Gene expression profile of human melanocytes derived from iPS cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE23805 | GEO | 2010/08/26
SECONDARY ACCESSION(S): PRJNA130689
REPOSITORIES: GEO
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Project description:This experiment was designed to show the similarity among normal human epidermal melanocytes, melanocytes derived from human 3F-induced pluripotent stem (iPS) cells, and human 3F-iPS cells. Human 3F-iPS cells without c-myc were established and then differentiated into melanocytes. The differentiated cells were collected and the gene expression profile was compared to normal human epidermal melanocytes (NHEMs) and orginal 3F-iPS cells.
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Project description:We used heterokaryon cell fusion based reprogramming and identified the cytokine IL6 as a potential regulator of reprogramming to pluripotency. We generated iPS clones using the four reprogramming factors (4F) Oct4, Klf4, Sox2, and c-Myc. In addition, iPS clones were generated using only three factors (3F: Oct4, Klf4, amd Sox2) with the addition of the cytokine IL6 to reprogramming culture conditions. Global RNA-Seq of the 3F + IL6 derived iPS clones was done for comparison with 4F-derived iPS clones, mouse embryonic stem cells and mouse embryonic fibroblasts. This study includes 8 samples: 2 independently derived 3F + IL6 iPS clones, 2 independently derived 4F iPS clones, 2 biological replicates of mouse D3-GFP ES cells, and 2 biological replicates of mouse embryonic fibroblasts (MEFs). The latter 6 samples are provided as references for the 3F + IL6 iPS clones. Poly-A RNA was isolated and prepared for sequencing using the Illumina TruSeq RNA kit (v2) to generate 50bp reads. Reads were aligned to mm10.
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Project description:Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin fibroblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially explained by incomplete promoter DNA methylation. This epigenetic mechanism underlies a robust form of memory that can be found in iPS cells generated by multiple laboratories using different methods, including RNA transfection. Incompletely silenced genes tend to be isolated from other genes that are repressed during reprogramming, indicating that recruitment of the silencing machinery may be inefficient at isolated genes. Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming. iPS cells were produced from melanocytes, fibroblasts, and hepatocytes, representing the three germ layers. Expression levels were profiled in the differentiated cells and their matched iPS cells, as well as 3 human ES cell lines (H1, H7 and H9) and their embroid bodies.
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Project description:Melanocytes are surrounded by diverse cells including sensory neurons in our skin, but their interaction and functional importance has been poorly investigated. In this study, we found that melanocytes and nociceptive neurons contact more in human skin color patch tissue than control. Co-culture with human iPS cell-derived sensory neurons significantly induced morphogenesis and pigmentation of human melanocytes. To reveal melanocytes-stimulating factors secreted from neurons, we performed proteomic analyses and identified RGMB in the sensory neuron-conditioned media. RGMB protein induced morphogenesis and melanin production of melanocytes, demonstrating that RGMB is a melanocyte-stimulating factor released from sensory neurons. Transcriptome analysis suggested that the melanosome transport machinery could be controlled by RGMB, which led us to identify vesicle production response of melanocytes upon RGMB treatment. This study discovered a role of sensory neurons to modulate multiple aspects of human melanocytes through secretion of a key factor RGMB.
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Project description:The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Towards this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines. We used microarrays to compare the gene expression profiles between human ES cell lines, iPS cell lines, fibroblasts and embryoid bodies, and to identify cell-line specific outlier genes.
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Project description:Purpose: Determine the mechanism of high mobility group box 1 (HMGB1)-induced signaling in melanocytes. Method: Primary human epidermal melanocytes were treated with HMGB1 (1 μg/ml) and incubated for 24 h. Total RNA (500 ng) from melanocytes were extracted and subjected to library synthesis. Results: HMGB1-treated melanocytes exhibited upregulation of cell death and type 1 interferon-related genes. Conclusion: HMGB1-induced melanocyte signaling was well evaluated using RNA sequencing.
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