Induced Pluripotent Stem Cells Show Metabolomic Differences to Embryonic Stem Cells in Polyunsaturated Phosphatidylcholines and Primary Metabolism

University of California Davis Genome Center, University of California Davis, Davis, California, United States of America.
PLoS ONE (Impact Factor: 3.23). 10/2012; 7(10):e46770. DOI: 10.1371/journal.pone.0046770
Source: PubMed

ABSTRACT Induced pluripotent stem cells are different from embryonic stem cells as shown by epigenetic and genomics analyses. Depending on cell types and culture conditions, such genetic alterations can lead to different metabolic phenotypes which may impact replication rates, membrane properties and cell differentiation. We here applied a comprehensive metabolomics strategy incorporating nanoelectrospray ion trap mass spectrometry (MS), gas chromatography-time of flight MS, and hydrophilic interaction- and reversed phase-liquid chromatography-quadrupole time-of-flight MS to examine the metabolome of induced pluripotent stem cells (iPSCs) compared to parental fibroblasts as well as to reference embryonic stem cells (ESCs). With over 250 identified metabolites and a range of structurally unknown compounds, quantitative and statistical metabolome data were mapped onto a metabolite networks describing the metabolic state of iPSCs relative to other cell types. Overall iPSCs exhibited a striking shift metabolically away from parental fibroblasts and toward ESCs, suggestive of near complete metabolic reprogramming. Differences between pluripotent cell types were not observed in carbohydrate or hydroxyl acid metabolism, pentose phosphate pathway metabolites, or free fatty acids. However, significant differences between iPSCs and ESCs were evident in phosphatidylcholine and phosphatidylethanolamine lipid structures, essential and non-essential amino acids, and metabolites involved in polyamine biosynthesis. Together our findings demonstrate that during cellular reprogramming, the metabolome of fibroblasts is also reprogrammed to take on an ESC-like profile, but there are select unique differences apparent in iPSCs. The identified metabolomics signatures of iPSCs and ESCs may have important implications for functional regulation of maintenance and induction of pluripotency.

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Available from: Dinesh Barupal, Sep 28, 2015
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    • "Moreover, those hypothetical induced pluripotent stem cells caused more immune rejections in recipient mice than normal embryonic stem cells [15] . In comparison with normal embryonic stem cells, those so-called induced pluripotent stem cells had different metabolic activities [16] [17] . In a major turn of events, the very same laboratory that pioneered these supposed stem cells has now reported that the believed human induced pluripotent stem cells were actually different from real human embryonic stem cells in several aspects [18] . "
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    ABSTRACT: The claimed human induced pluripotent stem cells (iPSCs) are not equivalent to human embryonic or adult stem cells. These should be redefined as induced pluripotent stem cell-like cells. We do not think that those so-called induced pluripotent stem cells will be a reliable and feasible source of stem cells for the foreseeable future.
    01/2015; 29(1):1-2. DOI:10.7555/JBR.29.20140166
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    • "It should be noted that the putrescine content depends not only on the biosynthetic ODC activity, but also on the level of the catabolic enzyme SSAT, which is low in stem cells, but increases across differentiation, such as following 1,25-dihydroxyvitamin- D3-mediated osteogenesis (Tjabringa et al. 2008). Reduction of the putrescine content has been indeed recently reported to be pivotal in cellular reprogramming of mouse fibroblasts to induced pluripotent stem cells (Meissen et al. 2012). Actually, SSAT has been indicated as a key metabolic regulator, able not only to regulate polyamine content , but also to directly affect HIF-1, NF-jB and integrinmediated signaling (Pegg 2008). "
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    ABSTRACT: The first step in skeleton development is the condensation of mesenchymal precursors followed by any of two different types of ossification, depending on the type of bone segment: in intramembranous ossification, the bone is deposed directly in the mesenchymal anlagen, whereas in endochondral ossification, the bone is deposed onto a template of cartilage that is subsequently substituted by bone. Polyamines and polyamine-related enzymes have been implicated in bone development as global regulators of the transcriptional and translational activity of stem cells and pivotal transcription factors. Therefore, it is tempting to investigate their use as a tool to improve regenerative medicine strategies in orthopedics. Growing evidence in vitro suggests a role for polyamines in enhancing differentiation in both adult stem cells and differentiated chondrocytes. Adipose-derived stem cells have recently proved to be a convenient alternative to bone marrow stromal cells, due to their easy accessibility and the high frequency of stem cell precursors per volume unit. State-of-the-art "prolotherapy" approaches for skeleton regeneration include the use of adipose-derived stem cells and platelet concentrates, such as platelet-rich plasma (PRP). Besides several growth factors, PRP also contains polyamines in the micromolar range, which may also exert an anti-apoptotic effect, thus helping to explain the efficacy of PRP in enhancing osteogenesis in vitro and in vivo. On the other hand, spermidine and spermine are both able to enhance hypertrophy and terminal differentiation of chondrocytes and therefore appear to be inducers of endochondral ossification. Finally, the peculiar activity of spermidine as an inducer of autophagy suggests the possibility of exploiting its use to enhance this cytoprotective mechanism to counteract the degenerative changes underlying either the aging or degenerative diseases that affect bone or cartilage.
    Amino Acids 11/2013; 46(3). DOI:10.1007/s00726-013-1607-9 · 3.29 Impact Factor
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    • "Using MS, Yanes et al. reported a reduction in the abundance of unsaturated metabolites (phospholipids) as ESCs undergo commitment to cardiac muscle cells and neurons (Yanes et al., 2010) conjecturing that stem cells differentiate in response to oxidative processes such as inflammation. Differences in polyunsaturated phosphatidylcholines and other metabolic compounds between mouse iPSCs and mESCs and between iPSCs and the parent fibroblasts undergoing reprogramming (Meissen et al., 2012). In addition, analysis of mESC extracts showed dependence of cell proliferation in vitro on threonine catabolism (Wang et al., 2009a). "
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    ABSTRACT: Isogenic stem cell populations display cell-to-cell variations in a multitude of attributes including gene or protein expression, epigenetic state, morphology, proliferation and proclivity for differentiation. The origins of the observed heterogeneity and its roles in the maintenance of pluripotency and the lineage specification of stem cells remain unclear. Addressing pertinent questions will require the employment of single-cell analysis methods as traditional cell biochemical and biomolecular assays yield mostly population-average data. In addition to time-lapse microscopy and flow cytometry, recent advances in single-cell genomic, transcriptomic and proteomic profiling are reviewed. The application of multiple displacement amplification, next generation sequencing, mass cytometry and spectrometry to stem cell systems is expected to provide a wealth of information affording unprecedented levels of multiparametric characterization of cell ensembles under defined conditions promoting pluripotency or commitment. Establishing connections between single-cell analysis information and the observed phenotypes will also require suitable mathematical models. Stem cell self-renewal and differentiation are orchestrated by the coordinated regulation of subcellular, intercellular and niche-wide processes spanning multiple time scales. Here, we discuss different modeling approaches and challenges arising from their application to stem cell populations. Integrating single-cell analysis with computational methods will fill gaps in our knowledge about the functions of heterogeneity in stem cell physiology. This combination will also aid the rational design of efficient differentiation and reprogramming strategies as well as bioprocesses for the production of clinically valuable stem cell derivatives.
    Biotechnology advances 09/2013; 31(7). DOI:10.1016/j.biotechadv.2013.09.001 · 9.02 Impact Factor
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