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Human induced pluripotent stem cells: diploid, chr7q deletion, spontaneous chr7 correction

ABSTRACT: Gene expression analysis, a) comparing isogenic karyotypically normal iPSCs to del7q-iPSCs, b) comparing del7q-iPSCs to spontaneously corrected iPSCs. The chr7q deletion results in reduced expression levels of a large number of genes in the chr7q deleted region

ORGANISM(S): Homo sapiens

PROVIDER: GSE65215 | GEO | 2015/02/16

SECONDARY ACCESSION(S): PRJNA273409

REPOSITORIES: GEO

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Human induced pluripotent stem cells: diploid, chr7q deletion, spontaneous chr7 correction

Project description:Gene expression analysis, a) comparing isogenic karyotypically normal iPSCs to del7q-iPSCs, b) comparing del7q-iPSCs to spontaneously corrected iPSCs. The chr7q deletion results in reduced expression levels of a large number of genes in the chr7q deleted region Two-condition experiment, del7q-iPSCs vs. isogenic normal iPSCs and del7q-iPSCs vs spontaneously corrected-iPSCs. Biological replicates: 3 control replicates, 3 del7q-iPSC replicates and 3 spontaneously corrected-iPSC replicates

2015-02-16 | E-GEOD-65215 | biostudies-arrayexpress

Human induced Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

Project description:Mapping deletions of Chr7 in human iPSC derived from patients cells through reprogramming Two-condition experiment, normal diploid iPSCs vs del7q-iPSCs

2015-02-16 | E-GEOD-65387 | biostudies-arrayexpress

GENETIC CORRECTION OF HUNTINGTON'S DISEASE PHENOTYPES IN INDUCED PLURIPOTENT STEM CELLS

Project description:Huntington's Disease (HD) is caused by a CAG expansion in the huntingtin gene. Expansion of the polyglutamine tract in the huntingtin protein results in massive cell death in the striatum of HD patients. We report that human induced pluripotent stem cells (iPSCs) derived from HD patient fibroblasts can be corrected by replacing the expanded CAG repeat with a normal repeat using homologous recombination, and that the correction persists in iPSC differentiation into DARPP-32 positive neurons in vitro and vivo. Further, correction of the HD-iPSCs normalized pathogenic HD signaling pathways (cadherin, TGF-?, BNDF, caspase activation), and reversed disease phenotypes such as susceptibility to cell death and altered mitochondrial bioenergetics in neural stem cells. The ability to make patient-specific, genetically corrected iPSCs from HD patients will provide relevant disease models in identical genetic backgrounds and is a critical step for the eventual use of these cells in cell replacement therapy. 16 experimental samples were used overall. There were 8 replicates per group, with one group being the control, and the other being the experimental. Comparison was carried out on the Nimblegen platform.

2012-06-14 | E-GEOD-37547 | biostudies-arrayexpress

Expression data from +7 hNPCs and diploid hNPCs

Project description:Human Neural progenitor cells have been found to have karyotypic abnormalities. In this study we explored the gene changes between hNPCs that are karyotypically normal and hNPCs with a trisomy of chromosome 7. We used Affymetrix GeneChips to study gene expression changes between karyotypically normal hNPCs and trisomy 7 hNPCs.

2009-10-01 | GSE18349 | GEO

RNA-seq analysis of MCT8-deficient and healthy control brain microvascular endothelial cells (BMECs) and neural cells

Project description:MCT8-deficient, healthy control and mutated/corrected isogenic iPSCs were differentiated into brain microvascular endothelial cells and neural cells. Neural cells were cultured with or without T3.

2017-04-04 | GSE97324 | GEO

GENETIC CORRECTION OF HUNTINGTON'S DISEASE PHENOTYPES IN INDUCED PLURIPOTENT STEM CELLS

Project description:Huntington's Disease (HD) is caused by a CAG expansion in the huntingtin gene. Expansion of the polyglutamine tract in the huntingtin protein results in massive cell death in the striatum of HD patients. We report that human induced pluripotent stem cells (iPSCs) derived from HD patient fibroblasts can be corrected by replacing the expanded CAG repeat with a normal repeat using homologous recombination, and that the correction persists in iPSC differentiation into DARPP-32 positive neurons in vitro and vivo. Further, correction of the HD-iPSCs normalized pathogenic HD signaling pathways (cadherin, TGF-β, BNDF, caspase activation), and reversed disease phenotypes such as susceptibility to cell death and altered mitochondrial bioenergetics in neural stem cells. The ability to make patient-specific, genetically corrected iPSCs from HD patients will provide relevant disease models in identical genetic backgrounds and is a critical step for the eventual use of these cells in cell replacement therapy.

