On multi-strain model for Hepatitis C

In this paper we present a multi-strain model for hepatitis C virus (HCV) including an immune response term. The model is presented and discussed. Also we argue that the added multi-strain term represents some basic properties of the immune system and that it should be included to study longer term behavior of the disease.     

On modeling two immune effectors two strain antigen interaction

In this paper we consider the fractional order model with two immune effectors interacting with two strain antigen. The systems may explain the recurrence of some diseases e.g. tuberculosis (TB). The stability of equilibrium points are studied. Numerical solutions of this model are given. Using integer order system the system oscillates. Using fractional order system the system converges to a stable internal equilibrium. Ulam-Hyers stability of the system has been studied.     

A chronic viral infection model with immune impairment

In this paper, a chronic viral infection model with cell-mediated immunity and immune impairment is proposed and studied, under the assumption that the presence of the antigen can both stimulate and impair immunity. It is shown that the virus persists in the host if the basic reproductive ratio of the virus is greater than 1. The immune cells persist when there is only one positive equilibrium. The system can exhibit two positive equilibria if the basic reproductive ratio of the virus is above a threshold. This allows a bistable behavior, and the immune cells persist or die out, i.e., infection will result in disease or immune control outcome, depending on the initial conditions. By theoretical analysis and numerical simulations, we show that therapy could shift the patient from a disease progression to an immune control outcome, despite that the therapy is not necessarily lifelong. This would allow the immune response to control the virus in the long term even in the absence of continued therapy.     

Oscillations and temporal signalling in cells

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce oscillations in gene expression or protein concentration using a framework of simple mathematical models. We focus on three eukaryotic genetic regulatory networks which show 'ultradian' oscillations, with a time period of the order of hours, and involve, respectively, proteins important for development (Hes1), apoptosis (p53) and immune response (NF-kappaB). We argue that underlying all three is a common design consisting of a negative feedback loop with time delay which is responsible for the oscillatory behaviour.     

A Single-Parameter Model of the Immune Response to Bacterial Invasion

The human immune response to bacterial pathogens is a remarkably complex process, involving many different cell types, chemical signals, and extensive lines of communication. Mathematical models of this system have become increasingly high-dimensional and complicated, as researchers seek to capture many of the major dynamics. In this paper, we argue that, in some important instances, preference should be given to low-dimensional models of immune response, as opposed to their high-dimensional counterparts. One such model is analyzed and shown to reflect many of the key phenomenological properties of the immune response in humans. Notably, this model includes a single parameter that, when combined with a single set of reference parameter values, may be used to quantify the overall immunocompetence of individual hosts.     

Residual Baculovirus in Insect Cell-Derived Influenza Virus-Like Particle Preparations Enhances Immunogenicity

Influenza virus-like particles are currently evaluated in clinical trials as vaccine candidates for influenza viruses. Most commonly they are produced in baculovirus- or mammalian- expression systems. Here we used different vaccination schemes in order to systematically compare virus-like particle preparations generated in the two systems. Our work shows significant differences in immunogenicity between the two, and indicates superior and broader immune responses induced by the baculovirus-derived constructs. We demonstrate that these differences critically influence protection and survival in a mouse model of influenza virus infection. Finally, we show that the enhanced immunogenicity of the baculovirus-derived virus-like particles is caused by contamination with residual baculovirus which activates the innate immune response at the site of inoculation.     

Towards understanding the immune system

It is proposed that using both self–non–self and danger theories give a better understanding of how the immune system works. It is proposed that comparing the immune system to the police force is useful in this case since the police respond both to danger or damage signals and foreign or suspicious behavior even if no danger signals existed. We also propose that due to low zone tolerance, immunotherapy needs to be combined with another treatment method for cancer, e.g., chemotherapy or/and radiotherapy, to get sufficient eradication of tumors. Finally, we propose that fractional order differential equations are more suitable than the familiar integer order differential equations. A fractional order example of two immune effectors attacking an antigen is given.     

Consensual immunity: success-driven development of T-helper-1 and T-helper-2 responses

Non-germline-encoded T- and B-cell receptors allow humans to effectively deal with rapidly mutating pathogens. Here, we argue that, in addition to determining the antigenic specificity of immune responses, the same receptor systems can also regulate the T-helper-1/T-helper-2 profile of immunity. Such a mechanism--based on feedback from distinct effector cells to dendritic cells, rather than on instruction from pathogens--uses the effectiveness of particular effector cells at targeting and destroying a pathogen as a reliable, experience-based criterion to induce and maintain the appropriately polarized response.     

