The caspase-8 dimerization/dissociation balance is a highly potent regulator of caspase-8, -3, -6 signaling

A nucleation barrier spring-loads the CBM signalosome for binary activation

Immune cells activate in binary, switch-like fashion via large protein assemblies known as signalosomes, but the molecular mechanism of the switch is not yet understood. Here, we employed an in-cell biophysical approach to dissect the assembly mechanism of the CARD-BCL10-MALT1 (CBM) signalosome, which governs nuclear transcription factor-κB activation in both innate and adaptive immunity. We found that the switch consists of a sequence-encoded and deeply conserved nucleation barrier to ordered polymerization by the adaptor protein BCL10. The particular structure of the BCL10 polymers did not matter for activity. Using optogenetic tools and single-cell transcriptional reporters, we discovered that endogenous BCL10 is functionally supersaturated even in unstimulated human cells, and this results in a predetermined response to stimulation upon nucleation by activated CARD multimers. Our findings may inform on the progressive nature of age-associated inflammation, and suggest that signalosome structure has evolved via selection for kinetic rather than equilibrium properties of the proteins.

The innate immune system is the body’s first line of defence against pathogens. Although innate immune cells do not recognize specific disease-causing agents, they can detect extremely low levels of harmful organisms or substances. In response, they activate signals that lead to inflammation, which tells other cells that there is an infection. Innate immune cells are turned on in a switch-like fashion, becoming active very quickly after interacting with a pathogen. This is due to the action of signalosomes, large complexes made up of several proteins that clump together to form long chains that activate the cell.

But how do these large protein complexes assemble quick enough to create the switch-like activation observed in innate immune cells? To answer this question, Rodríguez Gama et al. focused on the CBM signalosome, which is involved in triggering inflammation through the activation of a protein called NF-kB.

First, Rodríguez Gama et al. used genetic tools to determine that activating the CBM signalosome drives a switch-like activation of NF-kB in cells. This means that individual cells in a population either become fully activated or not at all in response to minute amounts of harmful substances.

Once they had established this, Rodríguez Gama et al. wanted to know which protein in the CBM signalosome was responsible for the switch. They found that one of the proteins in the signalosome, called BCL10, has a ‘nucleation barrier’ encoded in its sequence. This means that it is very hard for BCL10 to start clumping together, but once it does, the clumps grow on their own. The nucleation barrier describes exactly how hard it is for these clumps to get started, and is determined by how disorganized the protein is.

When a pathogen ‘stimulates’ an immune cell, a tiny template is formed that lowers the nucleation barrier so that BCL10 can then aggregate itself together, leading to the switch-like behaviour observed. The nucleation barrier allows there to be more than enough BCL10 present in the cell at all times – ready to clump together at a moment’s notice – and this permits the cell to detect very low levels of a pathogen.

Rodríguez Gama et al. then tested whether BCL10 from other animals also has a nucleation barrier. They found that this feature is conserved from cnidarians, such as corals or jellyfish, to mammals, including humans. This suggests that the use of nucleation barriers to regulate innate immune signalling has existed for a long time throughout evolution.

The work by Rodríguez Gama et al. broadens our understanding of how the innate immune system senses and responds to extremely low levels of pathogens. That BCL10 is always ready to clump together suggests it may be a driving force for chronic and age-associated inflammation. Additionally, the findings of Rodríguez Gama et al. also offer insights into how other signalosomes may become activated, and offer the possibility of new drugs aimed at modifying nucleation barriers.

Molecular Pathogenicity of Enteroviruses Causing Neurological Disease

Enteroviruses are single-stranded positive-sense RNA viruses that primarily cause self-limiting gastrointestinal or respiratory illness. In some cases, these viruses can invade the central nervous system, causing life-threatening neurological diseases including encephalitis, meningitis and acute flaccid paralysis (AFP). As we near the global eradication of poliovirus, formerly the major cause of AFP, the number of AFP cases have not diminished implying a non-poliovirus etiology. As the number of enteroviruses linked with neurological disease is expanding, of which many had previously little clinical significance, these viruses are becoming increasingly important to public health. Our current understanding of these non-polio enteroviruses is limited, especially with regards to their neurovirulence. Elucidating the molecular pathogenesis of these viruses is paramount for the development of effective therapeutic strategies. This review summarizes the clinical diseases associated with neurotropic enteroviruses and discusses recent advances in the understanding of viral invasion of the central nervous system, cell tropism and molecular pathogenesis as it correlates with host responses.

