Application of microarray technology for microbial diagnosis in stem cell cultures: a review

Zeroing in on the “holy grail”

Owing to differentiation and self-renewal capacity, hematopoietic stem cells clasp potentiality to engender all blood cell types, leading to their immense competence to play a diverse role in therapeutic applications. Although these stem cells are the most investigated and exploited until now, further research is still essential to comprehend their nature, fate, and potential. Enhanced usage of hematopoietic stem cells in research and therapeutics intensified the requirement of expansion and differentiation of hematopoietic stem cells under in vitro conditions. Since these cells remain in senescence for a prolonged period before isolation, selection of appropriate growth medium along with supplements and culture conditions are crucial to initiate their cell division and to designate their destiny. The precise equilibrium between self-renewal and differentiation of stem cells sustained by exclusive medium along with special growth or differentiation factors is accountable for generating diverse cell lineages. Maintenance of hematopoietic stem and progenitor cell lines along with the advancement of research work generate an inexorable demand for production and commercialization of specialized stem cell culture media, with or without serum along with specific growth factors and supplements. Media commercialization for precise stem cell types, culturing and differentiation is a cost-effective developing field. Here in this review, we are assembling various types of hematopoietic stem cell self-renewal, expansion and differentiation media along with supplements and culture conditions, either developed and used by various scientists or are available commercially.

How cell numbers are determined is not understood. Hedgehog-Gli activity is involved in precursor cell proliferation and stem cell self-renewal, and its deregulation sustains the growth of many human tumours. However, it is not known whether GLI1, the final mediator of Hh signals, controls stem cell numbers, and how its activity is restricted to curtail tumourigenesis. Here we have altered the levels of GLI1 and p53, the major tumour suppressor, in multiple systems. We show that GLI1 expression in Nestin+ neural progenitors increases precursor and clonogenic stem cell numbers in vivo and in vitro. In contrast, p53 inhibits GLI1-driven neural stem cell self-renewal, tumour growth and proliferation. Mechanistically, p53 inhibits the activity, nuclear localisation and levels of GLI1 and in turn, GLI1 represses p53, establishing an inhibitory loop. We also find that p53 regulates the phosphorylation of a novel N' truncated putative activator isoform of GLI1 in human cells. The balance of GLI1 and p53 functions, thus, determines cell numbers, and prevalence of p53 restricts GLI1-driven stem cell expansion and tumourigenesis.

Stem cells have the potential for self-renewal and differentiation. First stem cell cultures were derived 30 years ago from early developing mouse embryos. These are pluripotent embryonic stem (ES) cells. Efforts towards ES cell derivation have been attempted in other mammalian and non-mammalian species. Work with stem cell culture in fish started 20 years ago. Laboratory fish species, in particular zebrafish and medaka, have been the focus of research towards stem cell cultures. Medaka is the second organism that generated ES cells and the first that gave rise to a spermatogonial stem cell line capable of test-tube sperm production. Most recently, the first haploid stem cells capable of producing whole animals have also been generated from medaka. ES-like cells have been reported also in zebrafish and several marine species. Attempts for germline transmission of ES cell cultures and gene targeting have been reported in zebrafish. Recent years have witnessed the progress in markers and procedures for ES cell characterization. These include the identification of fish homologs/paralogs of mammalian pluripotency genes and parameters for optimal chimera formation. In addition, fish germ cell cultures and transplantation have attracted considerable interest for germline transmission and surrogate production. Haploid ES cell nuclear transfer has proven in medaka the feasibility of semi-cloning as a novel assisted reproductive technology. In this special issue on “Fish Stem Cells and Nuclear Transfer”, we will focus our review on medaka to illustrate the current status and perspective of fish stem cells in research and application. We will also mention semi-cloning as a new development to conventional nuclear transfer.

