Chromatin remodeling and stem cell theory of relativity

The role of m6A modification in the biological functions and diseases

N⁶-methyladenosine (m6A) is the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, especially within higher eukaryotic cells. m6A modification is modified by the m6A methyltransferases, or writers, such as METTL3/14/16, RBM15/15B, ZC3H3, VIRMA, CBLL1, WTAP, and KIAA1429, and, removed by the demethylases, or erasers, including FTO and ALKBH5. It is recognized by m6A-binding proteins YTHDF1/2/3, YTHDC1/2 IGF2BP1/2/3 and HNRNPA2B1, also known as "readers". Recent studies have shown that m6A RNA modification plays essential role in both physiological and pathological conditions, especially in the initiation and progression of different types of human cancers. In this review, we discuss how m6A RNA methylation influences both the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. We will mainly focus on recent progress in identifying the biological functions and the underlying molecular mechanisms of m6A RNA methylation, its regulators and downstream target genes, during cancer progression in above systems. We propose that m6A RNA methylation process offer potential targets for cancer therapy in the future.

Monitoring stem cell differentiation using Raman microspectroscopy: chondrogenic differentiation, towards cartilage formation

Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) has been demonstrated to be a powerful analytical tool, which provides detailed label free biochemical fingerprint information in a non-invasive way, for analysis of cells, tissues and body fluids. In this work, RMS is explored to monitor the process of Mesenchymal Stem Cell (MSC) differentiation into chondrocytes in vitro, providing a holistic molecular picture of cellular events governing the differentiation. Spectral signatures of the subcellular compartments, nucleolus, nucleus and cytoplasm were initially probed and characteristic molecular changes between differentiated and undifferentiated were identified. Moreover, high density cell micromasses were cultured over a period of three weeks, and a systematic monitoring of cellular molecular components and the progress of the ECM formation, associated with the chondrogenic differentiation, was performed. This study shows the potential applicability of RMS as a powerful tool to monitor and better understand the differentiation pathways and process.

Apelin: an endogenous peptide essential for cardiomyogenic differentiation of mesenchymal stem cells via activating extracellular signal-regulated kinase 1/2 and 5

Growing evidence has shown that apelin/APJ system functions as a critical mediator of cardiac development as well as cardiovascular function. Here, we investigated the role of apelin in the cardiomyogenic differentiation of mesenchymal stem cells derived from Wharton's jelly of human umbilical cord in vitro. In this research, we used RNA interference methodology and gene transfection technique to regulate the expression of apelin in Wharton's jelly-derived mesenchymal stem cells and induced cells with a effective cardiac differentiation protocol including 5-azacytidine and bFGF. Four weeks after induction, induced cells assumed a stick-like morphology and myotube-like structures except apelin-silenced cells and the control group. The silencing expression of apelin in Wharton's jelly-derived mesenchymal stem cells decreased the expression of several critical cardiac progenitor transcription factors (Mesp1, Mef2c, NKX2.5) and cardiac phenotypes (cardiac α-actin, β-MHC, cTnT, and connexin-43). Meanwhile, endogenous compensation of apelin contributed to differentiating into cells with characteristics of cardiomyocytes in vitro. Further experiment showed that exogenous apelin peptide rescued the cardiomyogenic differentiation of apelin-silenced mesenchymal stem cells in the early stage (1-4 days) of induction. Remarkably, our experiment indicated that apelin up-regulated cardiac specific genes in Wharton's jelly-derived mesenchymal stem cells via activating extracellular signal-regulated kinase (ERK) 1/2 and 5.

Recent Advances on Genetic and Physiological Bases of In Vitro Somatic Embryo Formation

Somatic embryogenesis involves a broad repertoire of genes, and complex expression patterns controlled by a concerted gene regulatory network. The present work describes this regulatory network focusing on the main aspects involved, with the aim of providing a deeper insight into understanding the total reprogramming of cells into a new organism through a somatic way. To the aim, the chromatin remodeling necessary to totipotent stem cell establishment is described, as the activity of numerous transcription factors necessary to cellular totipotency reprogramming. The eliciting effects of various plant growth regulators on the induction of somatic embryogenesis is also described and put in relation with the activity of specific transcription factors. The role of programmed cell death in the process, and the related function of specific hemoglobins as anti-stress and anti-death compounds is also described. The tools for biotechnology coming from this information is highlighted in the concluding remarks.

Concise review: Multidimensional regulation of the hematopoietic stem cell state

Hematopoietic stem cells (HSCs) are characterized by their unique function to produce all lineages of blood cells throughout life. Such tissue-specific function of HSC is attributed to their ability to execute self-renewal and multilineage differentiation. Accumulating evidence indicates that the undifferentiated state of HSC is characterized by dynamic maintenance of chromatin structures and epigenetic plasticity. Conversely, quiescence, self-renewal, and differentiation of HSCs are dictated by complex regulatory mechanisms involving specific transcription factors and microenvironmental crosstalk between stem cells and multiple compartments of niches in bone marrows. Thus, multidimensional regulatory inputs are integrated into two opposing characters of HSCs-maintenance of undifferentiated state analogous to pluripotent stem cells but execution of tissue-specific hematopoietic functions. Further studies on the interplay of such regulatory forces as "cell fate determinant" will likely shed the light on diverse spectrums of tissue-specific stem cells.

