Microarray analysis of novel cell lines representing two stages of metanephric mesenchyme differentiation

Clonal cell lines representing different developmental stages of the metanephric mesenchyme were made from transgenic mice with the Simian Virus 40 T-antigen (SV40 Tag) gene driven by the Hoxa 11 promoter. The resulting mK3 cell line represented early metanephric mesenchyme, prior to induction by the ureteric bud. These cells showed a spindle-shaped, fibroblast morphology. They expressed genes characteristic of early mesenchyme, including Hoxa 11, Hoxd 11, collagen I, and vimentin. Moreover, the mK3 cells displayed early metanephric mesenchyme biological function. In organ co-culture experiments they were able to induce growth and branching of the ureteric bud. Another cell line, mK4, represented later, induced metanephric mesenchyme undergoing epithelial conversion. These cells were more polygonal, or epithelial in shape, and expressed genes diagnostic of late mesenchyme, including Pax-2, Pax-8, Wnt-4, Cadherin-6, Collagen IV, and LFB3. To better define the gene expression patterns of kidney metanephric mesenchyme cells at these two stages of development, RNAs from the mK3 and mK4 cells were hybridized to Affymetrix GeneChip probe arrays. Over 4000 expressed genes were identified and thereby implicated in kidney formation. Comparison of the mK3 and mK4 gene expression profiles revealed 121 genes showing greater than a ten-fold difference in expression level. Several are known to be expressed during metanephric mesenchyme differentiation, but most had not been previously associated with this process. In situ hybridizations were used to confirm that selected novel genes were expressed in the developing kidney.     

In vitro models of intestinal epithelial cell differentiation

The intestinal epithelium is a particularly interesting tissue as (1) it is in a constant cell renewal from a stem cell pool located in the crypts which form, with the underlying fibroblasts, a stem cell niche and (2) the pluripotent stem cells give rise to four main cell types: enterocytes, mucus, endocrine, and Paneth cells. The mechanisms leading to the determination of phenotype commitment and cell-specific expressions are still poorly understood. Although transgenic mouse models are powerful tools for elucidating the molecular cascades implicated in these processes, cell culture approaches bring easy and elegant ways to study cellular behavior, cell interactions, and cell signaling pathways for example. In the present review, we will describe the major tissue culture technologies that allow differentiation of epithelial cells from undifferentiated embryonic or crypt cells. We will point to the necessity of the re-creation of a complex microenvironment that allows full differentiation process to occur. We will also summarize the characteristics and interesting properties of the cell lines established from human colorectal tumors.     

Multi-type branching models to describe cell differentiation programs

Cell proliferation and differentiation is described by a multi-type branching process, a probability model that defines the inheritance of cell type. Cell type is defined by (i) a repression index related to the time required for S-phase entry and (ii) phenotype as determined by cell markers and division history. The inheritance of cell type is expressed as the expected number and type of progeny cells produced by a mother cell given her type. Expressions for the expected number and type of cells produced by a multi-cellular (bulk culture) system are derived from the general model by making the simplifying assumption that cell generation times are independent. The multi-type Smith-Martin model (MSM) makes the further assumption that cell generation times are lag-exponentially distributed with phenotype transitions occurring just before entry into S-phase. The inheritance-modified MSM (IMSM) model includes the influence of generation time memory so that mother and daughter generation times are correlated. The expansion of human cord blood CD34⁺ cells by haematopoietic growth factors was division tracked in bulk culture using carboxyfluorescein diacetate, succinimidyl ester (CFDA-SE). The MSM model was fitted to division tracking data to indentify cell cycle length, and the rates of CD34 antigen down-regulation and apoptosis. The IMSM model was estimated for mouse granulocyte-macrophage progenitors using live cell imaging data. Multi-type branching models describe cell differentiation dynamics at both single- and multi-cell scales, providing a new paradigm for systematic analysis of stem and progenitor cell development.     

