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Simple Derivation of Transgene-Free iPS Cells by a Dual Recombinase Approach

ABSTRACT: Induced pluripotent stem cells (iPSCs) can be derived from somatic cells by the introduction of the transcription factors Oct4, Sox2, Klf4 and cMyc using various methods. Here, we describe a new approach for the derivation of murine iPSCs using a polycistronic non-viral inducible vector integrated into pseudo attP sites via the C31 integrase-mediated site-specific recombination and subsequent vector excision by Cre recombinase. The pluripotency of the derived iPSCs was proved by in vitro and in vivo tests. The derived transgene-free iPSCs reactivated the endogenous pluripotency genes like e.g. Oct4, Sox2 and Nanog and the global gene expression profiles of iPSCs lines are highly similar to ESCs and distinct from parental murine fibroblasts. We demonstrated the differentiation potential of iPSCs by generation cells of the three germ layers as well as we successfully created germline chimeric mice from transgene-free iPSCs. In this study, we presented an efficient method for the generation of transgene-free iPSCs using dual-recombinase technology.

ORGANISM(S): Mus musculus

PROVIDER: GSE51605 | GEO | 2014/03/29

SECONDARY ACCESSION(S): PRJNA224092

REPOSITORIES: GEO

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Simple Derivation of Transgene-Free iPS Cells by a Dual Recombinase Approach

Project description:Induced pluripotent stem cells (iPSCs) can be derived from somatic cells by the introduction of the transcription factors Oct4, Sox2, Klf4 and cMyc using various methods. Here, we describe a new approach for the derivation of murine iPSCs using a polycistronic non-viral inducible vector integrated into pseudo attP sites via the C31 integrase-mediated site-specific recombination and subsequent vector excision by Cre recombinase. The pluripotency of the derived iPSCs was proved by in vitro and in vivo tests. The derived transgene-free iPSCs reactivated the endogenous pluripotency genes like e.g. Oct4, Sox2 and Nanog and the global gene expression profiles of iPSCs lines are highly similar to ESCs and distinct from parental murine fibroblasts. We demonstrated the differentiation potential of iPSCs by generation cells of the three germ layers as well as we successfully created germline chimeric mice from transgene-free iPSCs. In this study, we presented an efficient method for the generation of transgene-free iPSCs using dual-recombinase technology. expression data of iPSCs/ESCs/MEFs

2014-03-29 | E-GEOD-51605 | biostudies-arrayexpress

Genotyping, generation and lysine 2-hydroxyisobutyrylation identification of the first human autosomal dominant osteopetrosis type II specific induced pluripotent stem cells

Project description:Background: Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell therapy. Methods: To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide analysis of lysine 2-hydroxyisobutyrylation in the ADO2-iPSCs and control cell lines was performed by high-resolution LC-MS/MS and a bioinformatics analysis. Results: WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband’s mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried the normal male karyotype (46, XY) and carried the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene was detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. Our proteomic profiling detected 7, 405 proteins and revealed 3,684 2-hydroxyisobutyrylated sites in 1,036 proteins in the ADO2-iPSCs. Conclusions: Our data indicated that mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with identified lysine 2-hydroxyisobutyrylation may be valuable for personalized and cell-based regenerative medicine in the future.

2022-02-15 | PXD014227 | Pride

The role of AF10 (Mllt10) in maintaining cell identity (RNA-Seq)

Project description:AF10 is a cofactor of the H3K79 methyltransferase DOT1L. To uncover the role of H3K79me in reprogramming to induced pluripotent stem cells (iPSCs), we bred reprogrammable mice encoding doxycycline inducible Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (OKSM) transgene with conditional flox (fl)-AF10 (Mllt10). We isolated mouse embryonic fibroblasts (MEFs), deleted AF10 with CRE-recombinase or treated cells with empty vector control, and initiated reprogramming in DOT1L chemical inhibitor SGC0946 or DMSO control. Gene expression was assessed using RNA-Seq and genome wide localization of H3K79me1 and H3K79me2 was determined by ChIP-Seq on day 4 of reprogramming.

2023-04-01 | GSE214139 | GEO

The role of AF10 (Mllt10) in maintaining cell identity (ChIP-Seq)

Project description:AF10 is a cofactor of the H3K79 methyltransferase DOT1L. To uncover the role of H3K79me in reprogramming to induced pluripotent stem cells (iPSCs), we bred reprogrammable mice encoding doxycycline inducible Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (OKSM) transgene with conditional flox (fl)-AF10 (Mllt10). We isolated mouse embryonic fibroblasts (MEFs), deleted AF10 with CRE-recombinase or treated cells with empty vector control, and initiated reprogramming in DOT1L chemical inhibitor SGC0946 or DMSO control. Gene expression was assessed using RNA-Seq and genome wide localization of H3K79me1, H3K79me2, and RNA Polymerase II (RNAPII) was determined by ChIP-Seq on day 4 of reprogramming.