Dynamics and potential impact of the immune response to chronic myelogenous leukemia

Recent mathematical models have been developed to study the dynamics of chronic myelogenous leukemia (CML) under imatinib treatment. None of these models incorporates the anti-leukemia immune response. Recent experimental data show that imatinib treatment may promote the development of anti-leukemia immune responses as patients enter remission. Using these experimental data we develop a mathematical model to gain insights into the dynamics and potential impact of the resulting anti-leukemia immune response on CML. We model the immune response using a system of delay differential equations, where the delay term accounts for the duration of cell division. The mathematical model suggests that anti-leukemia T cell responses may play a critical role in maintaining CML patients in remission under imatinib therapy. Furthermore, it proposes a novel concept of an “optimal load zone” for leukemic cells in which the anti-leukemia immune response is most effective. Imatinib therapy may drive leukemic cell populations to enter and fall below this optimal load zone too rapidly to sustain the anti-leukemia T cell response. As a potential therapeutic strategy, the model shows that vaccination approaches in combination with imatinib therapy may optimally sustain the anti-leukemia T cell response to potentially eradicate residual leukemic cells for a durable cure of CML. The approach presented in this paper accounts for the role of the anti-leukemia specific immune response in the dynamics of CML. By combining experimental data and mathematical models, we demonstrate that persistence of anti-leukemia T cells even at low levels seems to prevent the leukemia from relapsing (for at least 50 months). As a consequence, we hypothesize that anti-leukemia T cell responses may help maintain remission under imatinib therapy. The mathematical model together with the new experimental data imply that there may be a feasible, low-risk, clinical approach to enhancing the effects of imatinib treatment.     

Different immune correlates associated with tumor progression and regression: implications for prevention and treatment of cancer

Observations show that humans and animals respond immunologically to most cancers. Why does the immune system then fail to control cancer? We argue from the literature that there is a commonality in the regulation of responses against most murine tumors, and that a major mechanism of escape may be deviation of an effective Th1, cytotoxic T lymphocyte response to a less effective response with a Th2 component. We examined this hypothesis with two well-studied murine tumors. We found, following primary tumor implantation, that resistance correlates with Th1 responses and IgG2a antibody production and progression with mixed Th1/Th2 responses and production of IgG1 and IgG2a antibodies. Resistance is associated with a modulation of the anti-tumor response towards the Th1 pole in both systems. We conclude that the immune responses against these two tumors are in accord with our hypothesis, and argue that this is likely to be true of many human and murine tumors. The correlation of IgG isotype of anti-tumor antibody with the Th1/Th2 nature of the anti-tumor response readily allows one to longitudinally monitor the changing nature of the anti-tumor response. We suggest that such monitoring can guide immunotherapy to maximize the effectiveness of the host’s immune response against cancer.     

Differential production of IL-2 and IL-4 mRNA in vivo after primary sensitization

The study of lymphokines has been almost entirely conducted by utilizing in vitro assay systems, long term cell lines, and clones. Thus, little information is available concerning the production of lymphokines/cytokines in vivo after specific antigenic stimulation. In order to address this limitation, we have modified the mRNA phenotyping system to allow for the quantitation of lymphokine mRNA after antigenic stimulation in vivo. We report here the production of both IL-2 and IL-4 mRNA in vivo after primary sensitization with picryl chloride. However, the time course of IL-2 and IL-4 mRNA production is discordant. The majority of IL-2 mRNA expression occurs from 1 to 3 days after antigenic exposure, whereas IL-4 mRNA expression occurs mainly from day 3 through day 5. Thus, the production in vivo of these two lymphokine mRNA after sensitization with picryl chloride appears to occur as a "cascade." These results 1) demonstrate that IL-4 mRNA is induced during a primary immune response in vivo and 2) raise the possibility that the generation of an immune response in vivo may involve a specific sequential production of certain lymphokines.     

