Methods for making induced pluripotent stem cells: reprogramming à la carte

Pluripotent stem-cell lines can be obtained through the reprogramming of somatic cells from different tissues and species by ectopic expression of defined factors. In theory, these cells--known as induced pluripotent stem cells (iPSCs)--are suitable for various purposes, including disease modelling, autologous cell therapy, drug or toxicity screening and basic research. Recent methodological improvements are increasing the ease and efficiency of reprogramming, and reducing the genomic modifications required to complete the process. However, depending on the downstream applications, certain technologies have advantages over others. Here, we provide a comprehensive overview of the existing reprogramming approaches with the aim of providing readers with a better understanding of the reprogramming process and a basis for selecting the most suitable method for basic or clinical applications.     

Reliable noninvasive genotyping: fantasy or reality?

Noninvasive genotyping has not gained wide application, due to the notion that it is unreliable, and also because remedial measures are time consuming and expensive. Of the wide variety of noninvasive DNA sources, dung is the most universal and most widely used in studies. We have developed collection, extraction, and amplification protocols that are inexpensive and provide a high level of success in amplifying both mitochondrial and nuclear DNA from dung. Here we demonstrate the reliability of genotyping from elephant dung using these protocols by comparing results from dung-extracted DNA to results from blood-extracted DNA. The level of error from dung extractions was only slightly higher than from blood extractions, and conducting two extractions from each sample and a single amplification from each extraction was sufficient to eliminate error. Di-, tri-, and tetranucleotide loci were equally reliable, and low DNA quantity and quality and PCR inhibitors were not a major problem in genotyping from dung. We discuss the possible causes of error in genotyping with particular reference to noninvasive samples and suggest methods of reducing such error.     

Genetic design automation: engineering fantasy or scientific renewal?

The aim of synthetic biology is to make genetic systems more amenable to engineering, which has naturally led to the development of computer-aided design (CAD) tools. Experimentalists still primarily rely on project-specific ad hoc workflows instead of domain-specific tools, which suggests that CAD tools are lagging behind the front line of the field. Here, we discuss the scientific hurdles that have limited the productivity gains anticipated from existing tools. We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype.     

The aging signature: a hallmark of induced pluripotent stem cells?

The discovery that somatic cells can be induced into a pluripotent state by the expression of reprogramming factors has enormous potential for therapeutics and human disease modeling. With regard to aging and rejuvenation, the reprogramming process resets an aged, somatic cell to a more youthful state, elongating telomeres, rearranging the mitochondrial network, reducing oxidative stress, restoring pluripotency, and making numerous other alterations. The extent to which induced pluripotent stem cell (iPSC)s mime embryonic stem cells is controversial, however, as iPSCs have been shown to harbor an epigenetic memory characteristic of their tissue of origin which may impact their differentiation potential. Furthermore, there are contentious data regarding the extent to which telomeres are elongated, telomerase activity is reconstituted, and mitochondria are reorganized in iPSCs. Although several groups have reported that reprogramming efficiency declines with age and is inhibited by genes upregulated with age, others have successfully generated iPSCs from senescent and centenarian cells. Mixed findings have also been published regarding whether somatic cells generated from iPSCs are subject to premature senescence. Defects such as these would hinder the clinical application of iPSCs, and as such, more comprehensive testing of iPSCs and their potential aging signature should be conducted.     

Toxicities induced in cultured cells exposed to zearalenone: Apoptosis or mutagenesis?

Zearalenone (ZEN) is a fusarotoxin produced mainly by Fusarium graminearum in temperate and warm countries. ZEN has several adverse effects on humans and animals. It has a strong estrogenic activity associated with hyperestrogenism and leads to several physiological alterations in the reproductive tract. Even though the mutagenic and genotoxic proprieties of ZEN have been described recently, its molecular mechanisms of action are not completely understood. The aim of this study was to determine the involvement of other possible mechanisms in ZEN-induced toxicities. Each of the following toxicities, cytotoxicity, cell cycle perturbation, genotoxicity, and mutagenicity, was monitored in Vero cells exposed to ZEN. Our results showed that ZEN-reduced cell viability correlated to cell cycle perturbation-induced DNA fragmentation, resulting in DNA-laddering patterns on agar gel electrophoresis. This observation is consistent with apoptosis, which was confirmed by induction of apoptotic bodies. Moreover, ZEN induced in a concentration-dependant manner the formation of micronuclei and chromosome aberrations. This apparent contradiction between the apoptotic and mutagenic effects of ZEN can be explained by the modification of normal cellular regulation inducing apoptotic or antiapoptotic factors resulting from a lack of or an incorrect DNA-reparation in relation to cell exposure to the toxin.     