BackgroundStem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respectively.ResultsTo support standardized stem cell investigations, we have developed an Ontology for Stem Cell Investigations (OSCI). OSCI imports stem cell and cell line terms from CL and CLO, and investigation-related terms from existing ontologies. A novel focus of OSCI is its application in representing metadata types associated with various stem cell investigations. We also applied OSCI to systematically categorize experimental variables in an induced pluripotent stem cell line cell study related to bipolar disorder. In addition, we used a semi-automated literature mining approach to identify over 200 stem cell gene markers. The relations between these genes and stem cells are modeled and represented in OSCI.ConclusionsOSCI standardizes stem cells found in vivo and in vitro and in various stem cell investigation processes and entities. The presented use cases demonstrate the utility of OSCI in iPSC studies and literature mining related to bipolar disorder.

A wealth of evidence attests that the organs of developing embryos, particularly the developing brain, are acutely sensitive to chemical perturbations. However, scientists know very little about how exposures to specific endogenous chemicals actually impact human development or children’s ability to learn. And there are almost no data on how the vast majority of the 84,000 chemicals currently listed in the Toxic Substances Control Act (TSCA) Inventory1—including most of the 201 compounds known to be neurotoxic to adults and the 1,000 chemicals shown to be neurotoxic to animals2—may affect developing infants. It is also unclear whether testing with animals always provides accurate insights into human developmental susceptibility. A new line of research based on human stem cells is providing important insights into how chemicals may affect neonatal development. Stem cells are the master cells capable of producing some or all of the 200-plus different types of cells in the human body. In time, some researchers believe stem cells may enable scientists to amass far more data on how exposure to environmental chemicals affects human development, particularly the development of the brain. Now is a “critical time to be talking about stem cell research in the environmental health context,” says Tracey Woodruff, director of the Program on Reproductive Health and the Environment at the University of California, San Francisco (UCSF) Medical School.

Embryonic stem cells are pluripotent and capable of unlimited self-renewal. Elucidation of the underlying molecular mechanism may contribute to the advancement of cell-based regenerative medicine. In the present work, we performed a large scale analysis of the phosphoproteome in mouse embryonic stem (mES) cells. Using multiplex strategies, we detected 4581 proteins and 3970 high confidence distinct phosphosites in 1642 phosphoproteins. Notably, 22 prominent phosphorylated stem cell marker proteins with 39 novel phosphosites were identified for the first time by mass spectrometry, including phosphorylation sites in NANOG (Ser-65) and RE1 silencing transcription factor (Ser-950 and Thr-953). Quantitative profiles of NANOG peptides obtained during the differentiation of mES cells revealed that the abundance of phosphopeptides and non-phosphopeptides decreased with different trends. To our knowledge, this study presents the largest global characterization of phosphorylation in mES cells. Compared with a study of ultimately differentiated tissue cells, a bioinformatics analysis of the phosphorylation data set revealed a consistent phosphorylation motif in human and mouse ES cells. Moreover, investigations into phosphorylation conservation suggested that phosphoproteins were more conserved in the undifferentiated ES cell state than in the ultimately differentiated tissue cell state. However, the opposite conclusion was drawn from this conservation comparison with phosphosites. Overall, this work provides an overview of phosphorylation in mES cells and is a valuable resource for the future understanding of basic biology in mES cells.

Human embryonic stem (hES) cells are already transforming our vision of regenerative medicine and cell replacement therapies because of their unique ability to maintain themselves indefinitely and to form all cell types in the body. hES cell lines with genomes that are predisposed to disease can be used to develop cellular models of human pathologies. The generation of disease‐specific and/or genotypically diverse human stem cell lines that can differentiate into many cell types will have great value for understanding the biology of the cell types affected in disease and analysing disease mechanisms, screening for drug candidates that can slow or prevent disease‐related degeneration as well as toxicological testing and understanding the variation between patients in their responses to therapeutics. In addition, to prepare for cell‐based therapies, new technologies for the generation of stem cell lines that are histocompatible with or specific to individual patients will provide a strategy to overcome the challenges of immune rejection. Several different methods have been developed to make hES cells; to date, these all require the use of human female egg cells as a starting point. Recently, several laboratories have reported that adult cells from human skin and other sources can be induced to revert back to earlier stages of development and exhibit stem cell‐like properties. The methods for ‘reprogramming’ have been developing rapidly but generally involve putting multiple genes into skin cells and then exposing them to specific chemical environments tailored to hES cell growth. While these cells appear to have a developmental potential that is similar to that of hES cells, they are not derived from human embryos. To distinguish these reprogrammed cells from the embryo‐sourced hES cells, they are termed induced pluripotent stem (iPS) cells. The iPS technology is the source of much optimism; »The iPS technology is the source of much …

