Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA132087 | ENA |
REPOSITORIES: ENA
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Project description:The advent of human induced pluripotent stem (iPS) cells enables for the first time the derivation of unlimited numbers of patient-specific stem cells and holds great promise for regenerative medicine. However, realizing the full potential of iPS cells requires robust, precise and safe strategies for their genetic modification. Safe human iPS cell engineering is especially needed for therapeutic applications, as stem cell-based therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify iPS cells from patients with beta-thalassemia in a potentially clinically relevant manner. Our approach is based on the identification and selection of âsafe harborâ sites for transgene expression in the human genome. We show that thalassemia patient iPS cell clones harboring a transgene can be isolated and screened according to chromosomal position. We next demonstrate that iPS cell clones that meet our âsafe harborâ criteria resist silencing and allow for therapeutic levels of beta-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. Combined bioinformatics and functional analyses thus provide a robust and dependable approach for achieving desirable levels of transgene expression from selected chromosomal loci. This approach may be broadly applicable to introducing therapeutic or suicide genes into patient specific iPS cells for use in cell therapy. iPS cell clones were derived from beta-thalassemia patients. A single copy of beta-globin transgene cis-linked to locus control region (LCR) elements and an excisable Neo-eGFP transcription unit were inserted into these cell clones. beta-globin expression was induced by erythroid differentiation.
2010-10-26 | E-GEOD-24901 | biostudies-arrayexpress
Project description:The advent of human induced pluripotent stem (iPS) cells enables for the first time the derivation of unlimited numbers of patient-specific stem cells and holds great promise for regenerative medicine. However, realizing the full potential of iPS cells requires robust, precise and safe strategies for their genetic modification. Safe human iPS cell engineering is especially needed for therapeutic applications, as stem cell-based therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify iPS cells from patients with beta-thalassemia in a potentially clinically relevant manner. Our approach is based on the identification and selection of “safe harbor” sites for transgene expression in the human genome. We show that thalassemia patient iPS cell clones harboring a transgene can be isolated and screened according to chromosomal position. We next demonstrate that iPS cell clones that meet our “safe harbor” criteria resist silencing and allow for therapeutic levels of beta-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. Combined bioinformatics and functional analyses thus provide a robust and dependable approach for achieving desirable levels of transgene expression from selected chromosomal loci. This approach may be broadly applicable to introducing therapeutic or suicide genes into patient specific iPS cells for use in cell therapy.
2010-10-26 | GSE24901 | GEO
Project description:Delta-Beta thalassemia is an unusual variant of thalassemia caused by large deletions in the β globin gene cluster involving δ- and β-globin genes. The mutations are characterized by high fetal hemoglobin with significant phenotypic diversity. Routinely used diagnostic tests targeting point mutations and small insertions, deletions of the β-globin gene are not suitable for detection of large deletion mutations. This is overcome by either direct globin chain synthesis analysis or beta-cluster gene analysis using different methods. In the current study, we use direct globin chain analysis to diagnose a family with δβ-thalassemia using high resolution mass spectrometry.
2024-08-09 | PXD044775 | Pride
Project description:Reactivation of gamma-globin is considered a promising approach for the treatment of beta-thalassaemia and sickle cell disease. Therapeutic induction of gamma-globin expression is fraught with lack of suitable therapeutic targets. In order to identify new potential targets we analysed the changes in the proteome of human primary erythroid progenitor cells by treatment with decitabine, a known, yet not clinically safe, gamma-globin inducer. Significant differentially expressed proteins were identified which were involved in various biological pathways and functional categories.
2020-01-23 | PXD006889 | Pride
Project description:Clinical application of induced pluripotent stem (iPS) cells is limited by low efficiency of iPS derivation, and protocols that permanently modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPS cells towards clinically useful cell types are lacking. Here we describe a simple, non-mutagenic strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate anti-viral responses. We show that this approach can reprogram multiple human cell types to pluripotency with efficiencies that greatly surpass established protocols. We further show that the same technology can be used to efficiently direct the differentiation of RNA-induced pluripotent stem (RiPS) cells into terminally differentiated myogenic cells. Our method represents a safe, efficient strategy for somatic cell reprogramming and directing cell fates that has broad applicability for basic research, disease modeling and regenerative medicine. We isolated RNA from human RNA derived iPS cells, viral derived iPS cells, different human fibroblasts and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.
2010-09-30 | E-GEOD-23583 | biostudies-arrayexpress
Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
2018-08-02 | MSV000082680 | GNPS
Project description:Robust β-globin expression in erythroid cells derived from induced pluripotent stem cells (iPSCs) would increase the resolution with which red blood cell disorders such as sickle cell disease and β thalassemia can be modeled in vitro. To better quantify efforts in augmenting β-globin expression, we report the creation of a β-globin reporter iPSC line through the insertion of a GFP cassette after the endogenous β-globin promoter, allowing for the mapping of β-globin expression throughout erythroid development in real time at single cell resolution. Sorting live GFP+ and GFP- cells at the most mature stage of erythroid differentiation, followed by single cell RNA sequencing (scRNAseq), identifies features that distinguish GFP- from GFP+ β-globin expressing cells and allows for the dissection of the developmental and maturational status of iPSC-derived erythroid cells. Co-expression of embryonic, fetal and adult globins in individual cells indicates a yolk sac erythro-myeloid progenitor (EMP) stage of hematopoietic development, representing the onset of definitive erythropoiesis. Within this developmental program, scRNAseq analysis identifies a gradient of erythroid maturation with GFP+ β-globin expressing cells showing increased maturation. In addition, scRNAseq analysis reveals that definitively patterned iPSC-derived erythroblasts resemble their postnatal counterparts in terms of gene expression and essential biological processes, confirming their potential for disease modeling and regenerative medicine applications.
2018-07-31 | GSE111860 | GEO
Project description:Identification of Genomic Safe Harbors in the Anhydrobiotic Cell Line, Pv11
| PRJNA787263 | ENA
Project description:Induced pluripotent stem (iPS) cells give rise to neural stem cells, which are applicable for therapeutic transplantation in treatment of neural diseases. However, generation of neural stem cells from iPS cells requires a careful selection of safe iPS clones. We sought to determine whether direct induction of neural stem cells from partially reprogrammed somatic cells is able to generate safer cells rapidly. We have successfully established direct induction system from fibroblast to neural stem cells. To characterize these directly induced neural stem cells, Gene expression profiles were compared with iPS cell or ES cell-derived neurosphere. We used affymetrix microarrays to compare the global gene expression of neurospheres prepared several method. RNA extracted from neurospheres was hybridized to Affymetrix microarrays. The mouse strain used in this study except ES/iPS cells was C57BL/6.
2012-03-31 | E-GEOD-31598 | biostudies-arrayexpress
Project description:Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. Genomic instability induced by reprogramming or genetic modification would be a main issue for the safe use of these cells. We analyzed primary hIPSC lines and genetically modified derivatives by array-based comparative genomic hybridization.
2011-09-01 | E-MEXP-3316 | biostudies-arrayexpress