Resistance of short term activated T cells to CD95-mediated apoptosis correlates with de novo protein synthesis of c-FLIPshort

In the early phase of an immune response, T cells are activated and acquire effector functions. Whereas these short term activated T cells are resistant to CD95-mediated apoptosis, activated T cells in prolonged culture are readily sensitive, leading to activation-induced cell death and termination of the immune response. The translation inhibitor, cycloheximide, partially overcomes the apoptosis resistance of short term activated primary human T cells. Using this model we show in this study that sensitization of T cells to apoptosis occurs upstream of mitochondria. Neither death-inducing signaling complex formation nor expression of Bcl-2 proteins is altered in sensitized T cells. Although the caspase-8 inhibitor c-FLIP(long) was only slightly down-regulated in sensitized T cells, c-FLIP(short) became almost undetectable. This correlated with caspase-8 activation and apoptosis. These data suggest that c-FLIP(short), rather than c-FLIP(long), confers resistance of T cells to CD95-mediated apoptosis in the context of immune responses.     

Contributions of memory B cells to secondary immune response

The secondary immune response is one of the most important features of immune systems. During the secondary immune response, the immune system can eliminate the antigen, which has been encountered by the individual during the primary invasion, more rapidly and efficiently. Both T and B memory cells contribute to the secondary response. In this paper, we only concentrate on the functions of memory B cells. We explore a model describing the memory contributed by the specific long-lived clone which is maintained by continued stimulation with a small amount of antigens sequestered on the surfaces of the follicular dendritic cells (FDC). The behavior of the secondary response provided by the model can be compared with experimental observations. The model shows that memory B cells indeed play an important role in the secondary response. It is found that a single memory cell in a long-lived clone may not be long-lived. In the present note, the influences of relevant parameters on the secondary response are also explored.     

Spleen cells derived from male non-obese diabetic mice are capable of suppressing the autoantigen-specific production of interferon-gamma of female cells in vitro

Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes with a strong female predilection. Using co-culture systems with both female and male spleen cells, we found that spleen cells derived from male NOD mice suppress autoantigen (glutamic acid decarboxylase) induced production of interferon-gamma of female cells in vitro. In addition, this suppression appeared to be mediated by a soluble factor(s) produced by male cells in response to the same antigen. Our experimental systems might be useful for further understanding sex differences in autoimmunity as well as in the basic immune response.     

The Danger Is Growing! A New Paradigm for Immune System Activation and Peripheral Tolerance

Successful immune defense is a complex balancing act. In order to protect a host against invasion by harmful pathogens, an immune response must be rapid and vigorous, and must eliminate foreign invaders before their populations grow beyond control. That same immune response, however, must be selective enough to recognize and ignore commensal bacteria, environmental antigens and host tissue itself. How the immune system makes the crucial decision whether or not to attack a particular antigen has been a long-standing question central to the study of immunology. Here we show that the structure of the signaling network between regulatory T-cells and type 17 helper T-cells allows the immune system to selectively attack pathogens based on whether or not the pathogens represent a growing, and thus dangerous population. We term this mechanism for immune system activation the ‘Growth Detection Paradigm’, because it offers an entirely new explanation for immune system regulation and peripheral tolerance.     

The intrinsic immunogenic properties of cancer cell lines,immunogenic cell death,and how these influence host antitumor immune responses

Modern cancer therapies often involve the combination of tumor-directed cytotoxic strategies and generation of a host antitumor immune response. The latter is unleashed by immunotherapies that activate the immune system generating a more immunostimulatory tumor microenvironment and a stronger tumor antigen-specific immune response. Studying the interaction between antitumor cytotoxic therapies, dying cancer cells, and the innate and adaptive immune system requires appropriate experimental tumor models in mice. In this review, we discuss the immunostimulatory and immunosuppressive properties of cancer cell lines commonly used in immunogenic cell death (ICD) studies being apoptosis or necroptosis. We will especially focus on the antigenic component of immunogenicity. While in several cancer cell lines the epitopes of endogenously expressed tumor antigens are known, these intrinsic epitopes are rarely determined in experimental apoptotic or necroptotic ICD settings. Instead by far the most ICD research studies investigate the antigenic response against exogenously expressed model antigens such as ovalbumin or retroviral epitopes (e.g., AH1). In this review, we will argue that the immune response against endogenous tumor antigens and the immunopeptidome profile of cancer cell lines affect the eventual biological readouts in the typical prophylactic tumor vaccination type of experiments used in ICD research, and we will propose additional methods involving immunopeptidome profiling, major histocompatibility complex molecule expression, and identification of tumor-infiltrating immune cells to document intrinsic immunogenicity following different cell death modalities.Subject terms: Cancer models, Antigen-presenting cells, Immune cell death     