TRAIL receptor signaling: From the basics of canonical signal transduction toward its entanglement with ER stress and the unfolded protein response

The cytokine tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the large TNF superfamily that can trigger apoptosis in transformed or infected cells by binding and activating two receptors, TRAIL receptor 1 (TRAILR1) and TRAIL receptor 2 (TRAILR2). Compared to other death ligands of the same family, TRAIL induces apoptosis preferentially in malignant cells while sparing normal tissue and has therefore been extensively investigated for its suitability as an anti-cancer agent. Recently, it was noticed that TRAIL receptor signaling is also linked to endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). The role of TRAIL receptors in regulating cellular apoptosis susceptibility therefore is broader than previously thought. Here, we provide an overview of TRAIL-induced signaling, covering the core signal transduction during extrinsic apoptosis as well as its link to alternative outcomes, such as necroptosis or NF-κB activation. We discuss how environmental factors, transcriptional regulators, and genetic or epigenetic alterations regulate TRAIL receptors and thus alter cellular TRAIL susceptibility. Finally, we provide insight into the role of TRAIL receptors in signaling scenarios that engage the unfolded protein response and discuss how these findings might be translated into new combination therapies for cancer treatment.

Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform

Ligand binding to death receptors activates apoptosis in cancer cells. Stimulation of death receptors results in the formation of intracellular multiprotein platforms that either activate the apoptotic initiator Caspase-8 to trigger cell death, or signal through kinases to initiate inflammatory and cell survival signalling. Two of these platforms, the Death-Inducing Signalling Complex (DISC) and the RIPoptosome, also initiate necroptosis by building filamentous scaffolds that lead to the activation of mixed lineage kinase domain-like pseudokinase. To explain cell decision making downstream of death receptor activation, we developed a semi-stochastic model of DISC/RIPoptosome formation. The model is a hybrid of a direct Gillespie stochastic simulation algorithm for slow assembly of the RIPoptosome and a deterministic model of downstream caspase activation. The model explains how alterations in the level of death receptor-ligand complexes, their clustering properties and intrinsic molecular fluctuations in RIPoptosome assembly drive heterogeneous dynamics of Caspase-8 activation. The model highlights how kinetic proofreading leads to heterogeneous cell responses and results in fractional cell killing at low levels of receptor stimulation. It reveals that the noise in Caspase-8 activation-exclusively caused by the stochastic molecular assembly of the DISC/RIPoptosome platform-has a key function in extrinsic apoptotic stimuli recognition.

Cognitive Deficits Following a Post-Myocardial Infarct in the Rat Are Blocked by the Serotonin-Norepinephrine Reuptake Inhibitor Desvenlafaxine

Myocardial infarction (MI) in animal models induces cognitive deficits as well as the activation of caspase in the limbic system; both can be blocked by 2 weeks of treatment following MI using tricyclic antidepressants or selective serotonin uptake blockers. Here we used three different treatment schedules to test the short- and long-term effects of the combined serotonin-norepinephrine reuptake inhibitor desvenlafaxine on post-MI-associated cognitive deficits and caspase activation. MI was induced in 39 young adult rats, and 39 rats served as sham-operated controls. Desvenlafaxine (3 mg/kg/day, i.p.) or saline was administered according to one of three schedules: (1) for 2 weeks, starting right after surgery; (2) for 16 weeks, starting 2 weeks after surgery; (3) for 16 weeks, starting right after surgery. Behavior was tested 2 weeks (social interaction, passive avoidance) and 16 weeks (forced swimming, Morris water maze) after surgery. Caspase-3 and caspase-6 activities were measured 16 weeks after surgery. At 2 and 16 weeks post-surgery, saline-treated MI rats displayed performance deficits compared to desvenlafaxine-treated rats, regardless of the treatment schedule. Caspase-3 activity was higher in the amygdala (medial and lateral) and hippocampal CA3 region in untreated MI rats, whereas caspase-6 activity was higher in the CA1 region. Caspase-6 activity correlated positively with deficits in the Morris water maze. These results indicate that, independently of treatment schedules, various treatment schedules with desvenlafaxine can prevent MI-associated cognitive deficits and decrease caspase activities in the limbic system.

