Kick-starting the cell cycle: From growth-factor stimulation to initiation of DNA replication

Regulation of Cell Cycle Entry and Exit: A Single Cell Perspective

The transition between proliferating and quiescent states must be carefully regulated to ensure that cells divide to create the cells an organism needs only at the appropriate time and place. Cyclin-dependent kinases (CDKs) are critical for both transitioning cells from one cell cycle state to the next, and for regulating whether cells are proliferating or quiescent. CDKs are regulated by association with cognate cyclins, activating and inhibitory phosphorylation events, and proteins that bind to them and inhibit their activity. The substrates of these kinases, including the retinoblastoma protein, enforce the changes in cell cycle status. Single cell analysis has clarified that competition among factors that activate and inhibit CDK activity leads to the cell's decision to enter the cell cycle, a decision the cell makes before S phase. Signaling pathways that control the activity of CDKs regulate the transition between quiescence and proliferation in stem cells, including stem cells that generate muscle and neurons. © 2020 American Physiological Society. Compr Physiol 10:317-344, 2020.

Integration of cell biology, pharmacological modeling and statistical analysis: part I: cell biology and PK/PD in the Oncology paradigm

The motivation of this two-part review article is to provide a comprehensive picture of cancer, cancer drugs and the detection and treatment of cancer. In order to do so, this article integrates the cell biology and biophysics of cancer as well as the modeling of preclinical Oncology drug data and statistical analysis of Oncology clinical trials data. It also discusses novel cancer diagnostic tools and standard and potential treatment options.

An integrative biological approach to the analysis of tissue culture data: application to the antitumour agent RHPS4

We describe a mathematical model of cell growth and death and explain how it can be used to integrate data from classic tissue culture experiments on antitumour agents and thus aid the identification of their mechanism of action. Experimental data relating to time- and dose-dependent changes in growth rate, cell cycle distribution, plus apoptotic and senescent fractions, are reinterpreted in terms of modulations to kinetic parameters that describe the rates at which cells transit between phenotypic compartments. The mathematical model is analytical, in the sense that the kinetic parameters are calculated from the experimental data directly, without any fitting process. Since the kinetic parameters are much more directly related to potential molecular targets than are the experimentally measured quantities, this approach can provide a more informative picture of the mechanism of action of the antitumour agent under investigation. We demonstrate the potential value of our model by applying it to data from RHPS4 (3,11-difluoro-6,8,13-trimethyl-8H-quino [4,3,2-kl] acridinium methosulfate). This agent is a DNA-interactive pentacyclic acridine for which at least three potential mechanisms of antitumour activity have been identified. Firstly RHPS4 is a telomerase inhibitor, secondly it is a telomerase-independent destabiliser of telomeres, and thirdly it is a telomere-independent binder to genomic DNA. Each mechanism can induce a separate, but overlapping, pattern of cellular responses, making the interpretation of tissue culture data very complex. Here we study the time- and dose-dependent effects of RHPS4 on the HCT116 cell line, and develop a five-compartment mathematical model to interpret the data. Application of the model to the data suggests that RHPS4 increases the rate at which cells became senescent state but, rather surprisingly, actually inhibits the rate of cell death. As a control, we also apply the model to data describing the time- and dose-dependent effects of doxorubicin since its mechanism of action is better characterised.

A mesoscale model of G1/S phase transition in liver regeneration

The liver regenerates and maintains its function and size after injury by counterbalancing cell death with compensatory cell division. During liver regeneration, injured sites release cytokines, which stimulate normally quiescent hepatocytes to re-enter cell division cycle. Using a mesoscale approach, we have implemented the first mathematical model that describes cytokine-induced dedifferentiation of hepatocytes and the subsequent initiation of DNA synthesis (G0/G1 and G1/S phase transitions of the cell cycle). The model accurately reproduces experimentally measured kinetics of various signaling intermediates and DNA synthesis in hepatocytes for varying degrees of liver damage, in both wild type and knockout backgrounds. Liver regeneration is known to be a robust process, as liver mass reconstitution still occurs in various knockout mice (albeit with different kinetics). We analyze the robustness of the model using methods of control analysis. Moreover, we discuss the system's bandpass filtering properties and delays, which arise from feedbacks and nested feed-forward loops.

Differences of Cell Growth and Cell Cycle Regulators Induced by Basic Fibroblast Growth Factor Between Nifedipine Responders and Non-responders

Differences of cell proliferation, cell cycle, and G(1)/S transition regulatory proteins of gingival fibroblasts derived from nifedipine-reactive patient (NIFr) and nifedipine-non-reactive patient (NIFn) in the presence of basic fibroblast growth factor (bFGF) were investigated to elucidate the mechanism of gingival overgrowth associated with nifedipine, one of the Ca(2+)-channel blockers. The proliferation rate of NIFr cells in the presence of bFGF significantly increased than NIFn cells. The proportion of NIFr cells that had undergone progression to the S and G(2)/M phases from the G(0)/G(1) phase significantly increased compared to that in NIFn cells. Increases of pRB (Ser807/811), pCDK2 (Thr160), CDK2, and cyclin E protein levels in NIFr cells were greater than those in NIFn cells. The elevations of pRB (Ser780), RB, and cyclin A protein levels in NIFr cells did not differ from those of NIFn cells. The growth of NIFr cells was greater than that of NIFn cells as a result of the active G(1)/S transition of NIFr cells, as assessed by the increments of cyclin E, pCDK2, and pRB (ser807/811) protein in NIFr cells.