Theoretical analysis of Lumry-Eyring models in differential scanning calorimetry

A theoretical analysis of several protein denaturation models (Lumry-Eyring models) that include a rate-limited step leading to an irreversibly denatured state of the protein (the final state) has been carried out. The differential scanning calorimetry transitions predicted for these models can be broadly classified into four groups: situations A, B, C, and C′. (A) The transition is calorimetrically irreversible but the rate-limited, irreversible step takes place with significant rate only at temperatures slightly above those corresponding to the transition. Equilibrium thermodynamics analysis is permissible. (B) The transition is distorted by the occurrence of the rate-limited step; nevertheless, it contains thermodynamic information about the reversible unfolding of the protein, which could be obtained upon the appropriate data treatment. (C) The heat absorption is entirely determined by the kinetics of formation of the final state and no thermodynamic information can be extracted from the calorimetric transition; the rate-determining step is the irreversible process itself. (C′) same as C, but, in this case, the rate-determining step is a previous step in the unfolding pathway. It is shown that ligand and protein concentration effects on transitions corresponding to situation C (strongly rate-limited transitions) are similar to those predicted by equilibrium thermodynamics for simple reversible unfolding models. It has been widely held in recent literature that experimentally observed ligand and protein concentration effects support the applicability of equilibrium thermodynamics to irreversible protein denaturation. The theoretical analysis reported here disfavors this claim.     

Chromatin organization and differentiation in embryonic stem cell models

Embryonic stem cells derived from mammalian embryos represent indispensable tools for mammalian genetics. Their key features--self-renewal and pluripotency--enable them, on the one hand, to be propagated in culture almost indefinitely and, on the other, to be used to study the molecular details of cell commitment and differentiation. In the past few years, it has become clear that chromatin and epigenetic modifications have a central role in maintaining the gene expression programs that are important for both self-renewal and cell commitment. Therefore, studies focused on the chromatin profiles of embryonic stem cells are likely to be very informative for understanding pluripotency and the process of differentiation, and ultimately for using embryonic stem cells as a tool for cell replacement therapy or as models for the study of genetic diseases, cancer progression or drug testing.     

Two-carrier models for mediated transport I. Theoretical analysis of several two-carrier models

Several possible models of two sequential and two simultaneous carriers of different affinities are theoretically analysed. Following the analysis we suggest for each model an experimental procedure capable of testing and rejecting the model.     

Glycoproteomic analysis of glioblastoma stem cell differentiation

Cancer stem cells are responsible for tumor formation through self-renewal and differentiation into multiple cell types and thus represent a new therapeutic target for tumors. Glycoproteins play a critical role in determining the fates of stem cells such as self-renewal, proliferation, and differentiation. Here we applied a multilectin affinity chromatography and quantitative glycoproteomics approach to analyze alterations of glycoproteins relevant to the differentiation of a glioblastoma-derived stem cell line HSR-GBM1. Three lectins including concanavalin A (Con A), wheat germ agglutinin (WGA), and peanut agglutinin (PNA) were used to capture glycoproteins, followed by LC-MS/MS analysis. A total of 73 and 79 high-confidence (FDR < 0.01) glycoproteins were identified from the undifferentiated and differentiated cells, respectively. Label-free quantitation resulted in the discovery of 18 differentially expressed glycoproteins, wherein 9 proteins are localized in the lysosome. All of these lysosomal glycoproteins were up-regulated after differentiation, where their principal function was hydrolysis of glycosyl residues. Protein-protein interaction and functional analyses revealed the active involvement of lysosomes during the process of glioblastoma stem cell differentiation. This work provides glycoprotein markers to characterize differentiation status of glioblastoma stem cells that may be useful in stem-cell therapy of glioblastoma.     

Differential localization of two histidine kinases controlling bacterial cell differentiation

The bacterium C. crescentus coordinates cellular differentiation and cell cycle progression via a network of signal transduction proteins. Here, we demonstrate that the antagonistic DivJ and PleC histidine kinases that regulate polar differentiation are differentially localized as a function of the cell cycle. The DivJ kinase localizes to the stalked pole in response to a signal at the G1-to-S transition, while the PleC kinase is localized to the flagellar pole in swarmer and predivisional cells but is dispersed throughout the cell in the stalked cell. PleC, which is required for DivJ localization, may provide the cue at the G1-to-S transition that directs the polar positioning of DivJ. The dynamic positioning of signal transduction proteins may contribute to the regulation of polar differentiation at specific times during the bacterial cell cycle.     

Two-carrier models for mediated transport. I. Theoretical analysis of several two-carrier models.

Several possible models of two sequential and two simultaneous carriers of different affinities are theoretically analysed. Following the analysis we suggest for each model an experimental procedure capable of testing and rejecting the model.     