Molecular architecture of the DED chains at the DISC: regulation of procaspase-8 activation by short DED proteins c-FLIP and procaspase-8 prodomain

The CD95/Fas/APO-1 death-inducing signaling complex (DISC), comprising CD95, FADD, procaspase-8, procaspase-10, and c-FLIP, has a key role in apoptosis induction. Recently, it was demonstrated that procaspase-8 activation is driven by death effector domain (DED) chains at the DISC. Here, we analyzed the molecular architecture of the chains and the role of the short DED proteins in regulating procaspase-8 activation in the chain model. We demonstrate that the DED chains are largely composed of procaspase-8 cleavage products and, in particular, of its prodomain. The DED chain also comprises c-FLIP and procaspase-10 that are present in 10 times lower amounts compared with procaspase-8. We show that short c-FLIP isoforms can inhibit CD95-induced cell death upon overexpression, likely by forming inactive heterodimers with procaspase-8. Furthermore, we have addressed mechanisms of the termination of chain elongation using experimental and mathematical modeling approaches. We show that neither c-FLIP nor procaspase-8 prodomain terminates the DED chain, but rather the dissociation/association rates of procaspase-8 define the stability of the chain and thereby its length. In addition, we provide evidence that procaspase-8 prodomain generated at the DISC constitutes a negative feedback loop in procaspase-8 activation. Overall, these findings provide new insights into caspase-8 activation in DED chains and apoptosis initiation.

Cell-to-cell variability in cell death: can systems biology help us make sense of it all?

One of the most common observations in cell death assays is that not all cells die at the same time, or at the same treatment dose. Here, using the perspective of the systems biology of apoptosis and the context of cancer treatment, we discuss possible sources of this cell-to-cell variability as well as its implications for quantitative measurements and computational models of cell death. Many different factors, both within and outside of the apoptosis signaling networks, have been correlated with the variable responses to various death-inducing treatments. Systems biology models offer us the opportunity to take a more synoptic view of the cell death process to identify multifactorial determinants of the cell death decision. Finally, with an eye toward 'systems pharmacology', we discuss how leveraging this new understanding should help us develop combination treatment strategies to compel cancer cells toward apoptosis by manipulating either the biochemical state of cancer cells or the dynamics of signal transduction.

Systems biology of death receptor networks: live and let die

The extrinsic apoptotic pathway is initiated by death receptor activation. Death receptor activation leads to the formation of death receptor signaling platforms, resulting in the demolition of the cell. Despite the fact that death receptor-mediated apoptosis has been studied to a high level of detail, its quantitative regulation until recently has been poorly understood. This situation has dramatically changed in the last years. Creation of mathematical models of death receptor signaling led to an enormous progress in the quantitative understanding of the network regulation and provided fascinating insights into the mechanisms of apoptosis control. In the following sections, the models of the death receptor signaling and their biological implications will be addressed. Central attention will be given to the models of CD95/Fas/APO-1, an exemplified member of the death receptor signaling pathways. The CD95 death-inducing signaling complex (DISC) and regulation of CD95 DISC activity by its key inhibitor c-FLIP, have been vigorously investigated by modeling approaches, and therefore will be the major topic here. Furthermore, the non-linear dynamics of the DISC, positive feedback loops and bistability as well as stoichiometric switches in extrinsic apoptosis will be discussed. Collectively, this review gives a comprehensive view how the mathematical modeling supported by quantitative experimental approaches has provided a new understanding of the death receptor signaling network.

Intra- and interdimeric caspase-8 self-cleavage controls strength and timing of CD95-induced apoptosis

Apoptosis in response to the ligand CD95L (also known as Fas ligand) is initiated by caspase-8, which is activated by dimerization and self-cleavage at death-inducing signaling complexes (DISCs). Previous work indicated that the degree of substrate cleavage by caspase-8 determines whether a cell dies or survives in response to a death stimulus. To determine how a death ligand stimulus is effectively translated into caspase-8 activity, we assessed this activity over time in single cells with compartmentalized probes that are cleaved by caspase-8 and used multiscale modeling to simultaneously describe single-cell and population data with an ensemble of single-cell models. We derived and experimentally validated a minimal model in which cleavage of caspase-8 in the enzymatic domain occurs in an interdimeric manner through interaction between DISCs, whereas prodomain cleavage sites are cleaved in an intradimeric manner within DISCs. Modeling indicated that sustained membrane-bound caspase-8 activity is followed by transient cytosolic activity, which can be interpreted as a molecular timer mechanism reflected by a limited lifetime of active caspase-8. The activation of caspase-8 by combined intra- and interdimeric cleavage ensures weak signaling at low concentrations of CD95L and strongly accelerated activation at higher ligand concentrations, thereby contributing to precise control of apoptosis.