Although a normal karyotype is generally a requirement for stem cell lines, new applications are likely to emerge for stem cells with defined chromosomal aneuploidies. We therefore investigated the use of embryos found to be aneuploid on biopsy followed by preimplantation genetic diagnosis (PGD) with fluorescent in situ hybridization (FISH), and developmentally arrested embryos for stem cell derivation. Eleven stem cell lines were obtained from 41 embryos in 36 cultures, with higher success rate achieved from PGD-analyzed, developmentally advanced embryos (45%) than from clinically unsuitable non-PGD embryos (13%). The resulting stem cell lines were karyotyped, and surprisingly, six of the nine lines from aneuploid embryos as well as both lines from non-PGD embryos were karyotypically normal. Three lines from PGD embryos were aneuploid exhibiting trisomy 5, trisomy 16, and an isochromosome 13, respectively. None of the aneuploid lines presented the same anomally as the original PGD analysis. Our study has three important implications. First, we confirm the ability to produce stem cell lines from PGD-tested embryos as well as developmentally abnormal embryos, offering specialty stem cell lines for research into the clinically important aneuploidies. Second, we observe that stem cell derivation from apparently aneuploid embryos is often thwarted by underlying mosaicism and emerging dominance of the stem cell line by karyotypically normal cells. The corollary, however, is that regular production of normal stem cell lines from developmentally abnormal embryos ordinarity discarded opens a new source of embryos for stem cells, whether for research or for eventual therapeutic use within the donating families.

Sacrococcygeal teratomas (SCTs) are benign tumours of the newborn with absolute indication for surgery directly after birth. We recently described the presence of stem cells positive for the stem cell markers nanog and Oct4 in SCTs. Here we report the isolation of three stem cell lines from three different SCTs. Cells were propagated in mesenchymal or in embryonic stem cell medium. Non-clonal homogeneous stem cell lines were obtained after two to three passages and characterized in vitro by immunocytochemistry, RT-PCR, western blot, FACS analysis, and metaphase spreads. The differentiation potential was tested in vitro and in vivo. The isolated cell lines, which we refer to as human sacrococcygeal teratoma stem cells (hSctSCs), express nanog, Oct4 and stella, and are negative for malignancy markers alpha-fetoprotein and carcinoembryonic antigen. They can be induced in vitro to express neuronal, osteogenic, and chondrogenic traits. After grafting in vivo, spontaneous integration into the neural crest of the chick embryo and teratoma formation in the nude mouse were obtained. Our results indicate that SCTs are derived from remnants of the epiblast-derived primitive streak, which in the human embryo normally regresses but forms teratomas in children affected with SCT. The hSctSCs therefore may be comparable to mouse epiblast-derived stem cells (EpiSCs) and share characteristic features with human embryonic stem (hES) cells. Thus, SCT tissue obtained after surgery appears to be a novel source for the generation of human stem cells without the ethical implications associated with hES cells.

Chapter 43 - Growth Factors and the Serum-free Culture of Human Pluripotent Stem Cells

Heterogeneous, dynamic, and stochastic nature of mammalian spermatogenic stem cells.