2012-06-15 | GSE37547 | GEO

Induced-pluripotent stem-derived vascular endothelial cells in Down syndrome

Project description:To investigate the physiological characteristics of endothelial cells (EC) harboring trisomy 21 (T21), we establised isogenic pairs of T21-iPSCs and corrected disomy 21 (cDi21)-iPSCs We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 different iPSC-derived ECs.

2022-05-20 | GSE203257 | GEO

Concurrent progress of reprogramming and gene-correction to overcome limitation of gene therapy of ALK2 mutant iPSCs

Project description:To ameliorate the cumbersome processes of reprogramming and subsequent gene-editing in vulnerable iPSCs, we have developed a greatly simplified one-step procedure, simultaneously introducing reprogramming and gene-editing components into human fibroblast cells. This not only serves to save time, labor, and costs, but opens up a new arena of research that is beyond the current application of gene-editing methodologies due to restrictive reprogramming concerns, inhibitory pluripotency maintenance requirements, and vulnerability of single-cell dissociated iPSCs. We generated iPSCs (mALK2-iPSCs) derived from Fibrodysplasia ossificans progressiva (FOP)-fibroblast cells carrying the ACVR1 p.R206H mutation and gene-corrected ALK2-iPSCs (cALK2-iPSCs). To identify gene-correction effects on global gene expression, gene expression profiling was measured in cALK2-iPSCs and mALK2-iPSCs, calibrated to WT-iPSCs with duplication.

2015-05-12 | E-GEOD-68766 | biostudies-arrayexpress

Pathways Disrupted in Human ALS Motor Neurons Identified Through Genetic Correction of Mutant SOD1

Project description:Although many distinct mutations in a variety of genes are known to cause Amyotrophic Lateral Sclerosis (ALS), it remains poorly understood how they selectively impact motor neuron biology and whether they converge on common pathways to cause neural degeneration. Here, we have combined reprogramming and stem cell differentiation approaches with genome engineering and RNA sequencing to define the transcriptional changes that are induced in human motor neurons by mutant SOD1. Mutant SOD1 protein induced a transcriptional signature indicative of increased oxidative stress, reduced mitochondrial function, altered sub-cellular transport as well as activation of the ER stress and unfolded protein response pathways. Functional studies demonstrated that perturbations in these pathways were indeed the source of altered transcript levels. 5 samples, 2 patient-derived SOD1A4V and 3 isogenic control samples where the mutation has been corrected. All samples are motor neurons derived from induced pluripotent stem cells (iPSCs), and isolated after lentiviral infection with an Hb9:RFP construct and FACS purification. Each sample is a separate biological replicate.

2014-02-03 | E-GEOD-54409 | biostudies-arrayexpress

Universal correction of blood coagulation factor VIII in patient-derived induced pluripotent stem cells using CRISPR/Cas9

Project description:Confirmation of the nuclease acivities at the On- and Off-target sites; Hemophilia A (HA) is caused by genetic mutations in the blood coagulation factor VIII (FVIII). Genome editing approaches can be used to target the mutated site itself in patient-derived induced pluripotent stem cells (iPSCs). However, these approaches can be hampered by difficulty preparing thousands of editing platforms for each corresponding variant found in HA patients. Here, we report a universal approach to correct the various mutations in HA patient iPSCs by the targeted insertion of the FVIII gene into the human H11 site via CRISPR/Cas9. We derived corrected clones from two types of patient iPSCs with frequencies of up to 64% and 66%, respectively, without detectable unwanted off-target mutations. Moreover, we demonstrated that endothelial cells differentiated from the corrected iPSCs successfully secreted functional protein in vitro and functionally rescued the disease phenotype in vivo. This strategy may provide a universal therapeutic method for correcting all genetic variants found in HA patients.

2019-01-05 | GSE124663 | GEO

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