of CRX-LCA in retinal organoids that exhibit defective photoreceptor maturation by histology and gene profiling including diminished expression of visual opsins. Gene therapy by delivery of an additional correct CRX allele using an AAV vector partially restored photoreceptor phenotype and expression of phototransduction-related genes as revealed by single cell RNA-sequencing. Retinal organoids derived from iPSCs of a second dominant CRX-LCA patient carrying a K88N mutation revealed loss of opsin expression as a common phenotype, which could also be alleviated by AAV-mediated overexpression of CRX. Our studies provide the proof-of-concept for development of gene therapy for dominant CRX-LCA and other CRX-retinopathies.

2021-02-17 | GSE153099 | GEO

Gene therapy of dominant CRX-Leber congenital amaurosis using patient retinal organoids I

2021-02-17 | GSE152939 | GEO

Single cell RNA-seq of CRX+ cells obtained at day 90 of retinal organoid differentiation

Project description:Death of photoreceptors and/or Retinal Pigment Epithelium (RPE) cells is a common cause of age related and inherited retinal dystrophies, thus their replenishment from renewable stem cell sources is a well sought therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to differentiate into all key retinal cell types either in isolation or as part of three dimensional retinal organoids. Photoreceptor precursors have been isolated from differentiating human pluripotent stem cells either through application of cell surface markers or fluorescent reporter approaches and shown to share a transcriptional profile akin to foetal photoreceptors. In this study we investigated the transcriptional profile of CRX+ photoreceptor precursors derived from human embryonic stem cells (hESC) using single cell RNA sequencing and their engraftment capacity in an animal model of retinitis pigmentosa (C3H/rd1). Single cell RNA seq analysis revealed the presence of dominant cell cluster which displayed the hallmarks of early cone photoreceptor expression. When transplanted subretinally into the C3H/rd1 mice, the Crx positive cells settled next to the inner nuclear layer of host retina, matured into cone photoreceptors and made connections with the inner neurones of the host retina. Cellular transfer between the host retina and donor photoreceptors was investigated and shown to be minimal. Together our data provide valuable molecular insights into the transcriptional profile of human pluripotent stem cells derived CRX+ photoreceptor precursors and indicate their usefulness as a source of transplantable cone photoreceptors.

2019-04-01 | GSE112507 | GEO

Microarray analysis of Crx Knock-IN mice E168d2 and R90W

Project description:P10 retinal gene expression analysis of the homozygous Crx Knock-OUT or Knock-IN mice carrying the mutation E168d2 or R90W. Results provide important information about the retinal genes affected by mutations in the transcription factor Crx, which have been implicated in human retinopathies. PolyA RNA isolated from 3 Sex-matched (1M,1F) pairs of P10 mouse retinas from each genotype (WT, E168d2neo/d2neo, R90Wneo/Wneo, and Crx -/-)

2013-12-01 | E-GEOD-51184 | biostudies-arrayexpress

Mutations in BCOR, a novel co-repressor of OTX2/CRX, cause pediatric inherited retinal degeneration

Project description:Many transcription factors regulating the production, survival and function of photoreceptor cells in the retina have been identified, but little is known about transcriptional co-regulators in retinal health and disease. Here we show that BCL6 co-repressor (BCOR), a polycomb repressive complex I factor mutated in various cancers, negatively regulates photoreceptor gene expression. Using proteomics and promoter assays, we find that BCOR interacts with the photoreceptor transcription factors OTX2 and CRX, and reduces their ability to activate the promoters of photoreceptor-specific genes, such as Rhodopsin and Nrl. CUT&RUN sequencing further shows that BCOR shares genome-wide binding profiles with CRX/OTX2, consistent with a general co-repression activity. Finally, we identify missense variants in the human BCOR gene in six families with early-onset X-linked inherited retinal degeneration (IRD). Together, this work uncovers BCOR as a co-repressor of OTX2/CRX essential for photoreceptor cell biology and survival.

2022-09-10 | GSE168129 | GEO

Microarray analysis of Crx Knock-IN mice E168d2 and R90W

2013-12-01 | GSE51184 | GEO

OTX2 loss causes rod differentiation defect in CRX-associated congenital blindness

Project description:Leber congenital amaurosis (LCA) includes congenital or early-onset blinding diseases, characterized by vision loss together with nystagmus and nonrecordable electroretinogram (ERG). At least 19 genes are associated with LCA. While most LCA is recessive, mutations in the homeodomain transcription factor gene CRX lead to autosomal dominant LCA. The mechanism of CRX-LCA is not understood. Here, we report a new spontaneous mouse mutant carrying a frameshift mutation in Crx (CrxRip). We show that, unlike Crx-/- mouse retina, the dominant Crx c.763del1 mutation in CrxRip results in congenital blindness with complete loss of ERG, yet the photoreceptors do not degenerate. Dominant CRX frameshift mutations associated with LCA mimic the CrxRip phenotype that can be rescued by Crx. RNA-Seq profiling reveals progressive and complete loss of rod differentiation factor Nrl in CrxRip, while residual Nrl remains in Crx-/- retina. Moreover, Nrl partially restores the rod phenotype in CrxRip/+ mice. We show that the binding of Otx2 to Nrl promoter is obliterated in CrxRip mutant, and ectopic Otx2 can rescue the rod phenotype. Therefore, Otx2 is required to maintain Nrl expression in developing rods to consolidate rod fate. Our studies provide the mechanism of congenital blindness caused by dominant CRX mutations and should assist in therapeutic design. Retinal samples were harvested from WT, CrxRip/+, CrxRip/Rip, Crx-/- and Nrl-/- retina at postnatal days 2 and 21 for whole transcriptome sequencing (RNAseq). Each sample included 2 independent frozen retina and experiments were performed in duplicates. RNA-seq transcriptome libraries were constructed from 1 ?g of total RNA.

2014-01-13 | E-GEOD-52006 | biostudies-arrayexpress

Mouse retina LC-MSMS - Diurnal expression of proteins in the retina of the blind cone-rod homeobox (Crx(-/-) ) mouse and the 129/Sv mouse: a proteomic study

Project description:To investigate the role of the circadian clock of the photoreceptor cells in regulation of retinal protein rhythms, we have analyzed diurnal protein expression in the photoreceptor-deficient cone-rod homeobox knock out mouse (Crx-/-). Retinal homogenates of 129/sv and Crx-/- mice were analysed by 2D-PAGE. Differentially expressed spots were in-gel digested with trypsin and identified by LC-MS/MS. Data were used to search the Swiss-Prot protein database.

2017-04-04 | PXD005556 | Pride

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