Human embryonic stem (ES) cell lines have opened great potential and expectation for cell therapy and regenerative medicine. Monkey and human ES cell lines, which are very similar to each other, have been established from monkey blastocysts and surplus human blastocysts from fertility clinics.Nonhuman primate ES cell lines provide important research tools for basic and applicative research. Firstly, they provide wider aspects of investigation of the regulative mechanisms of stem cells and cell differentiation among primate species. Secondly, their usage does not need clearance or permission from the regulative rules in many countries that are associated with the ethical aspects of human ES cells, although human and nonhuman embryos and fetuses are very similar to each other. Lastly and most importantly, they are indispensable for animal models of cell therapy to test effectiveness, safety, and immunological reaction of the allogenic transplantation in a setting similar to the treatment of human diseases.So far, ES cell lines have been established from rhesus monkey (Macaca mulatta), common marmoset (Callithrix jacchus), and cynomolgus monkey (Macaca fascicularis), using blastocysts produced naturally or by in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). These cell lines seem to have very similar characteristics. They express alkaline phosphatase activity and stage-specific embryonic antigen (SSEA)-4 and, in most cases, SSEA-3. Their pluripotency was confirmed by the formation of embryoid bodies and differentiation into various cell types in culture and also by the formation of teratomas that contained many types of differentiated tissues including derivatives of three germ layers after transplantation into the severe combined immunodeficiency (SCID) mice.The noneffectiveness of the leukemia inhibitory factor (LIF) signal makes culture of primate and human ES cell lines prone to undergo spontaneous differentiation and thus it is difficult to maintain these stem cell colonies. Also, these ES cells are more susceptible to various stresses, causing difficulty with subculturing using enzymatic treatment and cloning from single cells. However, with various improvements in culture methods, it is now possible to maintain stable colonies of monkey ES cells using a serum-free medium and subculturing with trypsin treatment. Under such conditions, cynomolgus monkey ES cell lines can be maintained in an undifferentiated state with a normal karyotype and pluripotency even after prolonged periods of culture over 1 year. Such progress should facilitate many aspects of stem cell research using both nonhuman primate and human ES cell lines.

Dental pulp from deciduous (baby) teeth, which are discarded after exfoliation, represents an advantageous source of young stem cells. Herein, we discuss the methods of deciduous teeth stem cell (DTSC) isolation and cultivation. We show that based on these methods, at least three different stem cell populations can be identified: a population similar to bone marrow-derived mesenchymal stem cells, an epithelial stem-like cells, and/or a mixed population composed of both cell types. We analyzed the embryonic origin and stem cell niche of DTSCs with respect to the advantages they can provide for their future use in cell therapies and regenerative medicine. In vitro and in vivo differentiation of the DTSC populations, their developmental potential, immunological compatibility, tissue engineering, and transplantation use in studies in animal models are also the focus of the current report. We briefly describe the derivation of induced pluripotent stem (iPS) cells from DTSCs, which can be obtained more easily and efficiently in comparison with human fibroblasts. These iPS cells represent an interesting model for the investigation of pediatric diseases and disorders. The importance of DTSC banking is also discussed.

Stem cells have turned into promising tools for studying the mechanisms of development, regeneration, and for cell therapy of various disorders. Stem cells are found in the embryo and in most adult tissues participating in endogenous tissue regeneration. They are capable of autorenovation, often maintain their multipotency of differentiation into various tissues of their germ line and are, therefore, ideal candidates for cellular therapy taken that they can be unequivocally identified and isolated. In this review, we report stem cell marker expression used for identification of various stem cell lineages, including very small embryonic stem cells, neural, hematopoietic, mesenchymal, epithelial and limbal epithelial stem cells, endothelial progenitor cells, supra-adventitial adipose stromal cells, adipose pericytes, and cancer stem cells. These cells usually cannot be distinguished by a single stem cell marker, because their expression partially overlaps between lineages. Recent advances in flow cytometry allowing the simultaneous detection of various markers have facilitated stem cell identification for clinical diagnosis and research. So far experimental evidence suggests the existence of cells with different properties, i.e., the capability to different in various cell types. Several studies indicate that expression of classical markers for stem cell classification, such as CD34, CD45, and CD133, may differ between the virtually same stem and progenitor cells, i.e., endothelial progenitor or mesenchymal stem cells, when they were obtained from different tissues. This finding raises questions whether phenotypic differences are due to the source or if it is only caused by different isolation and experimental conditions.