AFT024 cell line in co-culture system using high pore density insert (HPDI) maintains hematopoietic stem/progenitor cells (HSCs/HPCs) as more primitive state through histone modification

BACKGROUND

It has been shown that the AFT024 stromal cell line sustains the engraftment capacity of human hematopoietic progenitor cells (HPCs) in vitro. However, the process by which AFT024 cell line maintains human HPCs is a more primitive state ex vivo remains unclear.

METHODS

Human umbilical cord blood (UCB)-derived fluorescent activated cell sorter (FACS)-purified CD34(+) CD38(-)hsc/HPCs were cultured with cytokines on hpdi (0.4 micron pore size) coated with irradiated AFT024 cells. The HSC/HPC and AFT024 cells contacted each other through 0.4 micron pores on HPDI membranes; the irradiated AFT024 cells could not migrate through the HPDI to contaminate the HSC/HPC. The frequency of CD34(+)Lin(-) cells was determined as HSCs/HPCs using flow cytometry. To evaluate their engraftment potential in vivo, the co-cultured cells were assayed as Long Term Culture-Initiating Cells (LTC-IC). To understand the process whereby AFT024 cells govern enhanced engraftment, we employed Western blot analysis for histone modifications.

RESULTS

There was a 30-fold increase in frequency of CD34(+)Lin(-) cells in co-cultures on HPDI coated on the outer bottom surface with irradiated AFT024 cells and cytokines in contrast to 6-fold among controls. Total colonies from LTC-IC increased approximately 1.5-fold among cells cultured with AFT024, compared with controls. More importantly, cells co-cultured with AFT024 showed a more primitive state with over-methylated h3k4 (Me-H3K4), under-methylated h3k9 (Di-Me-H3K4), and over-acetylated h4 (Ac-H4) compared with controls.

CONCLUSION

Our results suggested that co-culture of the AFT024 cell line with HPDI maintained hematopoietic progenitors as a more primitive state through histone modification.

Effect of 5-azacytidine: evidence for alteration of the multipotent ability of mesenchymal stem cells

The treatment of cardiac diseases by cell therapy continues to be challenged by a limited supply of appropriate cells. Although stem cells can generate myocytes after local delivery into the heart, this is often accompanied by the generation of several other cell types as a consequence of environment-driven differentiation. One strategy for overcoming dysregulated differentiation is the pretreatment of stem cells with the demethylation agent 5-azacytidine. The effects of 5-azacytidine on various stem cell types vary from cardiomyogenic differentiation to failure of differentiation or from adipogenic and chondrogenic differentiation to uncontrollable expression of a variety of genes. The underlying mechanisms remain poorly understood, and the effect of 5-azacytidine on the multipotent capacity of stem cells has never been addressed. This study was designed to investigate the changes induced by 5-azacytidine in mesenchymal stem cells (MSC), with particular focus on multipotency maintenance and the capacity of 5-azacytidine to boost myogenic differentiation. Our results show that MSCs retained their multipotent capacity after one pulse with 5-azacytidine, whereas additional pulses resulted in a restricted differentiation potential with concomitant increased ability to accomplish chondrogenic commitment. The induction of cardiac differentiation of MSCs was not observed unless the transcriptional activation of several genes was induced by random hypomethylation. Nevertheless, 5-azacytidine treatment promoted cell response to subsequent stimuli and generation of myogenic differentiation under permissive environmental conditions. Therefore, we assume that one pulse with 5-azacytidine might similarly promote the subsequent cardiac differentiation of MSCs, but it is dependent on the finding of adequate conditions for myocardial differentiation.

Biochemical analysis and quantification of hematopoietic stem cells by infrared spectroscopy

Identification of hematopoietic stem cells (HSCs) in different stages of maturation is one of the major issues in stem cell research and bone marrow (BM) transplantation. Each stage of maturation of HSCs is characterized by a series of distinct glycoproteins present on the cell plasma membrane surface, named a cluster of differentiation (CD). Currently, complicated and expensive procedures based on CD expression are needed for identification and isolation of HSCs. This method is under dispute, since the correct markers' composition is not strictly clear, thus there is need for a better method for stem cell characterization. In the present study, Fourier transform infrared (FTIR) spectroscopy is employed as a novel optical method for identification and characterization of HSCs based on their entire biochemical features. FTIR spectral analysis of isolated mice HSCs reveals several spectral markers related to lipids, nucleic acids, and carbohydrates, which distinguish HSCs from BM cells. The unique "open" conformation of HSC DNA as identified by FTIR is exploited for HSCs quantification in the BM. The proposed method of FTIR spectroscopy for HSC identification and quantification can contribute to stem cell research and BM transplantation.