2023-04-01 | GSE214141 | GEO

SNP genotyping array of human naive pluripotent stem cells

Project description:We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior differentiation ability compared with iPSCs derived from conventional methods.

2022-12-15 | GSE207525 | GEO

Dissecting pluripotency through the different OCT4 and SOX2 assembly configurations

Project description:The transcription factors OCT4 and SOX2 are required for generating induced pluripotent stem cells (iPSCs) and for maintaining embryonic stem cells (ESCs). To this end, OCT4 and SOX2 associate and bind to DNA in different configurations depending on the composite DNA element present in their target genes. Here, we have investigated the role of the different OCT4-SOX2 conformational arrangements in regulating and inducing pluripotency. To this end, we have generated SOX2 mutants that interfere with specific OCT4-SOX2 heterodimer configurations and we have assessed their abilities to generate iPSCs and to rescue ESC self-renewal. Our results demonstrate that the OCT4-SOX2 configuration that dimerizes on a Hoxb1-like composite, a canonical element with juxtaposed individual binding sites, plays a more critical role in the induction and maintenance of pluripotency than other OCT4-SOX2 configurations. Overall, the results of this study provide a new insight into the protein interactions required to establish a de novo pluripotent network and to maintain a true pluripotent cell fate.

2017-02-13 | GSE65345 | GEO

Gene expression profiles of human primed and naive pluripotent stem cells

Project description:We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior naive-specific differentiation ability compared with iPSCs derived from conventional methods.

2022-12-15 | GSE179475 | GEO

DNA methylation profiles of human primed and naive pluripotent stem cells

Project description:We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior naive-specific differentiation ability compared with iPSCs derived from conventional methods.

2022-12-15 | GSE179473 | GEO

Development of a method for quantitative analysis of in vivo interactions of pluripotency transcription factors Sox2, Oct4, Nanog by mass spectrometry

Project description:Protein-protein proximity of core pluripotency transcription factors plays an important role during cell reprogramming. Pluripotent embryonic stem (ES) cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. These proteins often bind to closely localized genomic sites. The precise mode by which Sox2, Oct4, and Nanog interact with DNA is likely to make a crucial contribution to their function. Here, a detailed protocol for in vivo detection and quantitative analysis of protein-protein proximity of Sox2 and Oct4 using Proximity Utilizing Biotinylation (PUB) method based on the use of the BAP/BirA (target/enzyme) system is described. The method includes design and cloning of DNA plasmid construct, transient transfection of HEK293T cells, Western blot analysis of nuclei fraction and LC-MS/MS analysis. Experiments with coexpression of BAP-X+BirA-Y (X, Y=Sox2, Oct4 and GFP as control) revealed strong biotinylation level of target proteins when X and Y were pluripotency transcription factors compared with control when X=GFP. Since mass spectrometry provides both high sensitivity and more accurate quantification of data a modified workflow was used, in which SDS-PAGE step was eliminated and His-tagged BAP-fused proteins from cell lysate were purified in 6M guanidine HCl buffer, washed, propionylated, digested directly on the Ni sepharose beads using trypsin and analysed on Q-TOF Impact II instrument. Using mass spectrometry allows making quantitative estimation of in vivo interaction of BAP-Sox2 and BirA-Oct4 which was demonstrated by measuring ratios of biotinylation levels of BAP fused either with Sox2 or GFP at different biotin pulse times. After vector preparation this protocol can be completed in seven working days.

2020-01-21 | PXD015756 | Pride

Pluripotency factor-induced lineage conversion involves transient passage through an iPS cell stage

Project description:Brief expression of pluripotency-associated factors such as OCT4, KLF4, SOX2 and c-MYC (OKSM), in combination with differentiation-inducing signals, was reported to trigger transdifferentiation of fibroblasts into alternative cell types. Here, we show that OKSM expression gives rise to both induced pluripotent stem cells (iPSCs) and iNSCs under conditions that were previously shown to induce only NSC transdifferentiation. Fibroblast-derived iNSC colonies silenced retroviral transgenes and reactivated silenced X chromosomes, both hallmarks of pluripotent stem cells. Moreover, lineage tracing via an Oct4-CreER labeling system demonstrated that virtually all iNSC colonies originate from cells transiently expressing Oct4, whereas ablation of Oct4-positive cells prevented iNSC formation. Lastly, use of an alternative transdifferentiation cocktail that lacks OCT4 and was reportedly unable to support induced pluripotency, yielded iPSCs and iNSCs carrying the Oct4-CreER-derived lineage label. Together, these data suggest that iNSC generation using OKSM and related reprogramming factors requires passage through a transient iPSC state. 5 samples were anlyzed in total, 2 induced pluripotent stem cells (iPSCs), 1 neural stem cells (NSCs) and 2 induced NSCs (iNSCs)

2015-04-30 | E-GEOD-65951 | biostudies-arrayexpress

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