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Rattus norvegicus

ABSTRACT: The potential mechanisms of NK-5962 on delaying the apoptosis of photoreceptor cells in a rat model of retinitis pigmentosa

PROVIDER: PRJDB12603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR332996_1.fastq.gz	Fastqsanger.gz
	DRR332996_2.fastq.gz	Fastqsanger.gz
	DRR332997_1.fastq.gz	Fastqsanger.gz
	DRR332997_2.fastq.gz	Fastqsanger.gz
	DRR332998_1.fastq.gz	Fastqsanger.gz

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Rattus norvegicus

Project description:The treatment of cyanine dye NK-4 against photoreceptor cell apoptosis in a rat model of Retinitis Pigmentosa

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PRPF8 CLIP seq for iPSC, kidney organoid, retinal organoid, and retinal epithelium derived from c.6926A>C RPE with Retinitis Pigmentosa patients and CRISPR/Cas9 corrected

Project description:Retinitis Pigmentosa is a group of inherited eye disorders characterized by progressive degeneration of photoreceptor cells in the retina, leading to vision loss and eventual blindness. One of the known genetic mutations associated with RP is the c.6926A>C mutation in the RPE (retinal pigment epithelium) cells. The dataset involves multiple experimental approaches and cell types, providing a comprehensive understanding of the disease and potential corrective strategies.

2024-03-13 | E-MTAB-13171 | biostudies-arrayexpress

The deubiquitinase Otud7b suppresses cone photoreceptor degeneration in mouse models of retinal degenerative diseases

Project description:Primary and secondary cone photoreceptor cell death in retinal degenerative diseases, including age-related macular degeneration and retinitis pigmentosa, leads to severe vision impairment and blindness. Regardless of the fact that protection of cone photoreceptor cells under stress conditions, such as retinal degenerative diseases, is crucial for maintaining vision, the underlying molecular mechanisms are unclear. Here, we investigated the function of the deubiquitinase Otud7b/Cezanne in the retina. We identified that Otud7b is predominantly expressed in photoreceptor cells in the mouse retina. While the ablation of Otud7b did not cause a significant defect in development and maturation of the mouse retina, Otud7b‒/‒ mice subjected to light-induced damage, which is one of the dry age-related macular degeneration models, exhibited increased cone photoreceptor degeneration. In addition, Otud7b deficiency in Mak‒/‒ mice, a retinitis pigmentosa mouse model, resulted in further cone photoreceptor degeneration. Moreover, neuronal cells deficient in Otud7b were susceptible to serum starvation, resulting in cell death. We found that NF-κB activity is increased in the Otud7b‒/‒ retinas exposed to light by RNA-sequencing analysis. Luciferase reporter assay also demonstrated increased NF-κB activation in Otud7b-deficient neuronal cells under stress. The neuronal cell death resulting from Otud7b deficiency was suppressed through the inhibition of NF-κB. Furthermore, we observed that inhibition of NF-κB attenuated cone photoreceptor degeneration in the light-exposed Otud7b‒/‒ retina. Together, the current study suggests that Otud7b deubiquitinase protects cone photoreceptor cells under stress conditions by modulating the NF-κB activity.

2024-03-12 | GSE239573 | GEO

Mouse retina single-cell RNA-seq of WT and two Nr2e3 mutant models to explore the role of Nr2e3 in cone and rod photoreceptor differentiation

Project description:Single-cell RNA-seq of mouse WT retinas and two Nr2e3 mutant retinas, ∆27 and ∆E8 (containing a 27 nucleotide in-frame deletion or a complete exon 8 deletion, respectively). The ∆27 retinas were used as a model for enhanced S-cone syndrome phenotype in humans, while the ∆E8 retinas show a progressive retinal degeneration similar to human retinitis pigmentosa patients. This data was used to explore the role of Nr2e3 in cone and rod photoreceptor differentiation.

2024-05-18 | E-MTAB-12183 | biostudies-arrayexpress

Rod photoreceptors degeneration in the rd1 model of retinitis pigmentosa involves a cascade of events leading to proteasome dysfunction

Project description:Retinitis pigmentosa is an inherited disease with sequential retinal degeneration of rod then cone photoreceptors leading to blindness. As in this human syndrome the rd1 mouse model carries a recessive mutation in the rod-specific cGMP phosphodiesterase beta subunit gene leading to rod followed by cone photoreceptor death. The cascade of early events leading to the induction of rod cell death through apoptosis remains unknown. We report a differential whole-genome expression profiling analysis of the wild-type and rd1 mouse retinal transcriptional program using high-density oligonucleotide microarrays with a time series experiment spanning the entire rod photoreceptor degeneration process. Among the 1252 genes found to be significantly differentially expressed, a key group of 19 loci showed distinct differences in expression early in development, suggesting that these genes of clinical interest may play a fundamental role in the induction of the rod photoreceptor degeneration.