Undifferentiated hematopoietic cells are characterized by a genome-wide undermethylation dip around the transcription start site and a hierarchical epigenetic plasticity

Evidence for the epigenetic regulation of hematopoietic stem cells (HSCs) is growing, but the genome-wide epigenetic signature of HSCs and its functional significance remain unclear. In this study, from a genome-wide comparison of CpG methylation in human CD34(+) and CD34(-) cells, we identified a characteristic undermethylation dip around the transcription start site of promoters and an overmethylation of flanking regions in undifferentiated CD34(+) cells. This "bivalent-like" CpG methylation pattern around the transcription start site was more prominent in genes not associated with CpG islands (CGI(-)) than CGI(+) genes. Undifferentiated hematopoietic cells also exhibited dynamic chromatin associated with active transcription and a higher turnover of histone acetylation than terminally differentiated cells. Interestingly, inhibition of chromatin condensation by chemical treatment (5-azacytidine, trichostatin A) enhanced the self-renewal of "stimulated" HSCs in reconstituting bone marrows but not "steady-state" HSCs in stationary phase bone marrows. In contrast, similar treatments on more mature cells caused partial phenotypic dedifferentiation and apoptosis at levels correlated with their hematopoietic differentiation. Taken together, our study reveals that the undifferentiated state of hematopoietic cells is characterized by a unique epigenetic signature, which includes dynamic chromatin structures and an epigenetic plasticity that correlates to level of undifferentiation.

In vitro differentiation of embryonic and adult stem cells into hepatocytes: state of the art

Stem cells are a unique source of self-renewing cells within the human body. Before the end of the last millennium, adult stem cells, in contrast to their embryonic counterparts, were considered to be lineage-restricted cells or incapable of crossing lineage boundaries. However, the unique breakthrough of muscle and liver regeneration by adult bone marrow stem cells at the end of the 1990s ended this long-standing paradigm. Since then, the number of articles reporting the existence of multipotent stem cells in skin, neuronal tissue, adipose tissue, and bone marrow has escalated, giving rise, both in vivo and in vitro, to cell types other than their tissue of origin. The phenomenon of fate reprogrammation and phenotypic diversification remains, though, an enigmatic and rare process. Understanding how to control both proliferation and differentiation of stem cells and their progeny is a challenge in many fields, going from preclinical drug discovery and development to clinical therapy. In this review, we focus on current strategies to differentiate embryonic, mesenchymal(-like), and liver stem/progenitor cells into hepatocytes in vitro. Special attention is paid to intracellular and extracellular signaling, genetic modification, and cell-cell and cell-matrix interactions. In addition, some recommendations are proposed to standardize, optimize, and enrich the in vitro production of hepatocyte-like cells out of stem/progenitor cells.

Pluripotency rush! Molecular cues for pluripotency, genetic reprogramming of adult stem cells, and widely multipotent adult cells

In the last few years, pluripotent stem cells have been the objective of intense investigation efforts. These cells are of paramount therapeutic interest, since they could be utilized: as in vitro models of disease, for pharmaceutical screening purposes, and for the regeneration of damaged organs. Over the years, pluripotent cells have been cultured from teratomas, the inner cell mass, and primordial germ cells. Accumulating informations have partially decrypted the molecular machinery responsible for the maintenance of a very primitive state, permitting the reprogramming of differentiated cells. Although the debate is still open, an extreme excitement is arising from two strictly related possibilities: pluripotent cells could be obtained from adult tissues with minimal manipulations or very rare pluripotent cells could be identified in adult tissues. This intriguing option will trigger new researches aimed both at identifying the possible biological role of pluripotent adult stem cells and at exploiting their potential clinical use. The present review article will summarize current knowledge of the molecular cues for pluripotency but also discusses whether pluripotent stem cells could be obtained from adult tissues.

Production of cloned pigs by nuclear transfer of preadipocytes following cell cycle synchronization by differentiation induction

Four methods of cell cycle synchronization of porcine preadipocytes for use as nuclear donors in somatic cell cloning were compared: serum starvation, differentiation induction, contact inhibition and roscovitine treatment. After three days of differentiation induction, the percentage of nuclear donor cells synchronized at the G0/G1 phase reached a peak value of 91.8%, which was significantly higher (P<0.05) than the percentage attained by serum starvation (84.9-89.8%), contact inhibition (78.3-83.7%) or roscovitine treatment (67.8-80.3%). Cell cycle synchronization by serum starvation, contact inhibition and roscovitine treatment all increased the percentage of apoptotic cells, while no increase was observed when the donor-cell cycle was synchronized by differentiation induction (Annexin V-positive: 15.7% to 19.3% vs. 7.7%, P<0.05; TUNEL-positive: 12.8% to 14.0% vs. 8.3%, P<0.05). Additionally, comparison of the in vitro development of nuclear transfer (NT) embryos formed from the nuclei of differentiation-induced or serum-starved preadipocytes revealed that, in both cases, a high proportion of embryos developed to the blastocyst stage (39.0 and 33.7%, respectively). In this study, NT embryos reconstructed with preadipocytes synchronized by differentiation induction were transferred to four recipient pigs, three of which gave birth to a total of 17 piglets (4.2%, 17/403). These results demonstrate that donor-cell cycle synchronization by differentiation induction enables effective production of cloned pigs. The findings also indicate that differentiation induction of multipotent cells is an excellent method of cell cycle synchronization that permits highly efficient synchronization of cells at the G0/G1 phase.

