High-dimensional switches and the modelling of cellular differentiation

Many genes have been identified as driving cellular differentiation, but because of their complex interactions, the understanding of their collective behaviour requires mathematical modelling. Intriguingly, it has been observed in numerous developmental contexts, and particularly haematopoiesis, that genes regulating differentiation are initially co-expressed in progenitors despite their antagonism, before one is upregulated and others downregulated. We characterise conditions under which three classes of generic "master regulatory networks", modelled at the molecular level after experimentally observed interactions (including bHLH protein dimerisation), and including an arbitrary number of antagonistic components, can behave as a "multi-switch", directing differentiation in an all-or-none fashion to a specific cell-type chosen among more than two possible outcomes. bHLH dimerisation networks can readily display coexistence of many antagonistic factors when competition is low (a simple characterisation is derived). Decision-making can be forced by a transient increase in competition, which could correspond to some unexplained experimental observations related to Id proteins; the speed of response varies with the initial conditions the network is subjected to, which could explain some aspects of cell behaviour upon reprogramming. The coexistence of antagonistic factors at low levels, early in the differentiation process or in pluripotent stem cells, could be an intrinsic property of the interaction between those factors, not requiring a specific regulatory system.     

LncRNA‐mRNA expression profiles and functional networks in osteoclast differentiation

Human osteoclasts are differentiated from CD14⁺ monocytes and are responsible for bone resorption. Long non‐coding RNAs (lncRNAs) have been proved to be significantly involved in multiple biologic processes, especially in cell differentiation. However, the effect of lncRNAs in osteoclast differentiation is less appreciated. In our study, RNA sequencing (RNA‐seq) was used to identify the expression profiles of lncRNAs and mRNAs in osteoclast differentiation. The results demonstrated that expressions of 1117 lncRNAs and 296 mRNAs were significantly altered after osteoclast differentiation. qRT‐PCR assays were performed to confirm the expression profiles, and the results were almost consistent with the RNA‐seq data. GO and KEGG analyses were used to predict the functions of these differentially expressed mRNA and lncRNAs. The Path‐net analysis demonstrated that MAPK pathway, PI3K‐AKT pathway and NF‐kappa B pathway played important roles in osteoclast differentiation. Co‐expression networks and competing endogenous RNA networks indicated that ENSG00000257764.2‐miR‐106a‐5p‐TIMP2 may play a central role in osteoclast differentiation. Our study provides a foundation to further understand the role and underlying mechanism of lncRNAs in osteoclast differentiation, in which many of them could be potential targets for bone metabolic disease.     

The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins

Regulation of cellular proliferation and differentiation during brain development results from processes requiring several regulatory networks to function in synchrony. MicroRNAs are part of this regulatory system. Although many microRNAs are evolutionarily conserved, recent evolution of such regulatory molecules can enable the acquisition of new means of attaining specialized functions. Here we identify and report the novel expression and functions of a human and higher primate-specific microRNA, miR-1290, in neurons. Using human fetal-derived neural progenitors, SH-SY5Y neuroblastoma cell line and H9-ESC-derived neural progenitors (H9-NPC), we found miR-1290 to be upregulated during neuronal differentiation, using microarray, northern blotting and qRT-PCR. We then conducted knockdown and overexpression experiments to look at the functional consequences of perturbed miR-1290 levels. Knockdown of miR-1290 inhibited differentiation and induced proliferation in differentiated neurons; correspondingly, miR-1290 overexpression in progenitors led to a slowing down of the cell cycle and differentiation to neuronal phenotypes. Consequently, we identified that crucial cell cycle proteins were aberrantly changed in expression level. Therefore, we conclude that miR-1290 is required for maintaining neurons in a differentiated state.     

Differentiation-induced alterations in cyclic AMP signaling in the Cath.a differentiated (CAD) neuronal cell line

Regulation of intracellular cyclic AMP is critical to the modulation of many cellular activities, including cellular differentiation. Moreover, morphological differentiation has been linked to subsequent alterations in the cAMP signaling pathway in various cellular models. The current study was designed to explore the mechanism for the previously reported enhancement of adenylate cyclase activity in Cath.a differentiated cells following differentiation. Differentiation of Cath.a differentiated cells stably expressing the D2L dopamine receptor markedly potentiated both forskolin- and A2-adenosine receptor-stimulated cAMP accumulation. This enhancement was accompanied by a twofold increase in adenylate cyclase 6 (AC6) expression and a dramatic loss in the expression of AC9. The ability of Ca2+ to inhibit drug-stimulated cAMP accumulation was enhanced following differentiation, as was D2L dopamine receptor-mediated inhibition of Galphas-stimulated cAMP accumulation. Differentiation altered basal and drug-stimulated phosphorylation of the cAMP-response element-binding protein, which was independent of changes in protein kinase A expression. The current data suggest that differentiation of the neuronal cell model, Cath.a differentiated cells induces significant alterations in the expression and function of both the proximal and distal portions of the cAMP signaling pathway and may impact cellular operations dependent upon this pathway.     

