Cancer cells are widely known to be protected from apoptosis,a phenomenon that is a major hurdle to successful anticancer therapy.Over-expression of several anti-apoptotic proteins,or mutations in proapoptotic factors...Cancer cells are widely known to be protected from apoptosis,a phenomenon that is a major hurdle to successful anticancer therapy.Over-expression of several anti-apoptotic proteins,or mutations in proapoptotic factors,has been recognized to confer such resistance.Development of new experimental strategies,such as in silico modeling of biological pathways,can increase our understanding of how abnormal regulation of apoptotic pathway in cancer cells can lead to tumour chemoresistance.Monte Carlo simulations are in particular well suited to study inherent variability,such as spatial heterogeneity and cell-to-cell variations in signaling reactions.Using this approach,often in combination with experimental validation of the computational model,we observed that large cell-to-cell variability could explain the kinetics of apoptosis,which depends on the type of pathway and the strength of stress stimuli.Most importantly,Monte Carlo simulations of apoptotic signaling provides unexpected insights into the mechanisms of fractional cell killing induced by apoptosis-inducing agents,showing that not only variation in protein levels,but also inherent stochastic variability in signaling reactions,can lead to survival of a fraction of treated cancer cells.展开更多
Death ligand mediated apoptotic activation is a mode of cell death that is widely used in cellular and physiological situations. Interest in studying death ligand induced apoptosis has increased due to the promising r...Death ligand mediated apoptotic activation is a mode of cell death that is widely used in cellular and physiological situations. Interest in studying death ligand induced apoptosis has increased due to the promising role of recombinant soluble forms of death ligands (mainly recombinant TRAIL) in anti-cancer therapy. A clear elucidation of how death ligands activate the type 1 and type 2 apoptotic pathways in healthy and cancer cells may help develop better chemotherapeutic strategies. In this work, we use kinetic Monte Carlo simulations to address the problem of type 1/ type 2 choice in death ligand mediated apoptosis of cancer cells. Our study provides insights into the activation of membrane proximal death module that results from complex interplay between death and decoy receptors. Relative abundance of death and decoy receptors was shown to be a key parameter for activation of the initiator caspases in the membrane module. Increased concentration of death ligands frequently increased the type 1 activation fraction in cancer cells, and, in certain cases changed the signaling phenotype from type 2 to type 1. Results of this study also indicate that inherent differences between cancer and healthy cells, such as in the membrane module, may allow robust activation of cancer cell apoptosis by death ligand induction. At the same time, large cell-to-cell variability through the type 2 pathway was shown to provide protection for healthy cells. Such elucidation of selective activation of apoptosis in cancer cells addresses a key question in cancer biology and cancer therapy.展开更多
B-cell receptor signaling in response to membrane-bound antigen increases with antigen affinity,a process known as affinity discrimination.We use computational modeling to show that B-cell affinity discrimination requ...B-cell receptor signaling in response to membrane-bound antigen increases with antigen affinity,a process known as affinity discrimination.We use computational modeling to show that B-cell affinity discrimination requires that kinetic proofreading predominate over serial engagement.We find that if B-cell receptors become signaling-capable immediately upon antigen binding,which results in decreasing serial engagement as affinity increases,then increasing affinity can lead to weaker signaling.Rather,antigen must stay bound to B-cell receptors for a threshold time of several seconds before becoming signaling-capable,a process similar to kinetic proofreading.This process overcomes the loss in serial engagement due to increasing antigen affinity,and replicates the monotonic increase in B-cell signaling with increasing affinity that has been observed in B-cell activation experiments.This finding matches well with the experimentally observed time(,20 s)required for the B-cell receptor signaling domains to undergo antigen and lipid raft-mediated conformational changes that lead to Src-family kinase recruitment.We hypothesize that the physical basis for a threshold time of antigen binding might lie in the formation timescale of B-cell receptor dimers.The time required for dimer formation decreases with increasing antigen affinity,thereby resulting in shorter threshold antigen binding times as affinity increases.Such an affinity-dependent kinetic proofreading requirement results in affinity discrimination very similar to that observed in biological experiments.B-cell affinity discrimination is critical to the process of affinity maturation and the production of high-affinity antibodies,and thus our results have important implications in applications such as vaccine design.展开更多
It is known from experiments that in the presence of soluble antigen,B-cell receptors(BCRs)assemble into microclusters and then collect into a macrocluster known as a‘cap’.However,the mechanisms of BCR cluster forma...It is known from experiments that in the presence of soluble antigen,B-cell receptors(BCRs)assemble into microclusters and then collect into a macrocluster known as a‘cap’.However,the mechanisms of BCR cluster formation during recognition of soluble antigens remain unclear.In previous work,we demonstrated that effective intrinsic attractions among BCRs can lead to the formation of small microclusters of BCR molecules.The effective intrinsic attractions could be caused by multivalent antigen binding,association with lipid rafts,or other biochemical factors.In the present study,we have developed and studied a Monte Carlo model of BCR clustering mediated by explicit binding and crosslinking of soluble bivalent antigens.Antigen crosslinking is shown to microcluster BCRs in an affinity-dependent manner and also in a biologically relevant timescale;however,antigen crosslinking alone does not appear to be sufficient for the formation of a single macrocluster of receptor molecules.We show that directed transport of BCRs is needed to drive the formation of large macroclusters.We constructed a simple model of directed transport,where BCR molecules diffuse towards the largest cluster or towards a random BCR microcluster,which results in a single macrocluster of receptor molecules.The mechanisms for both types of directed transport are compared using network-based metrics.We also develop and use appropriate network measures to analyze the effect of BCR and antigen concentration on BCR clustering,the stability of the formed clusters over time and the size of BCR–antigen crosslinked chains.展开更多
文摘Cancer cells are widely known to be protected from apoptosis,a phenomenon that is a major hurdle to successful anticancer therapy.Over-expression of several anti-apoptotic proteins,or mutations in proapoptotic factors,has been recognized to confer such resistance.Development of new experimental strategies,such as in silico modeling of biological pathways,can increase our understanding of how abnormal regulation of apoptotic pathway in cancer cells can lead to tumour chemoresistance.Monte Carlo simulations are in particular well suited to study inherent variability,such as spatial heterogeneity and cell-to-cell variations in signaling reactions.Using this approach,often in combination with experimental validation of the computational model,we observed that large cell-to-cell variability could explain the kinetics of apoptosis,which depends on the type of pathway and the strength of stress stimuli.Most importantly,Monte Carlo simulations of apoptotic signaling provides unexpected insights into the mechanisms of fractional cell killing induced by apoptosis-inducing agents,showing that not only variation in protein levels,but also inherent stochastic variability in signaling reactions,can lead to survival of a fraction of treated cancer cells.