Characterization and quantification of clonal heterogeneity among hematopoietic stem cells: a model-based approach

Hematopoietic stem cells (HSCs) show pronounced heterogeneity in self-renewal and differentiation behavior, which is reflected in their repopulation kinetics. Here, a single-cell-based mathematical model of HSC organization is used to examine the basis of HSC heterogeneity. Our modeling results, which are based on the analysis of limiting dilution competitive repopulation experiments in mice, demonstrate that small quantitative but clonally fixed differences of cellular properties are necessary and sufficient to account for the observed functional heterogeneity. The model predicts, and experimental data validate, that competitive pressures will amplify small clonal differences into large changes in the number of differentiated progeny. We further predict that the repertoire of HSC clones will evolve over time. Last, our results suggest that larger differences in cellular properties have to be assumed to account for genetically determined differences in HSC behavior as observed in different inbred mice strains. The model provides comprehensive systemic and quantitative insights into the clonal heterogeneity among HSCs with potential applications in predicting the behavior of malignant and/or genetically modified cells.

Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance

BACKGROUND

Despite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity.

RESULTS

In order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag). Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation.

CONCLUSION

The presented data provide a picture of the transcriptional profile of the pea SAM, and reveal possible roles of differentially expressed transcripts in meristem function and maintenance.

Embryonic stem cell biology

ES cell research represents an exploding field of exploration. Initially predicted to provide rapid cures for numerous human diseases, the clinical usefulness of ES cell-derived cells remains untested in humans. However, ES cells have rapidly expanded our knowledge of human development and the molecular details of differentiation. Our ability to generate relatively pure populations of specifically differentiated cells for transplantation has markedly improved. It is hoped that soon researchers will overcome the biologic impediments to successful treatment of human disease with ES cell-derived cells.

A role of Wnt/beta-catenin signals in hepatic fate specification of human umbilical cord blood-derived mesenchymal stem cells

Human umbilical cord blood-derived mesenchymal stem cells (UCBMSCs) are expected to be an excellent source of cells for transplantation. In addition, the stem cell plasticity of human UCBMSCs, which can transdifferentiate into hepatocytes, has been reported. However, the mechanisms involved remain to be clarified. To identify the genes and/or signals that are important in specifying the hepatic fate of human UCBMSCs, we analyzed gene expression profiles during the hepatic differentiation of UCBMSCs with human telomerase reverse transcriptase, UCBMSCs immortalized by infection with a retrovirus carrying telomerase reverse transcriptase, but whose differentiation potential remains unchanged. Efficient differentiation was induced by 5-azacytidine (5-aza)/hepatocyte growth factor (HGF)/oncostatin M (OSM)/fibroblast growth factor 2 (FGF2) treatment in terms of function as well as protein expression: 2.5-fold increase in albumin, 4-fold increase in CCAAT enhancer-binding protein alpha, 1.5-fold increase in cytochrome p450 1A1/2, and 8-fold increase in periodic acid-Schiff staining. Consequently, we found that the expression of Wnt/beta-catenin-related genes downregulated, and the translocation of beta-catenin was observed along the cell membrane and in the cytoplasm, although some beta-catenin was still in the nucleus. Downregulation of Wnt/beta-catenin signals in the cells by Fz8-small interference RNA treatment, which was analyzed with a Tcf4 promoter-luciferase assay, resulted in similar hepatic differentiation to that observed with 5-azacytidine/HGF/OSM/FGF2. In addition, the subcellular distribution of beta-catenin was similar to that of cells treated with 5-azacytidine/HGF/OSM/FGF2. In conclusion, the suppression of Wnt/beta-catenin signaling induced the hepatic differentiation of UCBMSCs, suggesting that Wnt/beta-catenin signals play an important role in the hepatic fate specification of human UCBMSCs.

Multipotent cells can be generated in vitro from several adult human organs (heart, liver, and bone marrow)

The aims of our study were to verify whether it was possible to generate in vitro, from different adult human tissues, a population of cells that behaved, in culture, as multipotent stem cells and if these latter shared common properties. To this purpose, we grew and cloned finite cell lines obtained from adult human liver, heart, and bone marrow and named them human multipotent adult stem cells (hMASCs). Cloned hMASCs, obtained from the 3 different tissues, expressed the pluripotent state-specific transcription factors Oct-4, NANOG, and REX1, displayed telomerase activity, and exhibited a wide range of differentiation potential, as shown both at a morphologic and functional level. hMASCs maintained a human diploid DNA content, and shared a common gene expression signature, compared with several somatic cell lines and irrespectively of the tissue of isolation. In particular, the pathways regulating stem cell self-renewal/maintenance, such as Wnt, Hedgehog, and Notch, were transcriptionally active. Our findings demonstrate that we have optimized an in vitro protocol to generate and expand cells from multiple organs that could be induced to acquire morphologic and functional features of mature cells even embryologically not related to the tissue of origin.

