ABSTRACT: This 89-node Boolean model of mammalian growth factor signaling can reproduce oscillations in PI3K signaling in cycling cells, and links these oscillations to the regulatory networks that drive each phase of cell cycle progression, as well as apoptosis. It builds on our previous work on modeling cell cycle progression as the interaction of two linked multi-stable switches (Deritei et al, Sci Rep 6:21957, 2016) and extends it to capture the role of Plk1 in cell cycle progression.
The resulting model reproduces the following experimentally documented cell behaviors:
— cyclic PI3K/AKT1 activity in dividing cells, which remain in sync with the cell cycle
— apoptosis in response to prolonged mitosis or mitotic catastrophe
— four distinct, experimentally documented cell fates caused by Plk1 inhibition, depending on the
timing of Plk1 loss; namely, G2 arrest, mitotic catastrophe, premature anaphase and chromosome mis-segregation leading to aneuploidy, and failure to complete cytokinesis following telophase, which can lead to genome duplication
— failure of cytokinesis and accumulation of binucleate telophase cells driven by hyperactive PI3K, hyperactive Ak1, or FoxO inhibition.
— the effect of a large number of knockdown / forced activation mutations
— PI3K degradation in response to high PI3K activation is driven by the Neddl4 ubiquitin ligase activated by PLCγ, while its re-synthesis requires nuclear re-accumulation of FoxO3.
— The degradation/re-synthesis cycle of PI3K occurs twice per division cycle, synchronized by Plk1-mediated inhibition of FoxO3 during metaphase/anaphase.
— Cells in which PI3K is inhibited after the start of DNA synthesis can nevertheless pre-commit to another cell cycle in the presence of saturating growth stimulation (passing the restriction point in late metaphase), albeit at lower rates than wild-type cells.
— Cell cycle defects in response to PI3K/Ak1 over-activation or FoxO knockdown are driven by a loss of Plk1 in telophase.
Project description:Progress through the division cycle of present day eukaryotic cells is controlled by a complex network consisting of (i) cyclin-dependent kinases (CDKs) and their associated cyclins, (ii) kinases and phosphatases that regulate CDK activity, and (iii) stoichiometric inhibitors that sequester cyclin-CDK dimers. Presumably regulation of cell division in the earliest ancestors of eukaryotes was a considerably simpler affair. Nasmyth (1995) recently proposed a mechanism for control of a putative, primordial, eukaryotic cell cycle, based on antagonistic interactions between a cyclin-CDK and the anaphase promoting complex (APC) that labels the cyclin subunit for proteolysis. We recast this idea in mathematical form and show that the model exhibits hysteretic behaviour between alternative steady states: a Gl-like state (APC on, CDK activity low, DNA unreplicated and replication complexes assembled) and an S/M-like state (APC off, CDK activity high, DNA replicated and replication complexes disassembled). In our model, the transition from G1 to S/M ('Start') is driven by cell growth, and the reverse transition ('Finish') is driven by completion of DNA synthesis and proper alignment of chromosomes on the metaphase plate. This simple and effective mechanism for coupling growth and division and for accurately copying and partitioning a genome consisting of numerous chromosomes, each with multiple origins of replication, could represent the core of the eukaryotic cell cycle. Furthermore, we show how other controls could be added to this core and speculate on the reasons why stoichiometric inhibitors and CDK inhibitory phosphorylation might have been appended to the primitive alternation between cyclin accumulation and degradation.