Amniotic fluid stem cells to study mTOR signaling in differentiation

The protein kinase mTOR is the central player within a pathway, which is known to be involved in the regulation of e.g., cell size, cell cycle, apoptosis, autophagy, aging and differentiation. mTOR activity responds to many signals, including cellular stress, oxygen, nutrient availability, energy status and growth factors. Deregulation of this enzyme is causatively involved in the molecular development of monogenic human diseases, cancer, obesity, type 2 diabetes or neurodegeneration. Recently, mTOR has also been demonstrated to control stem cell homeostasis. A more detailed investigation of this new mTOR function will be of highest relevance to provide more explicit insights into stem cell regulation in the near future. Different cellular tools, including adult stem cells, embryonic stem cells or induced pluripotent stem cells could be used to investigate the role of mTOR in mammalian stem cell biology. Here we discuss the potential of amniotic fluid stem cells to become a promising cellular model to study the role of signaling cascades in stem cell homeostasis.     

Amniotic fluid stem cells to study mTOR signaling in differentiation

The protein kinase mTOR is the central player within a pathway, which is known to be involved in the regulation of e.g., cell size, cell cycle, apoptosis, autophagy, aging and differentiation. mTOR activity responds to many signals, including cellular stress, oxygen, nutrient availability, energy status and growth factors. Deregulation of this enzyme is causatively involved in the molecular development of monogenic human diseases, cancer, obesity, type 2 diabetes or neurodegeneration. Recently, mTOR has also been demonstrated to control stem cell homeostasis. A more detailed investigation of this new mTOR function will be of highest relevance to provide more explicit insights into stem cell regulation in the near future. Different cellular tools, including adult stem cells, embryonic stem cells or induced pluripotent stem cells could be used to investigate the role of mTOR in mammalian stem cell biology. Here we discuss the potential of amniotic fluid stem cells to become a promising cellular model to study the role of signaling cascades in stem cell homeostasis.     

On the role of the peroxisome in cell differentiation and carcinogenesis

This article reviews the currently available data on the role of peroxisomal function in relation to the processes of cell differentiation and carcinogenesis. In regard to tumourigenesis, both genotoxic and non-genotoxic processes have been considered, and the peroxisomal relationships with these phenomena and with differentiation are described at the level of organelle characteristics, enzyme contents, and the involvement of retinoids, steroid hormones, oxygen free radicals, growth factors, apoptosis, omega-3 polyunsaturated fatty acids and the cellular signalling networks. Overall these data serve to illustrate the unique and distinctive role of the peroxisome in differentiation and carcinogenesis, and point to the advantages of considering the peroxisomal involvement in the holistic context of the differentiation dedifferentiation continuum rather than the narrower focus of non-genotoxic carcinogenesis. The review also outlines the potential for medical benefit arising from a fuller understanding of these peroxisomal affiliations.     

The statistical mechanics of complex signaling networks: nerve growth factor signaling

The inherent complexity of cellular signaling networks and their importance to a wide range of cellular functions necessitates the development of modeling methods that can be applied toward making predictions and highlighting the appropriate experiments to test our understanding of how these systems are designed and function. We use methods of statistical mechanics to extract useful predictions for complex cellular signaling networks. A key difficulty with signaling models is that, while significant effort is being made to experimentally measure the rate constants for individual steps in these networks, many of the parameters required to describe their behavior remain unknown or at best represent estimates. To establish the usefulness of our approach, we have applied our methods toward modeling the nerve growth factor (NGF)-induced differentiation of neuronal cells. In particular, we study the actions of NGF and mitogenic epidermal growth factor (EGF) in rat pheochromocytoma (PC12) cells. Through a network of intermediate signaling proteins, each of these growth factors stimulates extracellular regulated kinase (Erk) phosphorylation with distinct dynamical profiles. Using our modeling approach, we are able to predict the influence of specific signaling modules in determining the integrated cellular response to the two growth factors. Our methods also raise some interesting insights into the design and possible evolution of cellular systems, highlighting an inherent property of these systems that we call 'sloppiness.'     