Harnessing system models of cell death signalling for cytotoxic chemotherapy: towards personalised medicine approaches?

Most cytotoxic chemotherapeutics are believed to kill cancer cells by inducing apoptosis. Understanding the factors that contribute to impairment of apoptosis in cancer cells is therefore critical for the development of novel therapies that circumvent the widespread chemoresistance. Apoptosis, however, is a complex and tightly controlled process that can be induced by different classes of chemotherapeutics targeting different signalling nodes and pathways. Moreover, apoptosis initiation and apoptosis execution strongly depend on patient-specific, genomic and proteomic signatures. Here, we will review recent translational studies that suggest a critical link between the sensitivity of cancer cells to initiate apoptosis and clinical outcome. Next we will discuss recent advances in the field of system modelling of apoptosis pathways for the prediction of treatment responses. We propose that initiation of mitochondrial apoptosis, defined as the process of mitochondrial outer membrane permeabilisation (MOMP), is a dose-dependent decision process that allows for a prediction of individual therapy responses and therapeutic windows. We provide evidence in contrast that apoptosis execution post-MOMP may be a binary decision that dictates whether apoptosis is executed or not. We will discuss the implications of this concept for the future use of novel adjuvant therapeutics that specifically target apoptosis signalling pathways or which may be used to reduce the impact of cell-to-cell heterogeneity on therapy responses. Finally, we will discuss the technical and regulatory requirements surrounding the use and implications of system-based patient stratification tools for the future of personalised oncology.

Systems modelling methodology for the analysis of apoptosis signal transduction and cell death decisions

Systems biology and systems medicine, i.e. the application of systems biology in a clinical context, is becoming of increasing importance in biology, drug discovery and health care. Systems biology incorporates knowledge and methods that are applied in mathematics, physics and engineering, but may not be part of classical training in biology. We here provide an introduction to basic concepts and methods relevant to the construction and application of systems models for apoptosis research. We present the key methods relevant to the representation of biochemical processes in signal transduction models, with a particular reference to apoptotic processes. We demonstrate how such models enable a quantitative and temporal analysis of changes in molecular entities in response to an apoptosis-inducing stimulus, and provide information on cell survival and cell death decisions. We introduce methods for analyzing the spatial propagation of cell death signals, and discuss the concepts of sensitivity analyses that enable a prediction of network responses to disturbances of single or multiple parameters.

PI3K inhibition potentiates Bcl-2-dependent apoptosis in renal carcinoma cells

Inhibitors of PI3-K/Akt are currently being assessed clinically in patients with advanced RCC. Identification of therapeutic strategies that might enhance the efficacy of PI3-K/Akt inhibitors is therefore of great interest. As PI3-K inhibition would be expected to have many pro-apoptotic effects, we hypothesized that there may be unique synergy between PI3-K inhibitors and BH3-mimetics. Towards this end, we assessed the combination of the PI3K inhibitor LY 294002 and the Bcl-2 family inhibitor ABT-737 in RCC cell lines. We found that the combinatorial treatment with these agents led to a significant increase in PARP cleavage and cell death in all RCC cell lines. The synergized cell death was correlated with decreased levels of Mcl-1 and XIAP, and increased levels in Bim, and appears critically dependent upon the activation of caspase 3 and 8. The enhanced lethality observed with the combination also appears dependent upon the regulation of XIAP, Mcl-1 and Bim levels. Our results suggest that the combination of PI3-K inhibitors with BH3-mimetics may be a viable therapeutic strategy in RCC.