Differential role of epigenetic modulators in malignant and normal stem cells: a novel tool in preclinical in vitro toxicology and clinical therapy

Adult stem cells are primitive cells that undergo asymmetric division, thereby giving rise to one clonogenic, self-renewing cell and one cell able to undergo multipotent differentiation. Disturbance of this controlled process by epigenetic alterations, including imbalance of histone acetylation/histone deacetylation and DNA methylation/demethylation, may result in uncontrolled growth, formation of self-renewing malignant stem cells and eventually cancer. In view of this notion, several epigenetic modulators, in particular those with histone deacetylase inhibiting activity, are currently being tested in phase I and II clinical trials for their promising chemotherapeutic properties in cancer therapy. As chromatin modulation is also involved in regulation of differentiation, normal development, embryonic and adult stem cell functions and maintenance of their plasticity during embryonic organogenesis, the question can be raised whether predestined cell fate can be modified through epigenetic interference. And if so, could this strategy enforce adult stem cells to differentiate into different types of functional cells? In particular, functional hepatocytes seem important for preclinical toxicity screening of candidate drugs. This paper reviews the potential use and relevance of epigenetic modifiers, including inhibitors of histone deacetylases and DNA methyltransferases (1) to change cell fate and 'trans'differentiate normal adult stem cells into hepatocyte-like cells and (2) to cure disorders, caused by uncontrolled growth of malignant stem cells.

Muscle-specific expression of the smyd1 gene is controlled by its 5.3-kb promoter and 5'-flanking sequence in zebrafish embryos

Zebrafish SmyD1 is a SET and MYND domain-containing protein that plays an important role in myofiber maturation and muscle contraction. SmyD1 is required for myofibril organization and sarcomere assembly during myofiber maturation. Whole-mount in situ hybridization revealed that smyd1 mRNAs are specifically expressed in skeletal and cardiac muscles in zebrafish embryos. However, it is unknown if smyd1 is expressed in other striated muscles, such as cranial and fin muscles, and moreover, the regulatory elements required for its muscle-specific expression. We report here the analyses of smyd1 expression using smyd1-gfp transgenic zebrafish. smyd1-gfp transgenic zebrafish were generated using the 5.3-kb smyd1 promoter and its 5'-flanking sequence. GFP expression was found in the skeletal and cardiac muscles of smyd1-gfp transgenic embryos. GFP expression appeared stronger in slow muscles than fast muscles in transgenic zebrafish larvae. In addition, GFP expression was also detected in cranial and fin muscles of smyd1-gfp transgenic zebrafish larvae. In situ hybridization confirmed smyd1 mRNA expression in these tissues, suggesting that the expression of the smyd1-gfp transgene recapitulated that of the endogenous smyd1 gene. Deletion analysis revealed that the 0.5-kb sequence in the proximal promoter of smyd1 was essential for its muscle specificity. Together, these data indicate that smyd1 is specifically expressed in most, if not all, striated muscles, and the muscle specificity is controlled by the 5.3-kb promoter and flanking sequences.

Stem cell continuum: directed differentiation hotspots

OBJECTIVE

The purpose of this study was to evaluate the technique of stem cell-directed differentiation in the context of cell-cycle position. The hypothesis was that stem cells would have different sensitivities to an identical inductive signal through cell-cycle transit and that this would affect the outcome of its progeny.

MATERIALS AND METHODS

Differentiation of murine marrow lineage(negative)rhodamine-123(low-)Hoechst-33342(low) (LRH) stem cells was determined at different points in cell cycle under stimulation by thrombopoietin, flt3 ligand, and steel factor. LRH stem cells were subcultured in granulocyte macrophage colony-stimulating factor, granulocyte colony-stimulating factor, and steel factor at different points in cell cycle and differentiation determined 14 days later.

RESULTS

There was a significant, reproducible, and pronounced reversible increase in differentiation to megakaryocytes in early S-phase and to nonproliferative granulocytes in mid S-phase. Megakaryocyte hotspots also were seen on a clonal basis. Elevations of the transcription factor FOG-1 were seen at the hotspot along with increases in Nfe2 and Fli1.

CONCLUSIONS

We show that the potential of marrow stem cells to differentiate changes reversibly with cytokine-induced cell-cycle transit, suggesting that stem cell regulation is not based on the classic hierarchical model, but instead on a functional continuum. We propose that there is a tight linkage of commitment to a lineage and a particular phase of cell cycle. Thus, windows of vulnerability for commitment can open and close depending on the phase of cell cycle. These data indicate that stem cell differentiation occurs on a cell-cycle-related continuum with fluctuating windows of transcriptional opportunity.

