Some paradoxical effects of inhibitors of protein synthesis on protein turnover in cultured human cells

Lyapunov exponents and phase diagrams reveal multi-factorial control over TRAIL-induced apoptosis

Kinetic modeling, phase diagrams analysis, and quantitative single-cell experiments are combined to investigate how multiple factors, including the XIAP:caspase-3 ratio and ligand concentration, regulate receptor-mediated apoptosis.

Based on protein expression levels, Lyapunov-based phase diagrams predict which pathways are required for a cell to undergo receptor-mediated cell death.

Multiple inter-dependent factors, including the XIAP:caspase-3 ratio and ligand concentration, regulate the requirement for mitochondrial outer membrane permeabilization during receptor-mediated apoptosis.

The E3 ubiquitin ligase activity of XIAP is essential for maintaining the ‘snap-action' regulation of effector caspase activity.

Cell-to-cell variability in protein expression gives rise to mixed phenotypes in cell lines that map close to boundaries (separatrices) identified by Lyapunov exponent analysis.

In mammalian cells, extrinsic (receptor-mediated) apoptosis is triggered by binding of extracellular death ligands such as tumor necrosis factor (TNF) and TRAIL (TNF-related apoptosis-inducing ligand) to cognate receptors. When death receptors are activated, death inducing signaling complexes (DISCs) assemble causing activation and cleavage of initiator pro-caspases-8 and -10, which then cleave effector pro-caspases-3 and -7 in a multi-enzyme cascade (Riedl and Shi, 2004). Active effector caspases digest essential cellular proteins and activate the CAD nucleases that cleave genomic DNA, thereby killing cells. This cascade of DISC assembly followed by initiator and then effector caspase activation is sufficient to kill so-called type I cells (e.g. B lymphocytes), but most cell types exhibit a type II behavior in which mitochondrial outer membrane permeabilization (MOMP) is an essential step in the march to death (Scaffidi et al, 1998; Barnhart et al, 2003; Letai, 2008). Identifying factors that determine whether cells are type I or II is of practical and theoretical interest. From a practical perspective, whether a cell requires MOMP for apoptosis determines the potency of Bcl2 and similar oncogenes, the efficacy of anti-Bcl2 drugs such as navitoclax (ABT-263), and the sensitivity of cells to TRAIL and anti-TRAIL receptor antibodies, which are also investigational anti-cancer drugs (Newsom-Davis et al, 2009). From a theoretical perspective, the type I versus II choice exemplifies a common situation in mammalian cells in which overlapping signaling pathways play a greater or lesser role in controlling cell fate depending on cell type: it is remarkable that a simple three-step (receptor→initiator caspase→effector caspase) process is sufficient to trigger apoptosis in some cell types but that a much more complex route involving MOMP is required in others.

Attempts to understand why some cells require MOMP for cell death and others do not have identified differences in the oligomeric state of death ligand receptors and the efficiency of DISC formation as important variables. In cells in which DISCs form efficiently, initiator caspases are cleaved rapidly and sufficient effector pro-caspases are processed into their active forms to kill cells (type I cells; Scaffidi et al, 1999b). In type II cells, DISC formation seems to be less efficient, and it has been proposed that MOMP is required to amplify weak initiator caspase signals and thereby generate lethal effector caspase levels (Barnhart et al, 2003). However, it has recently become apparent that XIAP also plays a role in type I versus II choice: in XIAP knockout mice, liver cells switch from a type II to a type I phenotype (Jost et al, 2009) and XIAP is observed to be involved in the survival of type I cells treated with death ligands in culture (Maas et al, 2010).

In this paper, we attempt to place these observations in a quantitative context by analyzing a computational model of extrinsic cell death using a method drawn from dynamical system analysis, direct finite-time Lyapunov exponent (DLE) analysis. Our implementation of DLE analysis relates changes in the concentrations of protein in a model to an outcome several hours later. We computed DLEs for six regulators of apoptosis over a range of concentrations determined experimentally to represent a natural range of variation in parental or genetically modified tumor cell lines. This generated a phase space onto which individual cell lines could be mapped using quantitative immunoblotting data. Cell-to-cell variation was estimated by flow cytometry and also mapped onto the phase space. The most interesting regions of the space were those in which a small change in one or more initial protein concentration resulted in a dramatic change in phenotype. Such a boundary or separatrix was observed in slices of phase space corresponding XIAP versus pro-caspase-3 concentration (the [XIAP]:[caspase-3] ratio). In cells in which the ratio is low, a type I phenotype is predicted to occur; when the ratio is high, a type II phenotype is favored; and in cell lines that lie close to the separatrix, cell-to-cell variability is expected, with some cells exhibiting a type I phenotype and others a type II behavior. DLE analysis shows that the [XIAP]:[caspase-3] ratio is not the only controlling factor in type I versus II control: as receptor activity or ligand concentration increase, the position of the separatrix changes so as to expand the region in which the type I phenotype is favored.