The role of modelling in identifying drug targets for diseases of the cell cycle

The cell cycle is implicated in diseases that are the leading cause of mortality and morbidity in the developed world. Until recently, the search for drug targets has focused on relatively small parts of the regulatory network under the assumption that key events can be controlled by targeting single pathways. This is valid provided the impact of couplings to the wider scale context of the network can be ignored. The resulting depth of study has revealed many new insights; however, these have been won at the expense of breadth and a proper understanding of the consequences of links between the different parts of the network. Since it is now becoming clear that these early assumptions may not hold and successful treatments are likely to employ drugs that simultaneously target a number of different sites in the regulatory network, it is timely to redress this imbalance. However, the substantial increase in complexity presents new challenges and necessitates parallel theoretical and experimental approaches. We review the current status of theoretical models for the cell cycle in light of these new challenges. Many of the existing approaches are not sufficiently comprehensive to simultaneously incorporate the required extent of couplings. Where more appropriate levels of complexity are incorporated, the models are difficult to link directly to currently available data. Further progress requires a better integration of experiment and theory. New kinds of data are required that are quantitative, have a higher temporal resolution and that allow simultaneous quantitative comparison of the concentration of larger numbers of different proteins. More comprehensive models are required and must accommodate not only substantial uncertainties in the structure and kinetic parameters of the networks, but also high levels of ignorance. The most recent results relating network complexity to robustness of the dynamics provide clues that suggest progress is possible.

Phosphorylation of MCM4 by Cdc7 kinase facilitates its interaction with Cdc45 on the chromatin

Cdc7 kinase, conserved from yeasts to human, plays important roles in DNA replication. However, the mechanisms by which it stimulates initiation of DNA replication remain largely unclear. We have analyzed phosphorylation of MCM subunits during cell cycle by examining mobility shift on SDS-PAGE. MCM4 on the chromatin undergoes specific phosphorylation during S phase. Cdc7 phosphorylates MCM4 in the MCM complexes as well as the MCM4 N-terminal polypeptide. Experiments with phospho-amino acid-specific antibodies indicate that the S phase-specific mobility shift is due to the phosphorylation at specific N-terminal (S/T)(S/T)P residues of the MCM4 protein. These specific phosphorylation events are not observed in mouse ES cells deficient in Cdc7 or are reduced in the cells treated with siRNA specific to Cdc7, suggesting that they are mediated by Cdc7 kinase. The N-terminal phosphorylation of MCM4 stimulates association of Cdc45 with the chromatin, suggesting that it may be an important phosphorylation event by Cdc7 for activation of replication origins. Deletion of the N-terminal non-conserved 150 amino acids of MCM4 results in growth inhibition, and addition of amino acids carrying putative Cdc7 target sequences partially restores the growth. Furthermore, combination of MCM4 N-terminal deletion with alanine substitution and deletion of the N-terminal segments of MCM2 and MCM6, respectively, which contain clusters of serine/threonine and are also likely targets of Cdc7, led to an apparent nonviable phenotype. These results are consistent with the notion that the N-terminal phosphorylation of MCM2, MCM4, and MCM6 may play functionally redundant but essential roles in initiation of DNA replication.

Control of DNA replication: regulation and activation of eukaryotic replicative helicase, MCM

DNA replication is a key event of cell proliferation and the final target of signal transduction induced by growth factor stimulation. It is also strictly regulated during the ongoing cell cycle so that it occurs only once during S phase and that all the genetic materials are faithfully duplicated. DNA replication may be arrested or temporally inhibited due to a varieties of internal and external causes. Cells have developed intricate mechanisms to cope with the arrested replication forks to minimize the adversary effect on the stable maintenance of genetic materials. Helicases play a central role in DNA replication. In eukaryotes, MCM (minichromosome maintenance) protein complex plays essential roles as a replicative helicase. MCM4-6-7 complex possesses intrinsic DNA helicase activity which translocates on single-stranded DNA form 3' to 5'. Mammalian MCM4-6-7 helicase and ATPase activities are specifically stimulated by the presence of thymine-rich single-stranded DNA sequences onto which it is loaded. The activation appears to depend on the thymine content of this single-strand, and sequences derived from human replication origins can serve as potent activators of the MCM helicase. MCM is a prime target of Cdc7 kinase, known to be essential for activation of replication origins. We will discuss how the MCM may be activated at the replication origins by template DNA, phosphorylation, and interaction with other replicative proteins, and will present a model of how activation of MCM helicase by specific sequences may contribute to selection of replication initiation sites in higher eukaryotes.

Nonequilibrium capillary electrophoresis of equilibrium mixtures--a single experiment reveals equilibrium and kinetic parameters of protein-DNA interactions

We introduce a novel electrophoretic method, nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), and demonstrate its use for studying protein-DNA interactions. The equilibrium mixture of protein and DNA contains three components: free protein, free DNA, and the protein-DNA complex. A short plug of such a mixture is injected into the capillary, and the three components are separated under nonequilibrium conditions. The resulting electropherograms are composed of characteristic peaks and exponential curves. An easy nonnumerical analysis of a single electropherogram reveals two parameters: the equilibrium binding constant and the monomolecular rate constant of complex decay. The bimolecular rate constant of complex formation can then be calculated as the product of the two experimentally determined constants. NECEEM was applied to study the interaction between single-stranded DNA binding protein and a fluorescently labeled 15-mer oligonucleotide. It allowed us to measure for the first time the rate constant of complex decay for this important protein-DNA pair, k-1 = 0.03 s-1. The value of the equilibrium binding constant, Kb = 3.6 x 10-6 M-1, was in good agreement with those measured by other methods. As low as 10-18 mol of the protein was sufficient for the measurements. Thus, the new method is simple, informative, and highly sensitive. Moreover, it can be equally applied to other noncovalent protein-ligand complexes. These features of NECEEM make this method an indispensable tool in studies of macromolecular interactions. They also emphasize the potential role of NECEEM in the development of extremely sensitive protein assays using nucleotide aptamers.