The role of histone acetylation in regulating early gene expression patterns during early embryonic stem cell differentiation

We have examined the role of histone acetylation in the very earliest steps of differentiation of mouse embryonic stem cells in response to withdrawal of leukemia inhibitory factor (LIF) as a differentiation signal. The cells undergo dramatic changes in morphology and an ordered program of gene expression changes representing differentiation to all three germ layers over the first 3-5 days of LIF withdrawal. We observed a global increase in acetylation on histone H4 and to a lesser extent on histone H3 over this time period. Treatment of the cells with trichostatin A (TSA), a histone deacetylase inhibitor, induced changes in morphology, gene expression, and histone acetylation that mimicked differentiation induced by withdrawal of LIF. We examined localized histone acetylation in the regulatory regions of genes that were transcriptionally either active in undifferentiated cells, induced during differentiation, or inactive under all treatments. There was striking concordance in the histone acetylation patterns of specific genes induced by both TSA and LIF withdrawal. Increased histone acetylation in local regions correlated best with induction of gene expression. Finally, TSA treatment did not support the maintenance or progression of differentiation. Upon removal of TSA, the cells reverted to the undifferentiated phenotype. We concluded that increased histone acetylation at specific genes played a role in their expression, but additional events are required for maintenance of differentiated gene expression and loss of the pluripotent state.

Adult stem cell therapy: Dream or reality?

Adult stem cells may be an invaluable source of plastic cells for tissue regeneration. The bone marrow contains different subpopulations of adult stem cells easily accessible for transplantation. However the therapeutic value of adult stem cell is a question of debate in the scientific community. We have investigated the potential benefits of adult hematopoietic stem cell transplantation in animal models of demyelinating and motor neuron diseases. Our results suggest that transplantation of HSC have direct and indirect neuroregenerative and neuroprotective effects.

The constant variation: DNA methylation changes during preimplantation development

Studies on the DNA methylation changes in the mouse preimplantation embryo suggested a simple and attractive model explaining the process believed to be general in mammals. However, recent reports revealed marked differences between different species that abrogates the universal validity of the model. In order to find an explanation to the differences, we have analyzed the published mouse data and compared them to the observations available in other species. The emerging common theme is the high variability of the methylation at all scales of observation and all levels of organization. This variability is the likely consequence of a dynamic and active redistribution process of the cytosine methylation in the genome.

Can 5-azacytidine convert the adult stem cells into cardiomyocytes? A brief overview

From the first report that bone marrow cells (BMC) have stem cells characteristics, several studies have debated the possibility of intervening in myocardial remodeling after injury, for example myocardial infarction, by using BMC. The goal of this paper is to review the concept of whether the demethylating agent 5-azacytidine influences the myogenic differentiation of bone marrow-derived cells. The existing data seem to indicate that in vitro treatment with 5-azacytidine, even if not enough to generate mature CMC, promotes the in vivo and in vitro commitment of BMC into cells that express muscle-specific proteins and genes and, at a very low rate, show spontaneous contractions. It is probable this treatment makes the cells less responsive to other inductive factors secreted by the microenvironment that might modulate the differentiation. These data suggest that this approach may be used to prime cells prior to their transplantation in an injury area in the heart.

Epigenetic regulation of the imprinted U2af1-rs1 gene during retinoic acid-induced differentiation of embryonic stem cells

Epigenetic modifications such as DNA methylation and changes in chromatin structure are changes in the chemical composition or structure of DNA that work by regulating gene expression. Their mechanisms of action have been generally studied in imprinted genes. The present work analyzes the involvement of these mechanisms in the expression of the U2af1-rs1 imprinted gene during the differentiation process of embryonic stem (ES) cells induced by retinoic acid. By DNA digestion with methylation-dependent or independent restriction enzymes and consecutive Southern blot, we have found that methylation of the U2af1-rs1 gene increases in differentiated ES cells and in embryoid bodies. However, northern blot and real-time reverse transcription-polymerase chain reaction analysis showed a higher expression of the U2af1-rs1 gene in differentiated ES cells and in embryoid bodies than in undifferentiated ones. On the other hand, the sensitivity to DNase-I assay demonstrated an open chromatin conformation for differentiated cells with regard to undifferentiated ES cells. Our results suggest that the expression of the U2af1-rs1 gene would be regulated by changes in chromatin structure rather than by DNA methylation during the RA-induced process of differentiation of ES cells.

