[Are there immunological mechanisms for neurological memory?].
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Animals↗
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Immunity during cyclosporine therapy.
Cyclosporine is not cytotoxic but it inhibits the production of immunologic memory-building growth factors by CD4+ T lymphocytes. It also may have inhibitory effects on the effector phase of certain immune reactions. These inhibitory effects are largely reversible and when treatment is stopped, the immune competence of cyclosporine-treated patients returns to normal. In contrast, conventional cytotoxic immunosuppressive agents tend to exterminate the lymphocyte clones that are activated during therapy, and such clonal deletions may cause permanent loss of immunologic memory to those antigens because T lymphocytes are not readily restored in adults with involuted thymus. Most transplant patients have received cyclosporine in combination with various other immunosuppressive agents, and reports suggest that a combination of this drug and conventional immunosuppressive agents may be associated with increased early appearance of non-Hodgkin's lymphoma and, possibly, endocrine-related tumors. An increase in cancers has not been observed in patients treated with cyclosporine alone for such conditions as psoriasis and autoimmune diseases. Treatment of adults with cytotoxic immunosuppressive drugs may permanently delete T-lymphocyte clones that are required for control of latent oncogenic viruses or certain malignant cells. Because of this, when such patients are treated with cyclosporine, further suppression of T-cell function combined with impairment of cytokine-mediated stimulation of natural killer cells and cytotoxic macrophages may facilitate tumor growth. Consequently, it is predicted that if cyclosporine monotherapy is associated with an increased incidence of tumors, it would primarily affect psoriasis patients who are treated with cyclosporine after PUVA or methotrexate therapy. Eventually, comparison of cancer incidence in different categories of patients should resolve this issue.
Carcinogens↗
Enrichment of memory T cells and other profound immunological changes in the bone marrow from untreated breast cancer patients.
Previous studies with animal tumors showed that bone marrow (BM) is a privileged site where potentially lethal tumor cells are controlled in a dormant state by the immune system. Here, we investigated BM of breast cancer patients with respect to tumor cell content, immune activation status and memory T-cell content. BM-derived cells from primary operated breast cancer patients (n = 90) were compared with those from healthy donors (n = 10) and also with cells from respective blood samples. Cytokeratin 19-positive tumor cells were detected by nested polymerase chain reaction. Three-color flow cytometry was used to identify numbers and activation state of T cells, natural killer (NK) cells, monocytes/macrophages and subsets by a panel of monoclonal antibodies (mAbs). The proportion of memory T cells among the CD4 and CD8 T cells was much higher in BM of cancer patients than in healthy donors (p < 0.001). The extent of memory T-cell increase was related to the size of the primary tumor. Patient-derived BM memory CD8 T cells could be shown to contain specific HLA-A2/Her-2/neu(369-377) tetramer binding cells. Patients with disseminated tumor cells in their BM had more memory CD4 T cells and more CD56(+) CD8(+) cells than patients with tumor cell-negative BM. Only some of the immunological changes seen in BM samples of cancer patients were also detectable in peripheral blood samples. Our hypothesis that BM is a special compartment for immunological memory and tumor dormancy is supported by the above findings. The overall results reveal that BM is a valuable additional compartment for immune diagnosis in pathological conditions and possibly for follow-up treatment strategies.
Adult↗
Dynamics of one-pass germinal center models: implications for affinity maturation.
During an immune response, the affinity of antibodies that react with the antigen that triggered the response increases with time, a phenomenon known as affinity maturation. The molecular basis of affinity maturation has been partially elucidated. It involves the somatic mutation of immunoglobulin V-region genes within antigen-stimulated germinal center B cells and the subsequent selection of high affinity variants. This mutation and selection process is extremely efficient and produces large numbers of high affinity variants. Studies of the architecture of germinal centers suggested that B cells divide in the dark zone of the germinal center, then migrate to the light zone, where they undergo selection based on their interaction with antigen-loaded follicular dendritic cells, after which they exit the germinal center through the mantle zone. Kepler and Perelson questioned this architecturally driven view of the germinal center reaction. They, as well as others, argued that the large number of point mutations observed in germinal center B cell V-region genes, frequently 5 to 10 and sometimes higher, would most likely render cells incapable of binding the antigen, if no selection step was interposed between rounds of mutations. To clarify this issue, we address the question of whether a mechanism in which mutants are generated and then selected in one pass, with no post-selection amplification, can account for the observed efficiency of affinity maturation. We analyse a set of one-pass models of the germinal center reaction, with decaying antigen, and mutation occurring at transcription or at replication. We show that under all the scenarios, the proportion of high affinity cells in the output of a germinal center varies logarithmically with their selection probability. For biologically realistic parameters, the efficiency of this process is in clear disagreement with the experimental data. Furthermore, we discuss a set of, possibly counterintuitive, more general features of one-pass selection models that follow from our analysis. We believe that these results may also provide useful intuitions in other cases where a population is subjected to selection mediated by a selective force that decays over time.