Converted neural cells: induced to a cure?

Many neurodegenerative disorders such as Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS) and others often occur as a result of progressive loss of structure or function of neurons. Recently, many groups were able to generate neural cells, either differentiated from induced pluripotent stem cells (iPSCs) or converted from somatic cells. Advances in converted neural cells have opened a new era to ease applications for modeling diseases and screening drugs. In addition, the converted neural cells also hold the promise for cell replacement therapy (Kikuchi et al., 2011; Krencik et al., 2011; Kriks et al., 2011; Nori et al., 2011; Rhee et al., 2011; Schwartz et al., 2012). Here we will mainly discuss most recent progress on using converted functional neural cells to treat neurological diseases and highlight potential clinical challenges and future perspectives.     

NG2-glia as multipotent neural stem cells: fact or fantasy?

Cycling glial precursors-"NG2-glia"-are abundant in the developing and mature central nervous system (CNS). During development, they generate oligodendrocytes. In culture, they can revert to a multipotent state, suggesting that they might have latent stem cell potential that could be harnessed to treat neurodegenerative disease. This hope has been subdued recently by a series of fate-mapping studies that cast NG2-glia as dedicated oligodendrocyte precursors in the healthy adult CNS-though rare, neuron production in the piriform cortex remains a possibility. Following CNS damage, the repertoire of NG2-glia expands to include Schwann cells and possibly astrocytes-but so far not neurons. This reaffirms the central role of NG2-glia in myelin repair. The realization that oligodendrocyte generation continues throughout normal adulthood has seeded the idea that myelin genesis might also be involved in neural plasticity. We review these developments, highlighting areas of current interest, contention, and speculation.     

Induced pluripotent stem cells (iPSCs) as game-changing tools in the treatment of neurodegenerative disease: Mirage or reality?

Based on investigations, there exist tight correlations between neurodegenerative diseases' incidence and progression and aberrant protein aggregreferates in nervous tissue. However, the pathology of these diseases is not well known, leading to an inability to find an appropriate therapeutic approach to delay occurrence or slow many neurodegenerative diseases' development. The accessibility of induced pluripotent stem cells (iPSCs) in mimicking the phenotypes of various late-onset neurodegenerative diseases presents a novel strategy for in vitro disease modeling. The iPSCs provide a valuable and well-identified resource to clarify neurodegenerative disease mechanisms, as well as prepare a promising human stem cell platform for drug screening. Undoubtedly, neurodegenerative disease modeling using iPSCs has established innovative opportunities for both mechanistic types of research and recognition of novel disease treatments. Most important, the iPSCs have been considered as a novel autologous cell origin for cell-based therapy of neurodegenerative diseases following differentiation to varied types of neural lineage cells (e.g. GABAergic neurons, dopamine neurons, cortical neurons, and motor neurons). In this review, we summarize iPSC-based disease modeling in neurodegenerative diseases including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and Huntington's disease. Moreover, we discuss the efficacy of cell-replacement therapies for neurodegenerative disease.     

iPS cells—Alternative pluripotent cells to embryo stem cells

<正>Since the first murine and human embryonic stem cell lines were established by Drs. Evans and Kaufman [1] and Thomson et al. [2], respectively, great progress has been make in the field of     

CMA restricted to mammals and birds: myth or reality?

Chaperone-mediated autophagy (CMA) is a major pathway of lysosomal proteolysis essential for the control of intermediary metabolism. So far, the absence of any identifiable LAMP2A – a necessary and limiting protein for CMA – outside of the tetrapod clade, led to the paradigm that this cellular function was (presumably) restricted to mammals and birds. However, after we identified expressed sequences displaying high sequence homology with the mammalian LAMP2A in several fish species, our findings challenge that view and suggest that CMA likely appeared much earlier during evolution than initially thought. Hence, our results do not only shed an entirely new light on the evolution of CMA, but also bring new perspectives on the possible use of complementary genetic models, such as zebrafish or medaka for studying CMA function from a comparative angle/view.     

Preconditioning the hyperlipidemic myocardium: fact or fantasy?