2020-09-25 | GSE62020 | GEO

Investigating cone photoreceptor development using patient-derived NRLnull retinal organoids

Project description:Photoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degeneration are not well understood. Treatment strategies would benefit from an improved understanding of gene-expression patterns directing photoreceptor development, as many genes are implicated in both development and degeneration. Neural retina leucine zipper (NRL) is critical for rod photoreceptor genesis and degeneration, with NRL mutations known to cause enhanced S-cone syndrome and retinitis pigmentosa. While murine Nrl loss has been characterized, studies of human NRL can identify important insights for human retinal disease. Here we utilized human organoid models of retinal development to molecularly define developmental alterations in a human model of NRL loss. Consistent with the function of NRL in rod fate specification, human retinal organoids lacking NRL develop S-opsin dominant photoreceptor populations. We report generation of two distinct S-opsin expressing populations in NRL null retinal organoids and identify MEF2C as a candidate regulator of cone development.

2020-01-15 | GSE143669 | GEO

Project description:FGF21 via retinal glial modeling preserves photoreceptor function in retinitis pigmentosa

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RNA-seq of retinal organoids derived from RPGR patient-, control- and mutation-corrected-iPSC at different developmental stages

Project description:Retinitis pigmentosa (RP) is an irreversible and inherited retinopathy. RPGR mutations are the most common causes of this disease. It remains challenging to decipher the mechanism of RPGR mutation because of the lack of appropriate study models. The substitution of patient-specific diseased retina without ethical restrictions is desired and iPSC-derived 3D retina is the best choice. In our experiment, we generated iPSCs from one RP patient with 2-bp frameshift mutation in the exon14 of RPGR gene, which were differentiated into retinal organoids. Also we generated iPSCs from a normal control and differentiated those control-iPSCs into healthy retinal organoids. Samples of patient- and control-retinal organoids at W0, W7, W13 (two replicates), W18 (two replicates) and W22 (two replicates for patient) were collected for RNA-seq. Corrected-iPSC were derived from CRISPR/Cas9-mediated gene correction. Then we collected the corrected-iPSC derived retinal organoids at W0, W7, W13 (two replicates), W18 (two replicates) and W22 (two replicates) for RNA-seq. Through the RNA-seq data, we demonstrate that patient-specific iPSC-dervied 3D retinae can recapitulate disease progress of Retinitis Pigmentosa through presenting defects in photoreceptors' gene profile. CRISPR/Cas9-mediated gene correction can rescue photoreceptor gene profile. Those transcriptome are consistent with the phenotype and function.

2020-02-01 | E-MTAB-6490 | biostudies-arrayexpress

Inhibition of JNK ameliorates rod photoreceptor degeneration in a mouse model of retinitis pigmentosa

Project description:Retinitis pigmentosa (RP) is an inherited eye disease that causes progressive vision loss.To investigate the biological processes and molecular changes that occur in different cell types in the retinas in rd1 mice, a mouse model of retinitis pigmentosa, we performed single-cell RNA-seq to examine the transcriptomes of various retinal cells.

2024-06-23 | GSE261060 | GEO

The photoreceptor protective cGMP-analog Rp-8-Br-PET-cGMPS shows target-specificity in the degenerating mouse retina

Project description:The inherited eye disease Retinitis Pigmentosa (RP) causes the loss of photoreceptors by a still unknown cell death mechanism. During this degeneration, cGMP levels become elevated, leading to over-activation of the cGMP-binding protein cGMP-dependent protein kinase (PKG). cGMP analogs selectively modified to have inhibitory actions on PKG have aided in impeding photoreceptor death, and one such cGMP analog is Rp-8-Br-PET-cGMPS. However, cGMP analogs have previously been shown to interact with numerous targets, so to further evaluate Rp-8-Br-PET-cGMPS’ efficacy for therapies, it is necessary to comprehend its target-selectivity and what potential cellular mechanism(s) it may affect within the photoreceptors.

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