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Retinal Organoids derived from AIPL1-LCA Patient iPSCs Maintain Retinal Cytoarchitecture under Reduced AIPL1 Levels

ABSTRACT: In this study, we generated three-dimensional (3D) retinal organoids (ROs) from induced pluripotent stem cells (iPSCs) derived from an LCA4 patient carrying a Cys89Arg mutation in AIPL1. This study aimed to (i) explore whether the patient iPSC-derived ROs recapitulate LCA4 disease phenotype, and (ii) generate a clinically relevant resource to investigate the molecular mechanism of disease and safely test novel therapies for LCA4 in vitro.

ORGANISM(S): Homo sapiens

PROVIDER: GSE131877 | GEO | 2020/05/28

REPOSITORIES: GEO

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Retinal Organoids derived from AIPL1-LCA Patient iPSCs Maintain Retinal Cytoarchitecture under Reduced AIPL1 Levels

Project description:Retinal Organoids derived from AIPL1-LCA Patient iPSCs Maintain Retinal Cytoarchitecture under Reduced AIPL1 Levels

| PRJNA545219 | ENA

Transcriptomic comparison of 3D retinal organoids derived from retinitis pigmentosa patient harboring PDE6B mutation and non-phenotype control

Project description:Retinitis pigmentosa (RP) is a hereditary retinal degenerative disease. Although an increasing number of disease genes have been identified, the exact cellular mechanisms of RP remain largely unclear. Retinal organoids (ROs) derived from the induced pluripotent stem cells (iPSCs) of patients provide a potential but unvalidated platform for deciphering disease mechanisms. Here, we developed patient ROs with a PDE6B mutation.To investigate the transcriptional effects of the PDE6B mutation, comparison of bulk RNA-seq profiles were performed in patient and control ROs, which were collected from the mid-stage (D90, 120, 150 and 180) to late-stage (D230). Transcriptome analysis revealed a remarkably distinct gene expression profile in the patient ROs at late-stage.Gene Ontology (GO) analysis of the transcripts significantly different at D230 between the patient and control ROs indicated an enrichment of genes implicated in G-protein-coupled receptor activity, G-protein-coupled receptor signaling pathway and calcium ion binding.

2019-12-06 | GSE141531 | GEO

RNA-seq of retinal pigment epithelium (RPE) derived from human induced pluripotent stem cells (iPSCs): healthy control and USH1B patient iPSCs

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2023-08-22 | E-MTAB-12165 | biostudies-arrayexpress

Project description:Patient-derived models of brain metastases recapitulate human disseminated disease

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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.

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Nicotinamide promotes formation of retinal organoids from human pluripotent stem cells via enhanced neural cell fate commitment

Project description:Retinal organoids (ROs) derived from human pluripotent stem cells (hPSCs) recapitulate key features of human retinogenesis and thus provide a promising platform to study the mechanisms of retinal development and disease in a human context and to evaluate therapies. Although multiple differentiation protocols are currently in use, hPSCs exhibit tremendous variability in differentiation efficiency, with some cell lines consistently yielding few or even no ROs thus limiting their utility in research. To improve the efficiency and robustness of RO generation, we set out to identify factors that promote neural retina differentiation from hPSCs. We report here that nicotinamide (NAM) treatment at the early stage of differentiation significantly improved RO yield across 8 hPSC lines from different donors. Importantly, NAM treatment enabled efficient production of ROs from cell lines that would otherwise fail to generate meaningful number of ROs. Further analyses revealed that NAM treatment promotes neural commitment of hPSCs at the expense of non-neural ectodermal cell fate, which in turn increases eye field commitment and RO generation. This effect is mediated, at least in part, through inhibition of BMP signaling. Thus, our modified protocol with a simple NAM treatment improves the yield of ROs in all lines tested, and importantly greatly benefits to cell lines that previously proved to be intractable in retinal differentiation. Our data should facilitate the broader use of human ROs for disease modeling applications requiring the use of multiple cell lines or a larger scale of cell source such as therapy screening.

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Molecular signatures of human iPSCs highlight sex differences and cancer genes

2013-12-03 | GSE36233 | GEO

RNA-Seq profiling of dopaminergic neurons from iPSCs of Parkinson's disease patients

Project description:The fact that Parkinsons disease (PD) can arise from numerous genetic mutations suggests a unifying molecular pathology underlying the various genetic backgrounds. In order to address this hypothesis, an integrated approach utilizing in vitro disease modeling and comprehensive transcriptome profiling was taken to advance our understanding of PD progression and the concordant downstream signaling pathways across divergent genetic predispositions. To model PD in vitro, neurons harboring disease-causing mutations were generated from patient-specific, induced pluripotent stem cells (iPSCs) and found to recapitulate several disease-related phenotypes. Signs of degeneration in PD midbrain dopaminergic (mDA) neurons were observed, reflecting the cardinal feature of PD. In addition, novel gene expression signatures were revealed for PD mDA neurons, providing molecular insights to disease phenotype observed in vitro, including oxidative stress vulnerability and altered neuronal activity. Notably, detailed transcriptome profiling of PD neurons showed that elevated RBFOX1, a gene previously linked to neurodevelopmental diseases, is responsible for a pattern of alternative RNA processing associated with PD-specific phenotypes in vitro.

2016-06-07 | E-MTAB-4586 | biostudies-arrayexpress

Molecular signatures of human iPSCs highlight sex differences and cancer genes

Project description:We compared human female hiPSC lines (all derived from IMR-90 fibroblasts) that were XIST RNA-positive and XIST RNA-negative. We also examined the gene expression patterns for 2 female hIPSCs (derived from different disease model fibroblasts) that were also negative for XIST RNA. hiPS 12D-1 is derived from Huntington's Disease patient and 6C-1 is derived from a Type I Diabetes Mellitus patient (Park et al Nature 2008). hiPSCs (undifferentiated) were cultured to confluency then RNA was isolated using TriZOL (MEFs were removed using trypsin). cDNA was converted using NuGEN then hybridized to Affymetrix 3' arrays.

2013-12-03 | E-GEOD-36233 | biostudies-arrayexpress

Project description:PDAC patient-derived organoids mimic patient disease

| PRJNA471134 | ENA

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