Animals↗
Natural and induced tolerance in an immune network model.
It has been proposed that the immune system can be partitioned into central and peripheral immune systems. Recently, Carneiro et al. (1996a, b) proposed a network, model incorporating B and T lymphocytes that explicitly accounts for that partition. This model however, had some limitations that are tackled here. Two main changes were introduced: the average idiotypic connectivity is now an explicit function of time based on empirical evidence; and the activation of T lymphocytes by antigen is described by a log-bell shaped dose response curve. The new model, which also accounts for the CIS and PIS distinction, shows more reasonable results since the frequencies of tolerant, immune or autoimmune responses to an antigen are now correct. The model provides a new interpretation for tolerance induction during the neonatal period, and for the adult tolerance by low or high doses of antigen. It predicts that natural tolerance for antigens available during the neonatal period can be kept indefinitely upon their removal, while tolerance induced in the adult stages is rapidly lost upon transient removal of the antigen. A semiquantitative analysis of the model provides a simple explanation for the different results in terms of the frequency at which a limited set of canonical connectivity structures emerge during ontogenesis.
Animals↗
Antibody dynamics in childhood diseases: waning and boosting of immunity and the impact of vaccination.
The introduction of vaccination against acute diseases such as measles induced a dramatic decline in the prevalence of the disease, and a more gradual rise in the proportion of the population whose immunity is derived solely from vaccination. These two factors combine to constitute an important shift in the dynamics of immunity, especially in highly vaccinated populations. We develop a general model to describe both loss of immunity in the absence of disease, and boosting of immunity corresponding to subclinical infection in individuals whose immunity has waned. We consider the interaction between infection and immunity and identify the key parameters that determine the eradication threshold. We explore the dynamics in the years following the introduction of vaccination using a stochastic version of the model, and consider the effect of different assumptions concerning the nature of immunity. A comparison of the model results with recently published data suggests that heterogeneity in host immune response is an important feature of the antibody dynamics.
Antibodies, Viral↗
Infection, reinfection, and vaccination under suboptimal immune protection: epidemiological perspectives.
The SIR (susceptible-infectious-resistant) and SIS (susceptible-infectious-susceptible) frameworks for infectious disease have been extensively studied and successfully applied. They implicitly assume the upper and lower limits of the range of possibilities for host immune response. However, the majority of infections do not fall into either of these extreme categories. We combine two general avenues that straddle this range: temporary immune protection (immunity wanes over time since infection), and partial immune protection (immunity is not fully protective but reduces the risk of reinfection). We present a systematic analysis of the dynamics and equilibrium properties of these models in comparison to SIR and SIS, and analyse the outcome of vaccination programmes. We describe how the waning of immunity shortens inter-epidemic periods, and poses major difficulties to disease eradication. We identify a "reinfection threshold" in transmission when partial immunity is included. Below the reinfection threshold primary infection dominates, levels of infection are low, and vaccination is highly effective (approximately an SIR model). Above the reinfection threshold reinfection dominates, levels of infection are high, and vaccination fails to protect (approximately an SIS situation). This association between high prevalence of infection and vaccine failure emphasizes the problems of controlling recurrent infections in high-burden regions. However, vaccines that induce a better protection than natural infection have the potential to increase the reinfection threshold, and therefore constitute interventions with a surprisingly high capacity to reduce infection where reduction is most needed.
Communicable Disease Control↗
Contrasting B cell- and T cell-based protective vaccines.
A substantial research effort is devoted to the development of vaccines based on T cells. Such a vaccine would provide a means to protect against infection with HIV and stop the current pandemic. Here we investigate the possibility to develop a protective T cell-based vaccine. We do this by means of a mathematical model which describes the dynamics of a pathogen and the immune system in the early stages of infection. We compare an immune response that is near immediate--as is the case for a humoral response--with that of a response in which the effector cells have to be formed from precursor cells--as occurs in T cell responses. The latter applies to a T cell-based vaccine. A near immediate response is associated with a threshold number of effector cells above which an infection cannot take hold. For a T cell-based vaccine this threshold increases with the amount of antigen the immune system is exposed to. For small initial doses, as one would naturally expect to occur, this gives rise to impractically large thresholds. Thus, although a T cell vaccine might work against a high dose exposure, it might fail when exposed against to a low-dose exposure. This limits, we argue, the efficacy of T cell-based vaccines.
