Engineering neoantigen vaccines to improve cancer personalized immunotherapy

Immunotherapy treatments harnessing the immune system herald a new era of personalized medicine, offering considerable benefits for cancer patients. Over the past years, tumor neoantigens emerged as a rising star in immunotherapy. Neoantigens are tumor-specific antigens arising from somatic mutations, which are proceeded and presented by the major histocompatibility complex on the cell surface. With the advancement of sequencing technology and bioinformatics engineering, the recognition of neoantigens has accelerated and is expected to be incorporated into the clinical routine. Currently, tumor vaccines against neoantigens mainly encompass peptides, DNA, RNA, and dendritic cells, which are extremely specific to individual patients. Due to the high immunogenicity of neoantigens, tumor vaccines could activate and expand antigen-specific CD4+ and CD8+ T cells to intensify anti-tumor immunity. Herein, we introduce the origin and prediction of neoantigens and compare the advantages and disadvantages of multiple types of neoantigen vaccines. Besides, we review the immunizations and the current clinical research status in neoantigen vaccines, and outline strategies for enhancing the efficacy of neoantigen vaccines. Finally, we present the challenges facing the application of neoantigens.     

Tumor neoantigen heterogeneity impacts bystander immune inhibition of pancreatic cancer growth

The immunogenic clonal-fraction threshold in heterogeneous solid-tumor required to induce effective bystander-killing of non-immunogenic subclones is unknown. Pancreatic cancer poses crucial challenges for immune therapeutic interventions due to low mutational-burden and consequent lack of neoantigens. Here, we designed a model to incorporate artificial-neoantigens into genes-of -interest in cancer-cells and to test their potential to actuate bystander-killing. By precisely controlling a neoantigen's abundance in the tumor, we studied the impact of neoantigen frequency on immune-response and immune-escape. Our results showed single, strong, widely-expressed neoantigen could lead to robust antitumor response when over 80% of cancer cells express the neoantigen. Further, immunological assays demonstrated T-cell responses against non-target self-antigen on KRAS-oncoprotein, when we inoculated animals with a high frequency of tumor-cells expressing test-neoantigen. Using nanoparticle-based gene-therapy, we successfully altered tumor-microenvironment by perturbing interleukin-12 and interleukin-10 gene-expression. The subsequent microenvironment-remodeling reduced the neoantigen frequency threshold at which bioluminescent signal intensity for tumor-burden decreased 1.5-log-fold, marking robust tumor-growth inhibition, from 83% to 29%. Our results thus suggest bystander killing is inefficient in immunologically-cold tumors like pancreatic-cancer and requires high neoantigen abundance. However, bystander killing mediated antitumor response can be rescued by adjuvant-immune therapy.     

Mathematical model of immune processes

In the model the time lags of the antibody production and immune memory formation are taken into account explicitly. The antibody-antigen reaction is supposed to be very fast. The cases of a reproducing antigen as well as that of a non-reproducting antigen are considered. The conditions of the infinite increase of the antigen quantity and of the antigen elimination are obtained. For the rapidly reproducing antigen the latter condition includes the requirement for the time lag of the immune response to be not too short or not too long. In the case of the poorly catabolized non-reproducing antigen the cyclic appearance of the antibody producing cells due to the immune memory is described in the frame-work of the model.The mathematical structure of the model is similar to that of the Volterra-Lotka jequations. The only difference is the presence of the time lags in the non-linear terms. The time lags lead to the instability of the stationary state. In the prolonged reaction the antigen quantity may perform several oscillations before the elimination of the antigen.     

Mathematical model of the immune response]

A model of immune reaction is suggested, ahich takes into account the delay in the development of an immune response. The model depending on parameters values describes: an asymptotic decrease of antigene quantity, approach of its quantity towards constant value, periodic course of the illness, unlimited growth of the antigene quantity. It is shown that the course of the reaction essentially depends on the duration of delay. Parameters regions corresponding to different regimes are determined.     

Mathematical analysis of a model for a plant-herbivore system

The apple twig borer (Amphicerus bicaudatus) is an insect pest of the grape vine, causing considerable damage to the grape vine in early spring. A simple difference equation model is formulated and analysed for this plant-herbivore system based on two control strategies, cane removal and pesticide application. The system has two equilibria, one where the pest is present and one where the pest is absent. Regions are found in parameter space for global stability of the equilibria and in the absence of global stability it is shown that there exist periodic or quasiperiodic solutions.     

Mathematical model of the primary CD8 T cell immune response: stability analysis of a nonlinear age-structured system

The primary CD8 T cell immune response, due to a first encounter with a pathogen, happens in two phases: an expansion phase, with a fast increase of T cell count, followed by a contraction phase. This contraction phase is followed by the generation of memory cells. These latter are specific of the antigen and will allow a faster and stronger response when encountering the antigen for the second time. We propose a nonlinear mathematical model describing the T CD8 immune response to a primary infection, based on three nonlinear ordinary differential equations and one nonlinear age-structured partial differential equation, describing the evolution of CD8 T cell count and pathogen amount. We discuss in particular the roles and relevance of feedback controls that regulate the response. First we reduce our system to a system with a nonlinear differential equation with a distributed delay. We study the existence of two steady states, and we analyze the asymptotic stability of these steady states. Second we study the system with a discrete delay, and analyze global asymptotic stability of steady states. Finally, we show some simulations that we can obtain from the model and confront them to experimental data.     