We tested these predictions by manipulating XIAP and ligand levels in multiple cell lines and then followed cell death by imaging, flow cytometry, or clonogenic assays. We observed that when XIAP was knocked out (by homologous recombination) in the HCT116 colorectal cancer line, cells shifted from a pure type II to a type I phenotype, as predicted from the DLE phase diagram. SKW6.4 B-cell lymphoma cells were predicted to lie at a position in phase space that is insensitive to XIAP levels (within the range achievable by over-expression) and we confirmed this experimentally. Finally, T47D breast cancer cells were predicted—and observed—to straddle the separatrix and to exhibit cell-to-cell variability in fate, with some cells showing a type I and others a type II phenotype. As the concentration of TRAIL was increased, the ratio of type I to type II T47D cells increased, confirming the prediction that this ratio is controlled in a multi-factorial manner.

To extend our approach to mutations that change protein activity rather than protein level, we simulated the effects of changing rate constants that control ubiquitylation of caspase-3 following its binding to XIAP. We generated cells carrying a truncated form of XIAP that lacks the RING domain (XIAPΔRING) and cannot mediate the ubiquitylation of caspase-3 (this truncation leaves the affinity of XIAP for caspase-3 unchanged). We predicted and demonstrated experimentally that expression of XIAPΔRING disrupts normal snap-action control over caspase-3 activation. Our findings not only advance understanding of extrinsic apoptosis but also constitute a proof of principle for an approach to quantitative modeling of dynamic regulatory processes in diverse cell types.

Receptor-mediated apoptosis proceeds via two pathways: one requiring only a cascade of initiator and effector caspases (type I behavior) and the second requiring an initiator–effector caspase cascade and mitochondrial outer membrane permeabilization (type II behavior). Here, we investigate factors controlling type I versus II phenotypes by performing Lyapunov exponent analysis of an ODE-based model of cell death. The resulting phase diagrams predict that the ratio of XIAP to pro-caspase-3 concentrations plays a key regulatory role: type I behavior predominates when the ratio is low and type II behavior when the ratio is high. Cell-to-cell variability in phenotype is observed when the ratio is close to the type I versus II boundary. By positioning multiple tumor cell lines on the phase diagram we confirm these predictions. We also extend phase space analysis to mutations affecting the rate of caspase-3 ubiquitylation by XIAP, predicting and showing that such mutations abolish all-or-none control over activation of effector caspases. Thus, phase diagrams derived from Lyapunov exponent analysis represent a means to study multi-factorial control over a complex biochemical pathway.

Regulation of hexose transport in respiration deficient hamster lung fibroblasts

The transport of [3H]2-deoxy-D-glucose (2DG) and [3H]3-O-methyl-D-glucose (3-OMG) was elevated in a respiration deficient (NADH coenzyme Q [Co Q] reductase deficient) Chinese hamster lung fibroblast cell line (G14). This sugar transport increase was related to an increased Vmax for 2DG transport, 26.9 +/- 4.2 nmoles 2DG/mg protein/30 sec in the G14 cell line vs 9.5 +/- 0.6 nmoles 2DG/mg protein/30 sec in the parental V79 cell line. No differences were observed in their respective Km values for 2DG transport (3.9 +/- .6 vs. 3.0 +/- .13 mM). Factors which increase sugar transport (e.g., glucose deprivation, serum or insulin exposure) or decrease sugar transport (e.g., serum deprivation) in the parental V79 cell line had little effect on sugar transport in the G14 respiration deficient cell lines. Amino acid transport, specific 125I-insulin binding to cells, and insulin-stimulated DNA synthesis, however, were similar in both cell lines. Exposure of both cell lines to varying concentrations of cycloheximide (0.1-50 micrograms/ml) for 4 h resulted in differential effects on 2DG transport. In the parental cell line (V79) low cycloheximide concentrations resulted in decreased 2DG transport, while higher concentrations (greater than or equal to 1 microgram/ml) resulted in elevated 2DG transport. In the G14 cell line, 2DG transport decreased at all concentrations of cycloheximide (up to 50 micrograms/ml). The data indicate that the G14 mutant has been significantly and specifically affected in the expression of sugar transport activity and in the regulatory controls affecting sugar transport activity.