In vivo association of CReMM/CHD9 with promoters in osteogenic cells

Molecular mechanisms that control cell differentiation involve with chromatin remodeling activities. We recently identified Chromatin Related Mesenchymal Modulator (CReMM), a CHD protein expressed by mesenchymal cells. In this study, we analyzed CReMM expression on RNA and protein levels during embryonic development in mouse skeletal tissues. CReMM appears transiently during mesenchymal cell differentiation, being detected first in osteoprogenitors and declining in mature cells. A novel aspect of the study elaborates on in vivo association of CReMM with promoters in cells obtained by laser capture micro-dissection (LCM) technique from periosteum and endochondreal ossification regions. Using chromatin immunoprecipitation (ChIP), we proved that CReMM binds to skeletal tissue-specific promoters: CBFA1, biglycan, osteocalcin (OC), collagen-II, and myosin in a differential manner. The results imply that CReMM selectively interacts with analyzed promoters activated in the tissue at the appropriate time of development. The identification of CReMM and its tissue distribution and function provides an attractive clue for the study of transcriptional regulation of osteogenic cells' maturation.

Stem cell signalling networks in plants

The essential nature of meristematic tissues is addressed with reference to conceptual frameworks that have been developed to explain the behaviour of animal stem cells. Comparisons are made between different types of plant meristems with the objective of highlighting common themes that might illuminate underlying mechanisms. A more in depth comparison of the root and shoot apical meristems is made which suggests a common mechanism for maintaining stem cells. The relevance of organogenesis to stem cell maintenance is discussed, along with the nature of underlying mechanisms which help ensure that stem cell production is balanced with the depletion of cells through differentiation. Mechanisms that integrate stem cell behaviour in the whole plant are considered, with a focus on the roles of auxin and cytokinin. The review concludes with a brief discussion of epigenetic mechanisms that act to stabilise and maintain stem cell populations.

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs

Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.

In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis

Neural stem cells and neurogenesis persist in the adult mammalian brain subventricular zone (SVZ). Cells born in the rodent SVZ migrate to the olfactory bulb (Ob) where they differentiate into interneurons. To determine the gene expression and functional profile of SVZ neurogenesis, we performed three complementary sets of transcriptional analysis experiments using Affymetrix GeneChips: (1) comparison of adult mouse SVZ and Ob gene expression profiles with those of the striatum, cerebral cortex, and hippocampus; (2) profiling of SVZ stem cells and ependyma isolated by fluorescent-activated cell sorting (FACS); and (3) analysis of gene expression changes during in vivo SVZ regeneration after anti-mitotic treatment. Gene Ontology (GO) analysis of data from these three separate approaches showed that in adult SVZ neurogenesis, RNA splicing and chromatin remodeling are biological processes as statistically significant as cell proliferation, transcription, and neurogenesis. In non-neurogenic brain regions, RNA splicing and chromatin remodeling were not prominent processes. Fourteen mRNA splicing factors including Sf3b1, Sfrs2, Lsm4, and Khdrbs1/Sam68 were detected along with 9 chromatin remodeling genes including Mll, Bmi1, Smarcad1, Baf53a, and Hat1. We validated the transcriptional profile data with Northern blot analysis and in situ hybridization. The data greatly expand the catalogue of cell cycle components, transcription factors, and migration genes for adult SVZ neurogenesis and reveal RNA splicing and chromatin remodeling as prominent biological processes for these germinal cells.

Intestinal effects of long-lasting spermine ingestion by suckling rats

Spermine ingestion induces the precocious maturation of the small intestine in suckling rats. Previous observations suggest that spermine-induced intestinal maturation is a two-step phenomenon. The first step is the elimination of immature enterocytes (4-10 h post spermine ingestion) and the second step is the replacement of previous immature cells by adult-type enterocytes (2-3 days post initial spermine administration). The spermine-induced maturation is reversible when spermine administration is stopped. This work was undertaken in order to check whether the extension of polyamine administration (for 3-7 days) after the appearance of spermine-induced maturation can retain the mature state of the small intestine. Our results indicate that extension of spermine administration does not prevent some parameters (sucrase and maltase specific activities) reverting to a typical 'immature' value while others remain at a typical 'mature' level (mucosal weight and lactase specific activity). Our results show that there are at least two different mechanisms in required for the control of spermine-induced maturation of the small intestine.

Mesenchymal stem cells are recruited to striated muscle by NFAT/IL-4-mediated cell fusion

Mesenchymal stem cells (MSCs) or mesenchymal adult stem cells (MASCs) that are present in the stroma of several organs have been proposed to contribute to the regeneration of different tissues including liver, blood, heart, and skeletal muscle. Yet, it remains unclear whether MSCs can be programmed to differentiate cell-autonomously into fully functional cells or whether they are recruited by surrounding cells via fusion and thereby acquire specialized cellular functions. Here, we demonstrate that Wnt signaling molecules activate the expression of distinct sets of genes characteristic for cardiac and skeletal muscle cells in MASCs. However, such cells lack morphological criteria characteristic for functional muscle cells and do not show contractile activity. In contrast, MASCs fuse efficiently with native myotubes in an IL-4-dependent manner to form functional hybrid myotubes. Injection of genetically labeled MSCs into wild-type mouse blastocysts revealed a contribution to skeletal but not cardiac muscle development. Disruption of IL-4 and NFATc2/c3 reduced or prevented a contribution of adult stem cells to the development of Il-4 and NFATc2/c3 mutant embryos, further emphasizing the apparent inability of adult stem cells to differentiate fully into striated muscle in a cell-autonomous manner.