Project description:The duplication and segregation of chromosomes involve the dynamic re-organization of their internal structure by conserved architectural proteins, such as structural maintenance of chromosomes complexes (i.e., cohesin and condensin). Although the roles of these factors is actively investigated, a genome-wide view of chromosome dynamic architecture at both small and large-scales during cell division remains elusive. Here we report the first comprehensive 4D analysis of the Saccharomyces cerevisiae genome higher-order organization during the cell cycle, and investigate the roles of SMC in the observed structural transitions. During replication, cohesion establishment promotes long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. Mitotic chromosomes are then abruptly reorganized in anaphase by mechanical forces exerted by the mitotic spindle. The formation of a condensin-dependent loop, that bridges the centromere cluster with the rDNA loci, suggests that condensin-mediated forces may also directly facilitate segregation. This work provides a comprehensive overview of chromosome dynamics during the cell cycle of a unicellular eukaryote that recapitulates and unveils new features of highly conserved stages of the cell division. Overall design: Chromosome organization investigation through Hi-C
Project description:Transcript dynamics in mitotic exit mutants in the S. cerevisiae BF264-15D strain background. We examined the extent to which periodic cell-cycle transcription persisted in cells arrested in anaphase with intermediate level of B-cyclins. Overall design: Early G1 cells were obtained by α-factor arrest at 25°C and then released at 37°C for time-series microarray. This study includes new samples and re-analyzed samples from GSE8799, GSE32974 and GSE49650.
Project description:Sister chromatid cohesion relies on cohesins, a group of proteins that forms a ring-shaped complex embracing sister chromatids. Cohesion is established during S phase and is removed when cohesin Scc1 is cleaved by the protease separase at anaphase onset. During this process, the cohesin subunit Smc3 undergoes a cycle of acetylation: Smc3 acetylation by Eco1 in S phase stabilizes cohesin association with chromosomes, and its deacetylation by Hos1 in anaphase allows re-use of Smc3 in the next cell cycle. Here we find that Smc3 deacetylation by Hos1 has a more immediate effect in early anaphase of budding yeast. Without Hos1, sister chromatid separation and segregation are significantly delayed. Smc3 deacetylation facilitates removal of cohesins from chromosomes, without changing the Scc1 cleavage efficiency, thus promoting dissolution of cohesion. This action is probably due to disengagement of Smc1–3 heads, prompted by de-repression of their ATPase activity. We suggest Scc1 cleavage per se is insufficient for efficient dissolution of cohesion in early anaphase, but subsequent Smc3 deacetylation, which is triggered by Scc1 cleavage, is also required. Overall design: examination of cohesin subunit SMC1 distribution in S.cerevisiae
Project description:Mathematical model of the fission yeast cell cycle with checkpoint
controls at the G1/S, G2/M and metaphase/anaphase transitions. Model encoded by Matthieu Maire and submitted to BioModels by Krishna kumar Tiwari.
Project description:ABSTRACT: Condensin is a central regulator of mitotic genome structure, with mutants showing poorly condensed chromosomes and profound segregation defects. Here we identify the fission yeast NCT complex, comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), Casein Kinase II (CKII) and several TAFs, as a novel regulator of condensin function (where NCT mutants restore the formation of segregation-competent chromosomes in cells containing defective condensin). Synchronous ChIP-seq shows that NCT and condensin bind similar genomic regions, but only briefly co-localize during the periods of chromosome condensation and decondensation. These results are consistent with a model where NCT targets CKII to chromatin in a cell cycle-directed manner to modulate the activity of condensin during chromosome condensation and decondensation. DATA: Study includes ChIP-seq of fission yeast H3-K4Me3, H3-K36Me3, TBP, Taf7, Nrc1, Cka1 from aynchronous cells; Nrc1 and Cut3 (representing condensin) from four synchronized cell-cycle stages estimated as G2/M, Metaphase, Anaphase and G1/S.
Project description:The chromosomal condensin complex gives metaphase chromosomes structural stability. In addition, condensin is required for sister chromatid resolution during their segregation in anaphase. How condensin promotes chromosome resolution is poorly understood. Chromosome segregation during anaphase also fails after inactivation of topoisomerase II (topo II), the enzyme that removes catenation between sister chromatids left behind after completion of DNA replication. This has led to the proposal that condensin promotes DNA decatenation, but direct evidence for this is missing and alternative roles for condensin in chromosome resolution have been suggested. Using the budding yeast rDNA as a model, we now show that anaphase bridges in a condensin mutant are resolved by ectopic expression of a foreign (Chlorella virus) but not endogenous topo II. This suggests that catenation prevents sister rDNA segregation, and that yeast topo II is ineffective in decatenating the locus without condensin. Condensin and topo II colocalize along both rDNA and euchromatin, consistent with coordination of their activities. We investigate the physiological consequences of condensin-dependent rDNA decatenation and find that late decatenation determines the late segregation timing of this locus during anaphase. Regulation of decatenation therefore provides a means to finetune segregation timing of chromosomes in mitosis. Keywords: ChIP-chip, Cell Cycle Overall design: Comparison of the chromosomal association pattern of the condensin subunit Brn1 with that of topo II along budding yeast chromosomes. As control, the binding pattern of the cohesin subunit Scc1 is also included. (Figure 2 in the corresponding manuscript depicts the Brn1 association pattern as obtained from averaging two independent biological ChIP experiments C15_IP_2200_NOC and C16_IP_2200.)