Modulation of glutathione level during butyrate-induced differentiation in human colon derived HT-29 cells

Glutathione plays an important role in various cellular functions including cell growth and differentiation. In the present study, cell differentiation was induced by butyrate in human colon cell line HT-29 and cellular thiol status was assessed. It was observed that butyrate-induced differentiation was associated with decrease in cellular GSH level and this was prominent at early stages of differentiation. Buthionine sulfoximine (BSO), a specific cellular GSH depleting agent, did not induce differentiation in cells but potentiated the differentiation induced by butyrate. Both BSO and butyrate individually and together inhibited cell growth. These studies suggest that cellular GSH level is modulated in butyrate-induced differentiation and decrease of GSH at the initial stage might facilitate cellular differentiation.     

Use of evolved artificial regulatory networks to simulate 3D cell differentiation

Cell differentiation has a crucial role in both artificial and natural developments. This paper presents results from simulations in which a genetic algorithm (GA) was used to evolve artificial regulatory networks (ARNs) to produce predefined 3D cellular structures through the selective activation and inhibition of genes. The ARNs used in this work are extensions of a model previously used to create 2D geometrical patterns. The GA worked by evolving the gene regulatory networks that were used to control cell reproduction, which took place in a testbed based on cellular automata (CA). After the final chromosomes were produced, a single cell in the middle of the CA lattice was allowed to replicate controlled by the ARN found by the GA, until the desired cellular structures were formed. Two simple cubic layered structures were first developed to test multiple gene synchronization. The model was then applied to the problem of generating a 3D French flag pattern using morphogenetic gradients to provide cells with positional information that constrained cellular replication.     

Characterization and complementation analysis of sporogenous mutants of Dictyostelium discoideum

Sporogenous mutants of the cellular slime mold Dictyostelium discoideum are defined as mutants which are able to undergo terminal differentiation into spores in monolayer cultures in the presence of millimolar amounts of exogenous cyclic AMP. We describe the morphological development and cellular differentiation of a collection of 12 independently isolated sporogenous mutants of strain V12 M2. All mutants develop more rapidly than do wild-type at an air-water interface, display aberrant morphogenesis, and show overt spore and stalk differentiation as soon as 4 hr after starvation. All mutants differentiate in submerged monolayer culture in the presence of cAMP into variable proportions of spores and stalk cells. A number of the mutants also form both stalk cells and spores in submerged culture in the absence of exogenous cAMP. The spores formed by many of the mutants have a greatly reduced viability. Using parasexual genetics, we have found that two of the 12 mutants analyzed are dominant to wild-type and the remaining ten fall into a minimum of four complementation groups, the overall analysis thus yielding a minimum of four and a maximum of seven complementation groups. Intracellular cAMP levels in vegetative cells are significantly elevated in the two dominant mutants but are similar to wild type in all the other mutants.     

Cell mechanics: filaminA leads the way

Actin filaments are thought to be the major structural components of most eukaryotic cells, but reconstituted actin networks have yet to account for the remarkable strength exhibited by cellular networks. A new study has found that reconstituted networks that include the cross-linker filaminA can replicate many of the mechanical properties of cells if they are stressed prior to mechanical measurement.     

Emerging roles of the FBW7 tumour suppressor in stem cell differentiation

FBW7 is a ubiquitin E3 ligase substrate adaptor that targets many important oncoproteins-such as Notch, c-Myc, cyclin E and c-Jun-for ubiquitin-dependent proteolysis. By doing so, it plays crucial roles in many cellular processes, including cell cycle progression, cell growth, cellular metabolism, differentiation and apoptosis. Loss of FBW7 has been observed in many types of human cancer, and its role as a tumour suppressor was confirmed by genetic ablation of FBW7 in mice, which leads to the induction of tumorigenesis. How FBW7 exerts its tumour suppression function, and whether loss of FBW7 leads to de-differentiation or acquisition of stemness-a process frequently seen in human carcinomas-remains unclear. Emerging evidence shows that FBW7 controls stem cell self-renewal, differentiation, survival and multipotency in various stem cells, including those of the haematopoietic and nervous systems, liver and intestine. Here, we focus on the function of FBW7 in stem cell differentiation, and its potential relevance to human disease and therapeutics.     