果蝇先天性免疫研究进展

果蝇是生命科学与人类疾病研究的重要模式生物,虽然不具有人类高度专一的获得性免疫,但也有对病原微生物感染作出快速有效反应的先天性免疫应答系统,主要包括体液免疫,细胞免疫和黑化反应。文章结合国外最新研究,详细介绍果蝇体液免疫中控制抗菌肽合成的Toll信号通路和Imd信号通路中涉及的蛋白及其相互作用,并对果蝇细胞免疫中的吞噬、包埋功能和黑化反应作简要阐述。研究表明,果蝇的Toll和Imd信号通路分别与人类的TLR4和TNRF-1信号通路存在着惊人的相似之处,说明果蝇与人类在免疫调控通路方面可能存在着共同的进化起源。     

Viral dynamics model with CTL immune response incorporating antiretroviral therapy

We present two HIV models that include the CTL immune response, antiretroviral therapy and a full logistic growth term for uninfected $\text{ CD4}^+$ T-cells. The difference between the two models lies in the inclusion or omission of a loss term in the free virus equation. We obtain critical conditions for the existence of one, two or three steady states, and analyze the stability of these steady states. Through numerical simulation we find substantial differences in the reproduction numbers and the behaviour at the infected steady state between the two models, for certain parameter sets. We explore the effect of varying the combination drug efficacy on model behaviour, and the possibility of reconstituting the CTL immune response through antiretroviral therapy. Furthermore, we employ Latin hypercube sampling to investigate the existence of multiple infected equilibria.     

Control and inhibition analysis of complex formation processes

ABSTRACT: BACKGROUND: Proteolytic degradation of the extracellular matrix (ECM) is a key event in tumour metastasis and invasion. Matrix metalloproteinases (MMPs) are a family of endopeptidases that degrade most of the components of the ECM. Several broad-spectrum MMP inhibitors (MMPIs) have been developed, but have had little success due to side effects. Thus, it is important to develop mathematical methods to provide new drug treatment strategies. Matrix metalloproteinase 2 (MMP2) activation occurs via a mechanism involving complex formation that consists of membrane type 1 MMP (MT1-MMP), tissue inhibitor of matrix metalloproteinase 2 (TIMP2) and MMP2. Here, we focus on developing a method for analysing the complex formation process. RESULTS: We used control analysis to investigate inhibitor responses in complex formation processes. The essence of the analysis is to define the response coefficient which measures the inhibitory efficiency, a small fractional change of concentration of a targeting molecule in response to a small fractional change of concentration of an inhibitor. First, by using the response coefficient, we investigated models for general classes of complex formation processes: chain reaction systems composed of ordered steps, and chain reaction systems and site-binding reaction systems composed of unordered multi-branched steps. By analysing the ordered step models, we showed that parameter-independent inequalities between the response coefficients held. For the unordered multi-branched step models, we showed that independence of the response coefficients with respect to equilibrium constants held. As an application of our analysis, we discuss a mathematical model for the MMP2 activation process. By putting the experimentally derived parameter values into the model, we were able to conclude that the TIMP2 and MMP2 interaction is the most efficient interaction to consider in selecting inhibitors. CONCLUSIONS: Our result identifies a new drug target in the process of the MMP2 activation. Thus, our analysis will provide new insight into the design of more efficient drug strategies for cancer treatment.     

Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System

We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-ImmSim, such that it represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction. This is a key step for the simulation of the immune response, because it determines immunogenicity. The binding of the epitope, which is the immunogenic part of an invading pathogen, together with activation and cooperation from T helper cells, is required to trigger an immune response in the affected host. To determine a pathogen''s epitopes, we use existing prediction methods. In addition, we propose a novel method, which uses Miyazawa and Jernigan protein–protein potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype heterozygosity and homozygosity with respect to the influenza virus and show that there is an advantage to heterozygosity. Finally, we investigate the emergence of one or more dominating clones of lymphocytes in the situation of chronic exposure to the same immunogenic molecule and show that high affinity clones proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives for a better understanding of the immune system.