Project description:Macrophages accumulate with glioblastoma multiforme (GBM) progression, and can be acutely targeted via inhibition of colony stimulating factor-1 receptor (CSF-1R) to regress high-grade tumors in animal models. However, whether and how resistance emerges in response to sustained CSF-1R blockade is unknown. Here, we investigate whether long-term CSF-1R inhibition can stably regress GBM in preclinical trials. We show that while overall survival is significantly prolonged, tumors recur eventually in >50% of mice. Upon isolation and transplantation of recurrent tumor cells into naïve animals, gliomas re-establish sensitivity to CSF-1R inhibition, indicating that resistance is microenvironment-driven. PI3K pathway activity was elevated in recurrent GBM, driven by macrophage-derived IGF-1 and tumor cell IGF-1R. Consequently, combining IGF-1R or PI3K blockade with continuous CSF-1R inhibition in recurrent tumors significantly prolonged overall survival. By contrast, monotherapy with IGF-1R or PI3K inhibitors in rebound or treatment-naïve tumors was less effective, indicating the necessity of combination therapy to expose PI3K signaling-dependency in recurrent disease. Our findings thus reveal a potential therapeutic approach for treating resistance to CSF-1R inhibitors in the clinical setting. Overall design: 3 rebound neurosphere cell lines were assayed against 3 references to normal mouse liver
Project description:Entry into and exit from mitosis is driven by precisely-timed changes in protein abundance, and involves transcriptional regulation and protein degradation. However, the role of translational regulation in modulating cellular protein content during mitosis remains poorly understood. Here, using ribosome profiling, we show that translational, rather than transcriptional regulation is the dominant mechanism for modulating protein synthesis at mitotic entry. The vast majority of regulated mRNAs are translationally repressed, which contrasts previous findings of selective mRNA translational activation at mitotic entry. One of the most pronounced translationally repressed genes in mitosis is Emi1, an inhibitor of the anaphase promoting complex (APC), which is degraded during mitosis. We show that Emi1 degradation is insufficient for full APC activation and that simultaneous translational repression is required. These results provide a genome-wide view of protein translation during mitosis and suggest that translational repression may be used to ensure complete protein inactivation Ribosome profiling and mRNA-seq from 3 time points in the cell cycle
Project description:This a model from the article:
Kinetic analysis of a molecular model of the budding yeast cell cycle.
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. Mol Biol Cell
2000 Jan;11(1):369-91 10637314
The molecular machinery of cell cycle control is known in more detail for
budding yeast, Saccharomyces cerevisiae, than for any other eukaryotic organism.
In recent years, many elegant experiments on budding yeast have dissected the
roles of cyclin molecules (Cln1-3 and Clb1-6) in coordinating the events of DNA
synthesis, bud emergence, spindle formation, nuclear division, and cell
separation. These experimental clues suggest a mechanism for the principal
molecular interactions controlling cyclin synthesis and degradation. Using
standard techniques of biochemical kinetics, we convert the mechanism into a set
of differential equations, which describe the time courses of three major
classes of cyclin-dependent kinase activities. Model in hand, we examine the
molecular events controlling "Start" (the commitment step to a new round of
chromosome replication, bud formation, and mitosis) and "Finish" (the transition
from metaphase to anaphase, when sister chromatids are pulled apart and the bud
separates from the mother cell) in wild-type cells and 50 mutants. The model
accounts for many details of the physiology, biochemistry, and genetics of cell
cycle control in budding yeast.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. (2000) - version=1.0
The original CellML model was created by:
The University of Auckland
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