Ischemic heart disease is a leading cause of death worldwide. Myocardial ischemia results in reduced coronary flow, followed by diminished oxygen and nutrient supply to the heart. Reperfusion to an ischemic myocardium often augments the ischemic damage, known as ischemia-reperfusion (I/R) injury. Number of studies demonstrated that the hyperlipidemic myocardium is rather sensitive and more vulnerable to I/R-induced myocardial injury. Repeated brief ischemia and reperfusion cycles, termed as ischemic preconditioning, given before a sustained ischemia is known to reduce myocardial damage occur as a result of I/R. A plethora of evidence supports the fact that preconditioning is one of the promising interventional strategies having an ability to limit I/R-induced myocardial injury. Despite this fact, the preconditioning-mediated cardioprotection is blunted in chronic hyperlipidemic condition. This suggests that preconditioning is moderately a ‘healthy heart protective phenomenon’. The mechanisms by which chronic hyperlipidemia abrogates cardioprotective effects of preconditioning are uncertain and are not completely understood. The impaired opening of mitochondrial-K_ATP channels, eNOS uncoupling and excessive generation of superoxides in the hyperlipidemic myocardium could play a role in attenuating preconditioning-mediated myocardial protection against I/R injury. Moreover, hyperlipidemia-induced loss of cardioprotective effect of preconditioning is associated with redistribution of both sarcolemmal and mitochondrial Connexin 43. We addressed, in this review, the potential mechanisms involved in hyperlipidemia-induced impairment of myocardial preconditioning. Additionally, novel pharmacologic interventions to attenuate hyperlipidemia-associated exaggerated I/R-induced myocardial injury have been discussed.     

Microbial genomics: rhetoric or reality?

The availability of complete genome sequences of many bacterial species is facilitating numerous computational approaches for understanding bacterial genomes. One of the major incentives behind the genome sequencing of many pathogenic bacteria is the desire to better understand their diversity and to develop new approaches for controlling human diseases caused by these microorganisms. This task has become even more urgent with the rapid evolution of antibiotic resistance among many bacterial pathogens. Novel drug targets are required in order to design new antimicrobials against antibiotic-resistant pathogens. The complete genome sequences of an ever increasing number of pathogenic microbes constitute an invaluable resource and provide lead information on potential drug targets. This review focuses on in silico analyses of microbial genomes, their host-specific adaptations, with specific reference to genome architecture, design, evolution, and trends in computational identification of microbial drug targets. These trends underscore the utility of genomic data for systematic in silico drug target identification in the post-genomic era.     

Morphogens: experimental illusion or reality?

The main attention is paid to the critical analysis of experimental data on morphogenetically active substances, so called "morphogens". It is proposed to consider the morphogens as specific transmitters providing for definite phases of morphogenetic tissues interactions, rather than as vectors of "morphogenetic information". In the normal development, the most studied morphogenetic tissue interactions can be referred to as so called permissive inductions, since the cells of the vertebrate embryos (amphibians, avians) are early determined for development in the ectomeso--and endodermal directions. A slow progress in studying the morphogens can be due to the following causes. 1. Theoretical "inadequacy" of the former concepts on the essence and mechanisms of embryonic induction. The necessity to develop a new system of concepts in this area of developmental biology is stressed. 2. Incompleteness of knowledge about the properties of reacting tissues and the mechanisms of action of morphogens. The early gastrula ectoderm of amphibians, most frequently used for testing the morphogens, appears to be a heterogenous population of the cells with different properties and potencies. It is, therefore, impossible to standardize strictly the biotesting of morphogens. It is suggested that the use to this end of aggregates of cell "strains" from the gastrula ectoderm, rather than of the gastrula ectoderm itself, may be more adequate 3. Insufficiency of embryonic material for biochemical identification and isolation of natural morphogens. A study of so called heterogenous inductors might be of help; these latter can be considered as analogs of natural morphogens. But the similarity of natural and heterogenous inductors can be limited only by their final effect on target tissue. The data are provided on the chemical nature, properties and mechanisms of action for a number of natural and heterogenous inductors (vegetalizing, neuralizing, mesodermalizing, lens-inducing factors). A conclusion is drawn that specific antigens do exist normally but they should not be established as a special class of "informationally important" molecules. The information necessary for development is contained in target cells and the function of a morphogen consists in providing for a definite link in the chain of processes leading to the switching on or expression of one or another programme. Only syntheses of specific proteins can, apparently, be programmed, thus reflecting the "onset" of differentiation path for a cell.     

Invasive species: reality or myth?

In view of the recent debate on the future of invasion biology, we argue that species could be regarded as invasive only when after adaptation in non-native habitats they reach yet another fitness maximum. We suggest that invasion biologists need to unambiguously clarify what constitutes being “invasive” to refute those who call for an end to invasion biology.