The influence of urea and cell-surface protein on the behavior of nontumorigenic and chemically transformed cells

Alterations in cell-cell interactions induced by urea and urea-isolated cell-surface protein (CSP) were examined using the nontumorigenic mouse fibroblast 10T1/2 cell line and the malignantly transformed MCA daughter cell line as a model system. Both cell lines were exposed to urea and CSP, and contact inhibition was quantitated based on nuclear overlaps. The Abercrombie Overlap index was found to be dependent on cell density, and a new method of overlap analysis was developed based on the regression of the number of overlaps per microscope field on the number of cells per field. Urea had a differential effect on both protein and deoxyribonucleic acid synthesis and a differential effect on the overlap regression in the two cell lines. Urea increased the regression coefficient in the normal (10T1/2) cell line while decreasing it in the transformed (MCA) cell line to approximately equal levels of overlap. Added CSP had no effects on overlaps in the MCA line but increased overlaps in the 10T1/2 line to the level of the MCA control, suggesting that the CSP interactions were more specific than the urea interactions. Trypsin-derived cell-surface glycopeptide profiles of the two cell lines showed a difference consistent with previously reported differences between normal and transformed cell lines. However, the glycopeptide profile of the urea-isolated CSP from the normal 10T1/2 cell line and the trypsin-derived glycopeptides of the transformed MCA cell line were not significantly different in the high-molecular-weight region, suggesting that the relative abundance of CSP may be higher in the MCA line, and the fact that the addition of CSP to the 10T1/2 line increased overlap tendency to the level of the MCA line suggested that CSP is an important factor in the modulation of overlap tendency. Urea and CSP may exert their effects on overlap tendency by affecting the integrity or order of the cell-surface components. The increased overlap tendency of the 10T1/2 line in the presence of CSP was not associated with increased cell density. Density dependence of cell growth was apparently not directly related to density dependence of overlap tendency. Many xenobiotics have surface-active properties and are known to inhibit protein synthesis.(ABSTRACT TRUNCATED AT 400 WORDS)

Suppression of myocardial protein degradation in the rat during fasting. Effects of insulin, glucose, and leucine

To study the effects of leucine, glucose, and insulin on myocardial protein degradation in fed and fasted nutritional states, we developed and validated a sensitive method for measuring rates of total protein degradation in rat isolated left atrial preparations. Fasting resulted in a progressive decrease in myocardial protein breakdown to 71% of control over a 24-hour period, with no further reduction in degradation rate between 24 and 72 hours of fasting. Insulin (100 mU/ml) suppressed atrial protein degradation by 38% in fed animals (P less than 0.001) and by 51% in fasted animals (P less than 0.001). Glucose alone had no effect on protein degradation in either nutritional state. At 5 times normal plasma levels, leucine suppressed protein breakdown by 21% in fed and by 15% in fasted animals. The decrease in degradation induced by fasting and the absence of an effect of glucose are in contrast to the behavior reported for skeletal muscle.

Cycloheximide effect on DNA degradation and delta-crystallin synthesis in terminally differentiating lens cells

Low concentrations of a protein synthesis inhibitor, cycloheximide, were added throughout the process of in vitro differentiation of 11-day old embryonic chick lens cells. We found with low concentrations of cycloheximide (0.01 to 0.03 microgram/ml, 3 days of culture), that there was an almost complete delay of DNA degradation as observed on alkaline sucrose gradient. Identical concentrations and exposure time had no blocking effect on increased delta-crystallin synthesis as detected by immunoprecipitation and electrophoresis. Higher concentrations of cycloheximide (0.1 to 1 microgram/ml) showed a marked effect on DNA size and a net inhibition on delta-crystallin synthesis. Thus a selective effect of low doses of cycloheximide was observed on terminal differentiation suggesting that there was not a relationship between DNA degradation and delta-crystallin synthesis in these short term experiments. The investigations of minor proteins could be of interest as they may have a crucial role in intact nuclei cataracts.

Effects of multiplication stimulating activity (MSA) on AIB transport into myoblast and myotube cultures

The effects of a somatomedian analog, Temin's multiplication stimulating activity (MSA), on amino acid transport into muscle cells have been characterized in a series of experiments on myoblasts and myotubes in culture. Addition of MSA to serum-starved L6 myoblasts increased the rate of aminoisobutyrate (AIB) uptake 50-150% within five hours. This early effect on transport was followed by increases in cell number, protein content and 3H-thymidine incorporation. Kinetic analyses indicated that MSA increased the maximal velocity of AIB uptake but had no effect on the KM for AIB. When myoblasts were allowed to fuse (and dividing cells eliminated by addition of 10(-4) M cytosine arabinoside) the AIB transport system(s) remained similarly responsive to MSA. In myoblasts and in myotubes, both the basal and MSA-stimulated rate of AIB uptake were sodium-dependent processes; little stimrulation occurred if sodium was absent from the labeling medium. Further suggesting the involvement of cations in response to hormone, MSA stimulated uptake of the potassium analog, 86Rb+, and increase net intracellular potassium in both myoblasts and myotubes. MSA was active at concentrations equivalent to in vivo levels of somatomedins; neither insulin nor growth hormone had any effect at or near physiological concentrations.