AIDS Vaccines↗
Higher levels of HIV DNA in memory and naive CD4(+) T cell subsets of viremic compared to non-viremic patients after 18 and 24 months of HAART.
The degree of infection of memory and naive CD4(+) T cells in patients treated with HAART and with durable undetectable or detectable viral load in plasma was evaluated. The following two groups of patients were analyzed cross-sectionally: (i) patients with undetectable HIV RNA plasma levels during follow-up (responders); (ii) patients with no reduction or with rebound in HIV RNA levels during treatment (non-responders). Patients were examined following 6, 12, 18 and 24 months of HAART, respectively, by quantifying: (i) plasma HIV RNA load; (ii) CD4(+) T cells; (iii) memory and naive CD4(+) T cells; (iv) HIV DNA levels in memory and naive CD4(+) T cells. HIV RNA plasma levels were significantly higher in non-responders vs responders at each time point (P<0.02), while CD4(+) T cell counts as well as memory and naive CD4(+) T cell levels were comparable in both viremic and non-viremic patients. However, higher HIV DNA values were observed in both memory and naive CD4(+) T cells of non-responders vs responders after 18 and 24 months of HAART (P<0.02), suggesting an increased amount of HIV-infected naive CD4(+) T cells and a sustained high degree of infection of memory CD4(+) T cells. Immunological reconstitution following HAART might potentially be hampered in viremic patients despite the absolute increase in CD4(+) T cell counts.
Anti-HIV Agents↗
Migration and T-lymphocyte effector function.
The development of immunity depends upon the capacity of responding T cells to become mobilized from lymphoid tissues where they are primed to sites of antigen exposure, wherever they occur in the body. Activation-induced alterations in the ability of T cells to migrate signify a fundamental change in biological function. Considerable attention is now focused on identifying mechanisms that regulate the migration and persistence of T cells that disseminate to non-lymphoid compartments as effector cells, and those that are retained in the lymphoid compartment. There are many unanswered questions about the developmental relationships and roles in protective immunity of antigen-experienced T cells that partition in different tissues.
Cell Movement↗
Ongoing HIV dissemination during HAART.
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Anti-HIV Agents↗
Effector BCRs: inside information on IgG.
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B-Lymphocytes↗
Regulation of immune signal integration and memory by inflammation-induced chromosome conformation.
Three-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro Capture-C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements show that IL-4-driven conformation changes are required for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation can occur in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
Animals↗
The dynamics of germinal centre selection as measured by graph-theoretical analysis of mutational lineage trees.
We have developed a rigorous graph-theoretical algorithm for quantifying the shape properties of mutational lineage trees. We show that information about the dynamics of hypermutation and antigen-driven clonal selection during the humoral immune response is contained in the shape of mutational lineage trees deduced from the responding clones. Age and tissue related differences in the selection process can be studied using this method. Thus, tree shape analysis can be used as a means of elucidating humoral immune response dynamics in various situations.
Algorithms↗
Probabilistic learning in immune network: weighted tree matching model.
Adaptive learning properties (of clonal selection and affinity maturation) in the immune network model are investigated in this paper under a nonlinear data structural representation of the involved molecules. Weighted trees are constructed to model the multiple paratopes/epitopes on the antibodies/antigens. Parallel computing experiments are carried out for the canonical coding of these trees and the corresponding multiple matching interactions. Our experiments on real data have shown significant results on the cognitive properties of the immune network. These and other computational results are presented along with a discussion of future applications.
Amino Acid Sequence↗
An approach to modelling in immunology.
Like most other fields in biology, immunology has been revolutionised by the techniques of molecular biology and the resulting explosion in available experimental data. It is argued that efforts to integrate the data to gain insight into how various subsystems in the immune system interact and function require mathematical modelling and computer simulation in close collaboration with experimentalists. This paper illustrates some of the techniques available for modelling immune systems, and highlights the issues that should be borne in mind by anyone starting down the modelling path.
Animals↗
Large-scale cellular automata simulations of the immune system response.
The sequential nature of the process allowing the immune system to learn how to withstand pathogen agents is explored by means of large-scale computer simulation of the Celada-Seiden immunological automaton. In accord with our previous results, it is found that the learning process proceeds via a sequential cascade in affinity space.
B-Lymphocytes↗