In vitro analysis of cardiac progenitor cell differentiation

Cardiac myoblast commitment and differentiation were studied in the developing avian embryo. Single cell analysis of isolated cardiogenic cells grown in vitro established that stage 4 (newly gastrulated) mesodermal cells are capable of myocyte differentiation in the absence of intercellular contact or short range cellular interactions. While cardiac myocytes derived from single isolated progenitors expressed muscle-specific myosin heavy chains (MHC), atrial and ventricular MHCs characteristic of in vivo development were not detected. When the same progenitors were grown at high density or in organ cultures, cell-specific, expression of atrial and ventricular MHCs was observed, suggesting a role of cell density-dependent processes for differential MHC expression. Cardiogenic mesoderm (stages 4-8) was treated with the cocarcinogen 12-O-tetradecanoylphorbol-13-acetate (TPA), maintained as organ cultures, and assayed for muscle differentiation in an attempt to identify possible stage-specific variations in cardiac progenitors. TPA irreversibly blocked the differentiation of early (stages 4-7) progenitors. When exposed to TPA, stages 4-7 cardiogenic cells failed to synthesize several muscle-specific proteins as determined by immunochemical analysis of myosin synthesis and two-dimensional gel electrophoresis of 35S-labeled proteins isolated from cardiogenic cultures. In addition, stages 4-7, TPA-treated cells did not differentiate after the withdrawal of TPA. In contrast, TPA had no effect on the expression of several muscle-specific proteins in late (stage 8) cells including the cell-specific expression of atrial and ventricular MHCs.     

Theoretical analysis of cell separation based on cell surface marker density

A theoretical analysis was performed to determine the number of fractions a multidisperse, immunomagnetically labeled cell population can be separated into based on the surface marker (antigen) density. A number of assumptions were made in this analysis: that there is a proportionality between the number of surface markers on the cell surface and the number of immunomagnetic labels bound; that this surface marker density is independent of the cell diameter; and that there is only the presence of magnetic and drag forces acting on the cell. Due to the normal distribution of cell diameters, a "randomizing" effect enters into the analysis, and an analogy between the "theoretical plate" analysis of distillation, adsorption, and chromatography can be made. Using the experimentally determined, normal distribution of cell diameters for human lymphocytes and a breast cancer cell line, and fluorescent activated cell screening data of specific surface marker distributions, examples of theoretical plate calculations were made and discussed.     

Random-walk models of cell dispersal included in mechanobiological simulations of tissue differentiation

Computational models have shown that biophysical stimuli can be correlated with observed patterns of tissue differentiation, and simulations have been performed that predict the time course of tissue differentiation in, for example, long bone fracture healing. Some simulations have used a diffusion model to simulate the migration and proliferation of cells with the differentiating tissue. However, despite the convenience of the diffusion model, diffusion is not the mechanism of cell dispersal: cells disperse by crawling or proliferation, or are transported in a moving fluid. In this paper, a random-walk model (i.e., a stochastic model), with and without a preferred direction, is studied as an approach to simulate cell proliferation/migration in differentiating tissues and it is compared with the diffusion model. A simulation of tissue differentiation of gap tissue in a two-dimensional model of a bone/implant interface was performed to demonstrate the differences between diffusion vs. random walk with a preferred direction. Results of diffusion and random-walk models are similar with respect to the change in the stiffness of the gap tissue but rather different results are obtained regarding tissue patterning in the differentiating tissues; the diffusion approach predicted continuous patterns of tissue differentiation whereas the random-walk model showed a more discontinuous pattern-histological results are not available that can unequivocally establish which is most similar to experimental observation. Comparing isotropic to anisotropic random walk (preferred direction of proliferation and cell migration), a more rapid reduction of the relative displacement between implant and bone is predicted. In conclusion, we have shown how random-walk models of cell dispersal and proliferation can be implemented, and shown where differences between them exist. Further study of the random-walk model is warranted, given the importance of cell seeding and cell dispersal/proliferation in many mechanobiological problems.     

Smooth muscle cell differentiation: Mechanisms and models for vascular diseases

Background

Vascular smooth muscle cells (VSMCs) are mature cells that play critical roles in both normal and aberrant cardiovascular conditions. In response to various environmental cues, VSMCs can dedifferentiate from a contractile state to a highly proliferative synthetic state through the so-called ‘phenotypic switching’ process. Changes in VSMC phenotype contribute to numerous vascular-related diseases, including atherosclerosis, calcification, and restenosis following angioplasty. Adventitial VSMC progenitor cells also contribute to formation of the neointima.