Stress-inducible caspase substrate TRB3 promotes nuclear translocation of procaspase-3

Pseudokinase TRB3 is a stress-inducible nuclear protein, which has recently been shown to be involved in ER stress-induced apoptosis. However, it remains unclear how TRB3 contributes to the process. We recently demonstrated that TRB3 was cleaved by caspase-3 (CASP3) in vitro and also in apoptosis-induced cells. Thus, we investigate the role of TRB3 cleavage in the apoptotic process to address the above question. Overexpression studies revealed that the cleavage of TRB3 promoted CASP3/7 activation and apoptosis. In contrast, the anti-apoptotic effects were found under TRB3 non-cleavable conditions, such as ER stress, and also when the CASP3/7 activation was enhanced by knockdown of endogenous TRB3 expression. Interestingly, nuclear translocation of procaspase-3 (proCASP3) was observed in cells either overexpressing TRB3 or under tunicamycin-induced ER stress. Although forced cytoplasmic expression of proCASP3 enhanced apoptosis significantly, its nuclear expression did not produce any pro-apoptotic effect, suggesting that nuclear distribution of proCASP3 is not critical for the execution of apoptosis. Thus, TRB3 might prevent cytoplasmic activation of CASP3 by promoting proCASP3 entry into the nucleus, and thereby inhibit apoptosis. Taken together, our results suggest that TRB3, through its own cleavage, functions as a molecular switch between the cell survival and apoptotic pathways under stressful conditions.

Intrinsic cleavage of receptor-interacting protein kinase-1 by caspase-6

Necroptosis is a form of programmed cell death that occurs in the absence of caspase activation and depends on the activity of the receptor-interacting protein kinases. Inactivation of these kinases by caspase-mediated cleavage has been shown to be essential for successful embryonic development, survival and activation of certain cell types. The initiator of extrinsic apoptosis, caspase-8, which has a pro-death as well as a pro-life function, has been assigned this role. In the present study we demonstrate that caspase-6, an executioner caspase, performs this role during apoptosis induced through the intrinsic pathway. In addition, we demonstrate that in the absence of caspase activity, intrinsic triggers of apoptosis induce the receptor-interacting-kinase-1-dependent production of pro-inflammatory cytokines. We show that ubiquitously expressed caspase-6 has a supporting role in apoptosis by cleaving this kinase, thus preventing production of inflammatory cytokines as well as inhibiting the necroptotic pathway. These findings shed new light on the regulation of necroptosis as well as cell death in an inflammatory environment wherein cells receive both intrinsic and extrinsic death signals.

Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes

The TNF-R1 like receptor Fas is highly expressed on the plasma membrane of hepatocytes and plays an essential role in liver homeostasis. We recently showed that in collagen-cultured primary mouse hepatocytes, Fas stimulation triggers apoptosis via the so-called type I extrinsic signaling pathway. Central to this pathway is the direct caspase-8-mediated cleavage and activation of caspase-3 as compared to the type II pathway which first requires caspase-8-mediated Bid cleavage to trigger mitochondrial cytochrome c release for caspase-3 activation. Mathematical modeling can be used to understand complex signaling systems such as crosstalks and feedback or feedforward loops. A previously published model predicted a positive feedback loop between active caspases-3 and -8 in both type I and type II FasL signaling in lymphocytes and Hela cells, respectively. Here we experimentally tested this hypothesis in our hepatocytic type I Fas signaling pathway by using wild-type and XIAP-deficient primary hepatocytes and two recently characterized, selective caspase-3/-7 inhibitors (AB06 and AB13). Caspase-3/-7 activity assays and quantitative western blotting confirmed that fully processed, active p17 caspase-3 feeds back on caspase-8 by cleaving its partially processed p43 form into the fully processed p18 species. Our data do not discriminate if p18 positively or negatively influences FasL-induced apoptosis or is responsible for non-apoptotic aspects of FasL signaling. However, we found that caspase-3 also feeds back on Bid and degrades its own inhibitor XIAP, both events that may enhance caspase-3 activity and apoptosis. Thus, potent, selective caspase-3 inhibitors are useful tools to understand complex signaling circuitries in apoptosis.

A visual analytics approach for models of heterogeneous cell populations

In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in most populations of primary cells, cancer cells, and stem cells. Unfortunately, tools for in-depth analysis of population models are still missing. This problem originates from the complexity of population models. Particularly important are methods to determine the source of heterogeneity (e.g., genetics or epigenetic differences) and to select potential (bio-)markers. We propose an analysis based on visual analytics to tackle this problem. Our approach combines parallel-coordinates plots, used for a visual assessment of the high-dimensional dependencies, and nonlinear support vector machines, for the quantification of effects. The method can be employed to study qualitative and quantitative differences among cells. To illustrate the different components, we perform a case study using the proapoptotic signal transduction pathway involved in cellular apoptosis.

