Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Two Supporting Factors Greatly Improve the Efficiency of Human iPS Cell Generation

ABSTRACT: Human fibroblasts can be induced into pluripotent stem cells (iPS cells), but the reprogramming efficiency is quite low. Here, we screened a panel of candidate factors in the presence of OCT4, SOX2, KLF4 and c-MYC in an effort to improve the reprogramming efficiency from human adult fibroblasts. We found that p53 siRNA and UTF1 enhanced the efficiency of iPS cell generation up to 100-fold, even when the oncogene c-MYC was removed from the combinations. We further demonstrated that by using a novel combination of the four factors OCT4, SOX2, KLF4 and UTF1, iPS cells could be generated at a frequency at least 10 times higher than using the original four reprogramming factors without c-MYC. The iPS cells generated in this work have a similar gene expression profile and differentiation potential as human embryonic stem (hES) cells. In conclusion, two novel supporting factors that increase the efficiency of direct reprogramming have been identified, and a more-efficient method for the generation of human iPS cells has been developed in the absence of the oncogene c-MYC. Keywords: cell type comparison Total RNA from hFSF, hAFF, hES cells (H1, H7) and 7 established iPS cell lines were labeled with Cy5, hybridized to a human Oligo Microarray (Phalanx Human Whole Genome OneArray™, Phalanx Biotech) according to the manufacturer's protocol. Three technical repetitions were performed. After hybridization, arrays were scanned using GenePix 4000B scanner (Molecular Devices) and processed using the GenePix Pro 6.0 software (Molecular Devices). After removing control probes, a 14/33 presence call (SNR>=5 and foreground-background>0) was used to filter probes for the 33 microarrays, resulting in 12311 probes for further quantile normalization.

ORGANISM(S): Homo sapiens

SUBMITTER: hongkui deng

PROVIDER: E-GEOD-12922 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Two supporting factors greatly improve the efficiency of human iPSC generation.

Zhao Yang Y Yin Xiaolei X Qin Han H Zhu Fangfang F Liu Haisong H Yang Weifeng W Zhang Qiang Q Xiang Chengang C Hou Pingping P Song Zhihua Z Liu Yanxia Y Yong Jun J Zhang Pengbo P Cai Jun J Liu Meng M Li Honggang H Li Yanqin Y Qu Xiuxia X Cui Kai K Zhang Weiqi W Xiang Tingting T Wu Yetao Y Zhao Yiding Y Liu Chun C Yu Chen C Yuan Kehu K Lou Jinning J Ding Mingxiao M Deng Hongkui H

Cell stem cell 20081101 5

PMID: 18983962

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Project description:Introducing four transcription factors, Oct4, Sox2, Klf4 and c-Myc can reprogram both human and mouse somatic cells. first, the oncogenic properties of reprogramming factors such as Klf4 and c-Myc, second, the viral integrations of transcription factors in the genome of somatic cells which may also hinder a clinical setting and finally, the low efficiency of the generation of induced pluripotent stem cells (iPS). Some recent studies overcame the first two problems, the oncogenic properties and genomic integration of the reprogramming factors by either replacing Klf4 and/or c-Myc with small molecules or using different iPS protocols such as integration-free transcription factor inductions as well as introducing proteins. However, the slow reprogramming process and low efficiency of the iPS generation still need to be improved for either clinical application or studying the reprogramming mechanism. Different approaches including adding soluble Wnt3a, and generating iPS cells in hypoxic condition also showed increased efficiency in both 4 factors (Oct4/Sox2/Klf4/c-Myc) or less factors combination without further genetic manipulation. In the current study, we show that basic fibroblast growth factor (bFGF) dramatically increased the efficiency of iPS generation and shortened the reprogramming timing of mouse embryonic fibroblast (MEF) cells in both 4 factors (4F Oct4/Sox2/Klf4/c-Myc) and 3 factors (3F Oct4/Sox2/Klf4) combination without further exogenous genetic manipulation. RNA samples to be analyzed on microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion. 300 ng of total RNA per sample was used as input into a linear amplification protocol (Ambion), which involved synthesis of T7-linked double-stranded cDNA and 12 hrs of in-vitro transcription incorporating biotin-labelled nucleotides. Purified and labelled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and accompanying software. Samples were hybridized as biological replicates.

Project description:Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility to generate patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4, Sox2, c-Myc, and Klf4. Considering that ectopic expression of c-Myc causes tumourigenicity in offspring and retroviruses themselves can cause insertional mutagenesis, the generation of iPS cells with a minimal number of factors may hasten the clinical application of this approach. Here, we show that adult mouse neural stem cells (NSCs) express higher endogenous levels of Sox2 and c-Myc than ES cells and that exogenous Oct4 together with either Klf4 or c-Myc are sufficient to generate iPS cells from NSCs. These two-factor (2F) iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germline, and form chimeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors. Experiment Overall Design: 8 hybridizations in total. Experiment Overall Design: NSC derived iPS cells by 2 factors (Oct4 and Klf4) in triplicate: Experiment Overall Design: - iPS cell_2F_1 Experiment Overall Design: - iPS cell_2F_2 Experiment Overall Design: - iPS cell_2F_3 Experiment Overall Design: Embryonic Stem cells (ESC) in triplicate: Experiment Overall Design: - ESC_1 Experiment Overall Design: - ESC_2 Experiment Overall Design: - ESC_3 Experiment Overall Design: NSC cultures in duplicates: Experiment Overall Design: - NSC_2 Experiment Overall Design: - NSC_3 Experiment Overall Design: NSC derived iPS cells by 4 factors (Oct4, Sox2, c-Myc and Klf4) in triplicate: Experiment Overall Design: - iPS cell_4F_1 Experiment Overall Design: - iPS cell_4F_2 Experiment Overall Design: - iPS cell_4F_3

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Two Supporting Factors Greatly Improve the Efficiency of Human iPS Cell Generation

Publications

Two supporting factors greatly improve the efficiency of human iPSC generation.

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