Methods/Results

Herein, we review both, the roles of VSMC differentiation in vascular diseases, and the in vitro models used to investigate the molecular mechanisms involved in the regulation of VSMC differentiation and phenotype modulation.

Conclusion

A comprehensive understanding of VSMC behavior in vascular diseases is essential to identify new therapeutic targets for the prevention and treatment of cardiovascular diseases.

     

Theoretical analysis of epigenetic cell memory by nucleosome modification

Chromosomal regions can adopt stable and heritable alternative states resulting in bistable gene expression without changes to the DNA sequence. Such epigenetic control is often associated with alternative covalent modifications of histones. The stability and heritability of the states are thought to involve positive feedback where modified nucleosomes recruit enzymes that similarly modify nearby nucleosomes. We developed a simplified stochastic model for dynamic nucleosome modification based on the silent mating-type region of the yeast Schizosaccharomyces pombe. We show that the mechanism can give strong bistability that is resistant both to high noise due to random gain or loss of nucleosome modifications and to random partitioning upon DNA replication. However, robust bistability required: (1) cooperativity, the activity of more than one modified nucleosome, in the modification reactions and (2) that nucleosomes occasionally stimulate modification beyond their neighbor nucleosomes, arguing against a simple continuous spreading of nucleosome modification.     

Theoretical models of cellular dielectrophoresis

Dielectrophoresis, the motion of neutral particles induced by a non-uniform electric field, is useful in separating and comparing single-celled organisms. The rate of dielectrophoretic collection in a region of higher field, called the “yield”, depends strongly upon the physiological state of the organism, upon the frequency of the field, and upon the conductivity of the suspending medium. The resulting yield spectrum is complex.     

Embryonic stem cell differentiation models: cardiogenesis, myogenesis, neurogenesis, epithelial and vascular smooth muscle cell differentiation in vitro

Embryonic stem cells, totipotent cells of the early mouse embryo, were established as permanent cell lines of undifferentiated cells. ES cells provide an important cellular system in developmental biology for the manipulation of preselected genes in mice by using the gene targeting technology. Embryonic stem cells, when cultivated as embryo-like aggregates, so-called ‘embryoid bodies’, are able to differentiate in vitro into derivatives of all three primary germ layers, the endoderm, ectoderm and mesoderm. We established differentiation protocols for the in vitro development of undifferentiated embryonic stem cells into differentiated cardiomyocytes, skeletal muscle, neuronal, epithelial and vascular smooth muscle cells. During differentiation, tissue-specific genes, proteins, ion channels, receptors and action potentials were expressed in a developmentally controlled pattern. This pattern closely recapitulates the developmental pattern during embryogenesis in the living organism. In vitro, the controlled developmental pattern was found to be influenced by differentiation and growth factor molecules or by xenobiotics. Furthermore, the differentiation system has been used for genetic analyses by ‘gain of function’ and ‘loss of function’ approaches in vitro. This revised version was published online in July 2006 with corrections to the Cover Date.     

Parameter resolution in two models for cell survival after radiation

The resolvability of model parameters for the linear-quadratic and the repair-misrepair models for cell survival after radiation has been studied by Monte Carlo simulations as a function of the number of experimental data points collected in a given dose range and the experimental error. Statistical analysis of the results reveals the range of experimental conditions under which the model parameters can be resolved with sufficient accuracy, and points out some differences in the operational aspects of the two models.     

Theoretical analysis of two ACO approaches for the traveling salesman problem

Bioinspired algorithms, such as evolutionary algorithms and ant colony optimization, are widely used for different combinatorial optimization problems. These algorithms rely heavily on the use of randomness and are hard to understand from a theoretical point of view. This paper contributes to the theoretical analysis of ant colony optimization and studies this type of algorithm on one of the most prominent combinatorial optimization problems, namely the traveling salesperson problem (TSP). We present a new construction graph and show that it has a stronger local property than one commonly used for constructing solutions of the TSP. The rigorous runtime analysis for two ant colony optimization algorithms, based on these two construction procedures, shows that they lead to good approximation in expected polynomial time on random instances. Furthermore, we point out in which situations our algorithms get trapped in local optima and show where the use of the right amount of heuristic information is provably beneficial.