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Single cell transcriptomics of hepatostellate organoids derived from DKC1 A353V mutant and DKC1 A353V corrected iPSCs

ABSTRACT: Single cell transcriptomics of hepatostellate organoids derived from DKC1 A353V mutant and DKC1 A353V corrected iPSCs

PROVIDER: PRJNA780948 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16959615_1.fastq.gz	Fastqsanger.gz
	SRR16959615_2.fastq.gz	Fastqsanger.gz
	SRR16959616_1.fastq.gz	Fastqsanger.gz
	SRR16959616_2.fastq.gz	Fastqsanger.gz
	SRR16959617_1.fastq.gz	Fastqsanger.gz

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Single cell transcriptomics of hepatostellate organoids derived from DKC1 A353V mutant and DKC1 A353V corrected iPSCs

Project description:We model liver phenotypes associated with telomere dysfunction using DC patient-derived iPS cells and isogenic controls with CRISPR/Cas9-mediated homology-directed repair correction of the disease-causing DKC1 mutation. Differentiation of these cells into hepatocyte-like cells or hepatic stellate cells indicates that the parenchymal hepatocytes are primarily affected by telomere dysfunction. We develop an admixed hepatostellate organoid culture model which further reveals that mutant hepatocytes exert dominant effects on hepatic stellate cells regardless of stellate cell genotype. Hepatostellate organoids containing DKC1-mutant hepatocytes exhibit hyperplasia in both the hepatocyte compartment and, remarkably, in stellate cells. Moreover, mutant hepatocytes can induce hallmarks of stellate cell activation independently of stellate cell genotype. Interestingly, mutant hepatostellate organoids also contain off-target PLVAP+ endothelial cells reminiscent of scar-associated endothelium observed in non-DC cirrhosis patients.

2022-02-28 | GSE188987 | GEO

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

scRNA-seq of cerebral organoids derived from CBP mutant iPSCs

Project description:CREB-binding protein (CBP/CREBBP) is a histone acetyltransferase essential for human development. Mutations in CBP are associated with Menke–Hennekam syndrome (MKHK), a neurodevelopmental disorder. To examine the impact of a disease-associated mutation, we performed single-cell RNA sequencing (scRNA-seq) on day 32 cerebral organoids derived from isogenic wild-type and CBP R1868 mutant human induced pluripotent stem cells (iPSCs). This scRNA-seq data captures cellular heterogeneity and gene expression programs during early neurodevelopment and reveals how the CBP R1868W mutation influences lineage specification and transcriptional states in human cerebral organoids.

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RNA-seq profiling of cerebral organoids derived from CBP mutant iPSCs

Project description:CREB-binding protein (CBP/CREBBP) is a histone acetyltransferase essential for human development. Mutations in CBP are associated with Menke–Hennekam syndrome (MKHK), a neurodevelopmental disorder. To examine the impact of a disease-associated mutation, we performed RNA sequencing on cerebral organoids derived from isogenic wild-type and CBP R1868 mutant human induced pluripotent stem cells (iPSCs) at Day6, Day12, Day18 and Day30 of differentiation. This time-course RNA-seq data captures gene expression programs during early neurodevelopment and reveals how the CBP R1868W mutation influences transcriptional states in human cerebral organoids.

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scRNA-seq of cerebral organoids derived from CBP mutant iPSCs

Project description:scRNA-seq of cerebral organoids derived from CBP mutant iPSCs

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Bulk RNA-seq of MilliporeSigma SCC300 human iPSC-derived colon organoids compared with undifferentiated human iPSCs and MilliporeSigma SCC321 human patient-derived colon organoids

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Project description:The use of patient-derived induced pluripotent stem (iPS) cells as treatment for genetic diseases entails genetic repair or transfer of genetic information as a prerequisite. We have chosen the murine model of tyrosinemia type 1 (fumarylacetoacetate hydrolase deficiency; FAH(-/-) mice) as a paradigm for hereditary metabolic liver disorders and evaluated fibroblast-derived FAH(-/-)-iPS cell lines as targets for gene correction. By aggregating FAH(-/-)-iPS cells with tetraploid embryos, we obtained FAH-/--iPS cellâderived mice, which exhibited the phenotype of the founding FAH(-/-)-mice. We then rescued the diseased phenotype by lentiviral transduction of FAH-cDNA and performed embryo aggregation with these gene-corrected FAHgc-iPS cells to obtain viable healthy mice. Our results demonstrate that iPS cell technology is a valid approach to establish mouse disease models directly from somatic cells bearing genetic defects. Furthermore, established iPS cell lines can be genetically manipulated without loss of pluripotency for treatment of genetic diseases. 6 samples: 1 MEF, 1ESC, 4 iPSCs

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RNA-seq profiling of cerebral organoids derived from CBP mutant iPSCs

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DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis

Project description:Higher expression of Dyskerin Pseudouridine Synthase 1 (DKC1) associates with poor prognosis in colorectal cancer (CRC) patients. However, the mechanism associated with DKC1 upregulation, and its functional significance in disease pathogenesis and therapeutic resistance remains largely unexplored. Here, we performed global transcriptome sequencing outlining the molecular mechanism associated with DKC1 depletion in CRC. We show a positive feedback loop between canonical WNT signaling and DKC1, which orchestrates DKC1 expression. Moreover, we show the role of altered sphingolipid metabolism upon DKC1 abrogation in imparting CRC oncogenicity and first-line chemotherapeutic resistance.

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DKC1: a robust prognostic factor and potential therapeutic target in Multiple Myeloma

Project description:Multiple Myeloma (MM) is an incurable plasma cell malignancy. Dyskerin pseudouridine synthase 1 (DKC1), a nucleolar protein, is essential for RNA modification and cellular homeostasis, yet its role in MM remains unclear. Here, we report that elevated DKC1 expression independently predicted poor outcomes in MM and further refined prognostic stratification beyond the ISS system. Functional assays showed that DKC1 promoted MM cell proliferation, survival, and colony formation, whereas DKC1 knockdown or pharmacological inhibition of DKC1 by pyrazofurin inhibited proliferation and colonies, induced apoptosis, and suppressed tumor growth in xenografts. Mechanistically, DKC1 promotes tumor progression by stabilizing ATF5 mRNA through pseudouridylation, a direct post-transcriptional mechanism evidenced by site-specific pseudouridine mapping. Together, these findings highlight DKC1 as both a critical prognostic biomarker and a promising therapeutic target.

2026-04-15 | GSE308784 | GEO

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