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.

Stratified corneal limbal epithelial cells are protected from UVB-induced apoptosis by elevated extracellular K⁺

The goal of this study was to determine whether elevated [K(+)] protects stratified corneal epithelial cells from entering apoptosis following exposure to ambient levels of UVB radiation. Human corneal limbal epithelial (HCLE) cells were stratified to form multilayered constructs in culture. The cells were exposed to UVB doses of 100-250 mJ/cm(2) followed by incubation in medium with 5.5-100 mM K(+). The protective effect of K(+) was determined by measuring the caspase-3 and -8 activity and TUNEL staining of the stratified HCLE constructs. In response to UVB exposure, activation of apoptotic pathways peaked at 24 h. Caspase-8 in stratified cells was activated by exposure to UVB at 100-250 mJ/cm(2), and activity was significantly reduced in response to 50 or 100 mM K(+). Caspase-3 was activated in the stratified cells in response to 100-250 mJ/cm(2) UVB and showed a significant reduction in activity in response to 25, 50 or 100 mM K(+). DNA fragmentation, as indicated by TUNEL staining, was elevated after exposure to 200 mJ/cm(2) UVB, and decreased following incubation with 25-100 mM K(+). These results show that in a culture system that models the intact corneal epithelium, elevated extracellular K(+) can reduce UVB-induced apoptosis which is believed to be initiated by loss of K(+) from cells. This is the basis of damage to the corneal epithelium caused by UVB exposure. Based on these observations it is suggested that the relatively high K(+) concentration in tears (20-25 mM) may play a role in protecting the corneal epithelium from ambient UVB radiation.

A bifunctional allosteric site in the dimer interface of procaspase-3

The dimer interface of caspase-3 contains a bifunctional allosteric site in which the enzyme can be activated or inactivated, depending on the context of the protein. In the mature caspase-3, the binding of allosteric inhibitors to the interface results in an order-to-disorder transition in the active site loops. In procaspase-3, by contrast, the binding of allosteric activators to the interface results in a disorder-to-order transition in the active site. We have utilized the allosteric site to identify a small molecule activator of procaspase and to characterize its binding to the protease. The data suggest that an efficient activator must stabilize the active conformer of the zymogen by expelling the intersubunit linker from the interface, and it must interact with active site residues found in the allosteric site. Small molecule activators that fulfill the two requirements should provide scaffolds for drug candidates as a therapeutic strategy for directly promoting procaspase-3 activation in cancer cells.

Measuring and modeling apoptosis in single cells

Cell death plays an essential role in the development of tissues and organisms, the etiology of disease, and the responses of cells to therapeutic drugs. Here we review progress made over the last decade in using mathematical models and quantitative, often single-cell, data to study apoptosis. We discuss the delay that follows exposure of cells to prodeath stimuli, control of mitochondrial outer membrane permeabilization, switch-like activation of effector caspases, and variability in the timing and probability of death from one cell to the next. Finally, we discuss challenges facing the fields of biochemical modeling and systems pharmacology.

Ion channel inhibitors block caspase activation by mechanisms other than restoring intracellular potassium concentration

Ion fluxes at the plasma membrane have an important role in early stages of apoptosis. Accordingly, plasma membrane depolarization and gain of Na(+) and loss of K(+) are initial events in apoptosis. We have studied the effect of staurosporine (STS), a well-established apoptosis inducer, on the membrane potential of HeLa cells to determine the nature of STS-activated ion conductances and their role in the activation of different caspases. We observed that STS can activate tetraethylammonium (TEA(+)) and 4-aminopyridine-sensitive K(+) channels and flufenamic-sensitive cation channels as an early response. The combination of these ion channel inhibitors significantly reduced cytochrome c (cyt c) release and activation of caspase-9, -3 and -8. STS also induced a large reduction in the intracellular [K(+)] that was not blocked by the ion channel inhibitors. Our data suggest that reduction in the [K(+)](i) is necessary but not sufficient and that ion channel inhibitors block activation of caspase-3 by two different mechanisms: the inhibitors of K(+) channels by reducing cyt c release while flufenamic acid by a different, unrelated mechanism that does not involve cation channels at the plasma membrane. Our data also imply that these ion channels activated by STS are not responsible for the reduction in the [K(+)](i) associated with apoptosis.