文摘Death ligand mediated apoptotic activation is a mode of cell death that is widely used in cellular and physiological situations. Interest in studying death ligand induced apoptosis has increased due to the promising role of recombinant soluble forms of death ligands (mainly recombinant TRAIL) in anti-cancer therapy. A clear elucidation of how death ligands activate the type 1 and type 2 apoptotic pathways in healthy and cancer cells may help develop better chemotherapeutic strategies. In this work, we use kinetic Monte Carlo simulations to address the problem of type 1/ type 2 choice in death ligand mediated apoptosis of cancer cells. Our study provides insights into the activation of membrane proximal death module that results from complex interplay between death and decoy receptors. Relative abundance of death and decoy receptors was shown to be a key parameter for activation of the initiator caspases in the membrane module. Increased concentration of death ligands frequently increased the type 1 activation fraction in cancer cells, and, in certain cases changed the signaling phenotype from type 2 to type 1. Results of this study also indicate that inherent differences between cancer and healthy cells, such as in the membrane module, may allow robust activation of cancer cell apoptosis by death ligand induction. At the same time, large cell-to-cell variability through the type 2 pathway was shown to provide protection for healthy cells. Such elucidation of selective activation of apoptosis in cancer cells addresses a key question in cancer biology and cancer therapy.
基金The authors thank Dr Emanual Maverakis,Dr Aaron Dinner and Dr Stephen Kaattari for proofreading the manuscript and offering valuable advice.PT and SR are supported by NIH grant AI074022.
文摘B-cell receptor signaling in response to membrane-bound antigen increases with antigen affinity,a process known as affinity discrimination.We use computational modeling to show that B-cell affinity discrimination requires that kinetic proofreading predominate over serial engagement.We find that if B-cell receptors become signaling-capable immediately upon antigen binding,which results in decreasing serial engagement as affinity increases,then increasing affinity can lead to weaker signaling.Rather,antigen must stay bound to B-cell receptors for a threshold time of several seconds before becoming signaling-capable,a process similar to kinetic proofreading.This process overcomes the loss in serial engagement due to increasing antigen affinity,and replicates the monotonic increase in B-cell signaling with increasing affinity that has been observed in B-cell activation experiments.This finding matches well with the experimentally observed time(,20 s)required for the B-cell receptor signaling domains to undergo antigen and lipid raft-mediated conformational changes that lead to Src-family kinase recruitment.We hypothesize that the physical basis for a threshold time of antigen binding might lie in the formation timescale of B-cell receptor dimers.The time required for dimer formation decreases with increasing antigen affinity,thereby resulting in shorter threshold antigen binding times as affinity increases.Such an affinity-dependent kinetic proofreading requirement results in affinity discrimination very similar to that observed in biological experiments.B-cell affinity discrimination is critical to the process of affinity maturation and the production of high-affinity antibodies,and thus our results have important implications in applications such as vaccine design.
基金ASR,PKT and SR are supported from National Institutes of Health grant AI074022.
文摘It is known from experiments that in the presence of soluble antigen,B-cell receptors(BCRs)assemble into microclusters and then collect into a macrocluster known as a‘cap’.However,the mechanisms of BCR cluster formation during recognition of soluble antigens remain unclear.In previous work,we demonstrated that effective intrinsic attractions among BCRs can lead to the formation of small microclusters of BCR molecules.The effective intrinsic attractions could be caused by multivalent antigen binding,association with lipid rafts,or other biochemical factors.In the present study,we have developed and studied a Monte Carlo model of BCR clustering mediated by explicit binding and crosslinking of soluble bivalent antigens.Antigen crosslinking is shown to microcluster BCRs in an affinity-dependent manner and also in a biologically relevant timescale;however,antigen crosslinking alone does not appear to be sufficient for the formation of a single macrocluster of receptor molecules.We show that directed transport of BCRs is needed to drive the formation of large macroclusters.We constructed a simple model of directed transport,where BCR molecules diffuse towards the largest cluster or towards a random BCR microcluster,which results in a single macrocluster of receptor molecules.The mechanisms for both types of directed transport are compared using network-based metrics.We also develop and use appropriate network measures to analyze the effect of BCR and antigen concentration on BCR clustering,the stability of the formed clusters over time and the size of BCR–antigen crosslinked chains.