Are bone marrow stem cells plastic or heterogenous--that is the question

The concept that bone marrow (BM) may contain heterogeneous populations of stem cells was surprisingly not taken carefully enough into consideration in several recently reported experiments demonstrating so-called plasticity or trans-dedifferentiation of hematopoietic stem cells (HSC). These studies, without including proper controls to exclude this possibility, often lead to wrong interpretations. Accumulated evidence suggests that in addition to hematopoietic stem cells (HSC), bone marrow (BM) also harbors versatile subpopulations of tissue-committed stem cells (TCSC) and perhaps even more primitive pluripotent stem cells (PSC), and that these rare cells accumulate in bone marrow during ontogenesis, and being a mobile population of cells are released from BM into peripheral blood after tissue injury to regenerate damaged organs. Thus, the presence of TCSC/PSC in BM tissue should be considered before experimental evidence is interpreted simply as trans-dedifferentiation/plasticity of HSC. In this review, we will discuss this alternative explanation of plasticity of HSC, providing data from others and our laboratory that supports the concept that BM-derived stem cells are heterogeneous.

The Stem State: Plasticity Is Essential, Whereas Self-Renewal and Hierarchy Are Optional

The prevailing stem cell concept is derived from the large body of evidence available on the structure of the blood-generating system. Hemopoiesis is organized such that a multipotent stem cell, endowed with self-renewal capacity, is viewed as being positioned at the origin of a hierarchical tree of branching specificities, increasing maturity and decreasing self-renewal ability. Data accumulated in recent years on various stem cell systems often contradict this traditional view of stem cells and are reviewed herein. It is suggested that other options should be considered and put to experimental scrutiny; it is argued that the organization of the hemopoietic system may not represent a general structure of stem cell systems. The basic trait of the stem state is proposed to be plasticity. Self-renewal is not a specific stem cell trait; rather, it is exhibited by some mature cell types, whereas other particular stem cells are endowed with relatively poor renewal ability. Hierarchical structuring is also proposed to be an optional stem cell trait and may exist only in specific tissues where it serves the need for rapid expansion. The stem state is therefore defined by the highest degree of plasticity of a cell, within the repertoire of cell types present in the organism.

Histone deacetylase activity is essential for the expression of HoxA9 and for endothelial commitment of progenitor cells

The regulation of acetylation is central for the epigenetic control of lineage-specific gene expression and determines cell fate decisions. We provide evidence that the inhibition of histone deacetylases (HDACs) blocks the endothelial differentiation of adult progenitor cells. To define the mechanisms by which HDAC inhibition prevents endothelial differentiation, we determined the expression of homeobox transcription factors and demonstrated that HoxA9 expression is down-regulated by HDAC inhibitors. The causal involvement of HoxA9 in the endothelial differentiation of adult progenitor cells is supported by the finding that HoxA9 overexpression partially rescued the endothelial differentiation blockade induced by HDAC inhibitors. Knockdown and overexpression studies revealed that HoxA9 acts as a master switch to regulate the expression of prototypical endothelial-committed genes such as endothelial nitric oxide synthase, VEGF-R₂, and VE-cadherin, and mediates the shear stress–induced maturation of endothelial cells. Consistently, HoxA9-deficient mice exhibited lower numbers of endothelial progenitor cells and showed an impaired postnatal neovascularization capacity after the induction of ischemia. Thus, HoxA9 is regulated by HDACs and is critical for postnatal neovascularization.

Bone marrow as a home of heterogenous populations of nonhematopoietic stem cells

Evidence is presented that bone marrow (BM) in addition to CD45(positive) hematopoietic stem cells contains a rare population of heterogenous CD45(negative) nonhematopoietic tissue committed stem cells (TCSC). These nonhematopoietic TCSC (i) are enriched in population of CXCR4(+) CD34(+) AC133(+) lin(-) CD45(-) and CXCR4(+) Sca-1(+) lin(-) CD45(-) in humans and mice, respectively, (ii) display several markers of pluripotent stem cells (PSC) and (iii) as we envision are deposited in BM early in development. Thus, since BM contains versatile nonhematopoietic stem cells, previous studies on plasticity trans-dedifferentiation of BM-derived hematopoietic stem cells (HSC) that did not include proper controls to exclude this possibility could lead to wrong interpretations. Therefore, in this spotlight review we present this alternative explanation of 'plasticity' of BM-derived stem cells based on the assumption that BM stem cells are heterogenous. We also discuss a potential relationship of TCSC/PSC identified by us with other BM-derived CD45(negative) nonhematopoietic stem cells that were recently identified by other investigators (eg MSC, MAPC, USSC and MIAMI cells). Finally, we discuss perspectives and pitfalls in potential application of these cells in regenerative medicine.