Relation of Cholesterol to Astrocytic Differentiation in C-6 Glial Cells

Abstract: The relation of cellular cholesterol content to a biochemical expression of astrocytic differentiation was investigated in cultured C-6 glial cells. The astrocytic marker, glutamine synthetase, was studied. Cellular sterol content was perturbed with compactin, a specific inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase and, thereby, cholesterol biosynthesis. Depletion of cellular sterol resulted in 72 h in a more than twofold increase in glutamine synthetase activity. Production of various degrees of sterol depletion with different concentrations of compactin demonstrated a striking inverse relationship between glutamine synthetase activity and the cellular sterol/phospholipid molar ratio. That the effect of compactin, in fact, is mediated by depletion of sterol was shown further by prevention of the compactin-induced increase in synthetase activity by simultaneous addition of exogenous cholesterol. Moreover, addition of cholesterol alone to the culture medium led to both a decrease in glutamine synthetase activity and an increase in the sterol/phospholipid molar ratio. The possibility that the compactin-induced increase in glutamine synthetase activity is caused by an increase in synthesis of the enzyme was suggested by prevention of the increase by cycloheximide. The data suggest that astrocytic differentiation is stimulated by a decrease in cellular sterol content. When considered with our previous observation that oli-godendroglial differentiation is inhibited by such a decrease, the findings suggest that cellular sterol content is a critical determinant of the direction of glial differentiation, i.e., whether along astrocytic or oligodendroglial lines.     

Mechanical stimuli on C2C12 myoblasts affect myoblast differentiation, focal adhesion kinase phosphorylation and galectin-1 expression: a proteomic approach

Mechanical forces are crucial in the regulation of cell morphology and function. At the cellular level, these forces influence myoblast differentiation and fusion. In this study, we applied mechanical stimuli to embryonic muscle cells using magnetic microbeads, a method shown to apply stress to specific receptors on the cell surface. We showed that mechanical stimuli promote an increase in FAK (focal adhesion kinase) phosphorylation. In order to further shed light in the process of myoblast-induced differentiation by mechanical stimuli, we performed a proteomic analysis. Thirteen proteins were found to be affected by mechanical stimulation including galectin-1, annexin III and RhoGDI (Rho guanine-nucleotide-dissociation inhibitor). In this study, we demonstrate how the combination of this method of mechanical stimuli and proteomic analysis can be a powerful tool to detect proteins that are potentially interacting in biochemical pathways or complex cellular mechanisms during the process of myoblast differentiation. We determined an increase in expression and changes in cellular localization of galectin-1 in mechanically stimulated myoblasts. A potential involvement of galectin-1 in myoblast differentiation is presented.     

Mouse ES cell lines show a variable degree of chondrogenic differentiation in vitro

Pluripotent mouse embryonic stem (ES) cells differentiate in vitro spontaneously into cell types of all three primary germ layers when cultivated as cell aggregates, so-called 'embryoid bodies'. Many reports have shown that this system recapitulates cellular developmental processes and gene expression patterns of early embryogenesis. During ES cell differentiation, efficient and directed differentiation into a specific cell type is influenced by many parameters, for example, the batch of the serum used or the application of growth factors and signalling molecules. Because all ES cell lines are considered to be pluripotent, one should not expect remarkable differences regarding their spontaneous differentiation efficiencies. However, here we show that different ES cell lines exhibit a variable degree of spontaneous chondrogenic differentiation indicating that lines with a specific differentiation capacity could be selected. This is an important aspect if ES cells are applied for tissue regeneration.     

In search of the molecular mechanism by which small stress proteins counteract apoptosis during cellular differentiation

Many differentiation programs are accompanied by an increase in small heat shock proteins (sHsps) level. Most of the time transient, this accumulation takes place during the early phase of the process and is correlated with the growth arrest that precedes the differentiation. Important biochemical modifications of sHsps occur, such as changes in phosphorylation and oligomerization. The fact that these proteins are induced independently of the signal that triggers differentiation, of the differentiation type, and of the cell type strongly suggests their involvement in fundamental mechanisms of cellular differentiation. Moreover, impairment of sHsps accumulation leads to abortion of the differentiation program and, subsequently, to a massive commitment to cell death. Recent advances in this field of research are presented as well as the hypothesis that should be tested to unravel the mode of action of these proteins during cellular differentiation.