Mathematical model of the human ankle joint

It has been suspected that the mechanical environment in which a particular joint functions has an effect on the initiation or progression of degenerative joint disease. The objective of this study is to define the mechanical environment of the ankle joint, specifically, the contact areas and pressure distributions, through the development and analysis of a simplified mathematical model. Since the state of pressure across articular surfaces during function is influenced by joint incongruity, cartilage thickness profile and the geometry of the opposing surfaces, these factors have been incorporated into the model formulation. Mathematical analysis of the model has resulted in pressure distributions in both the anterior-posterior and medial-lateral directions and contact area growth plots which correlate well with observed ankle contact patterns obtained from in vitro investigations. The significance of joint incongruity to these pressure distributions and to the relative immunity of the ankle joint to primary osteoarthritis is discussed.     

Mathematical model of a three-stage innate immune response to a pneumococcal lung infection

Pneumococcal pneumonia is a leading cause of death and a major source of human morbidity. The initial immune response plays a central role in determining the course and outcome of pneumococcal disease. We combine bacterial titer measurements from mice infected with Streptococcus pneumoniae with mathematical modeling to investigate the coordination of immune responses and the effects of initial inoculum on outcome. To evaluate the contributions of individual components, we systematically build a mathematical model from three subsystems that describe the succession of defensive cells in the lung: resident alveolar macrophages, neutrophils and monocyte-derived macrophages. The alveolar macrophage response, which can be modeled by a single differential equation, can by itself rapidly clear small initial numbers of pneumococci. Extending the model to include the neutrophil response required additional equations for recruitment cytokines and host cell status and damage. With these dynamics, two outcomes can be predicted: bacterial clearance or sustained bacterial growth. Finally, a model including monocyte-derived macrophage recruitment by neutrophils suggests that sustained bacterial growth is possible even in their presence. Our model quantifies the contributions of cytotoxicity and immune-mediated damage in pneumococcal pathogenesis.     

Human immune responses to the UK human anthrax vaccine

The IgG anti-protective antigen subclass antibody response of individuals who had been infected with anthrax was compared with that of healthy individuals immunized with the UK licensed anthrax vaccine. The predominant subclass in both groups was IgG1. In addition, IgG3 was seen in convalescent serum while vaccinees produced IgG2, IgG3 and IgG4 subclass. The significance of these results is discussed. Further work is required to determine the role of antibodies in mediating protective immunity in man.     

Endocannabinoids in the immune system and cancer

The present review focuses on the role of the endogenous cannabinoid system in the modulation of immune response and control of cancer cell proliferation. The involvement of cannabinoid receptors, endogenous ligands and enzymes for their biosynthesis and degradation, as well as of cannabinoid receptor-independent events is discussed. The picture arising from the recent literature appears very complex, indicating that the effects elicited by the stimulation of the endocannabinoid system are strictly dependent on the specific compounds and cell types considered. Both the endocannabinoid anandamide and its congener palmitoylethanolamide, exert a negative action in the onset of a variety of parameters of the immune response. However, 2-arachidonoylglycerol appears to be the true endogenous ligand for peripheral cannabinoid receptors, although its action as an immunomodulatory molecule requires further characterization. Modulation of the endocannabinoid system interferes with cancer cell proliferation either by inhibiting mitogenic autocrine/paracrine loops or by directly inducing apoptosis; however, the proapoptotic effect of anandamide is not shared by other endocannabinoids and suggests the involvement of non-cannabinoid receptors, namely the VR1 class of vanilloid receptors. In conclusion, further investigations are needed to elucidate the function of endocannabinoids as immunosuppressant and antiproliferative/cytotoxic agents. The experimental evidence reviewed in this article argues in favor of the therapeutic potential of these compounds in immune disorders and cancer.     

Mathematical model comparisons of potential non-typeable Haemophilus influenzae vaccine effects

Vaccines to prevent acute otitis media (AOM) caused by non-typeable Haemophilus influenzae (NTHi) are under development. Because NTHi is highly variable and colonization rates are high, special vaccine characteristics and trial designs might be needed. We examined in mathematical models the equilibrium NTHi-caused AOM rate given hypothetical vaccines that generated immunity identical to corresponding maximal naturally acquired immunity. Vaccines were examined with single effects and combinations of immunity affecting (1) AOM rates given colonization (pathogenicity), (2) susceptibility to colonization, and (3) contagiousness given colonization. Percent reductions in AOM across all preschool children were (1) 34%, (2) 31%, (3) 9%, (1 and 2) 57%, (2 and 3) 50%, and (1, 2, and 3) 75%. Effects on children in daycare vs. not in daycare were (1) 18 vs. 48%, (2) -1 vs. 57%, (3) 13 vs. 5%, (1 and 2) 30 vs. 79%, (2 and 3) 33 vs. 60%, and (1, 2, and 3) 64 vs. 85%. Pure pathogenicity effects (1 alone) will need to be supplemented by transmission effects. The effects of susceptibility (2 alone) are diminished or negative because children protected against colonization have lower levels of immunity to (1) and (3) than unvaccinated children. For trials to predict population effects, both colonization and AOM outcomes must be studied and all three effects must be evaluated. This need arises because, unlike H. influenzae type B, high NTHi exposure diminishes cumulative vaccine effects and high colonization rates generate rapid accumulation of natural immunity that alters the indirect effects of vaccine immunity on transmission differently by age and daycare status.     

Characterisation of the immune response to the UK human anthrax vaccine

The UK human anthrax vaccine consists of the alum-precipitated culture supernatant of Bacillus anthracis Sterne. In addition to protective antigen (PA), the key immunogen, the vaccine also contains a number of other bacteria- and media-derived proteins. These proteins may contribute to the transient side effects experienced by some individuals and could influence the development of the PA-specific immune response. Bacterial cell-wall components have been shown to be potent immunomodulators. B. anthracis expresses two S-layer proteins, EA1 and Sap, which have been demonstrated to be immunogenic in animal studies. These are also immunogenic in man so that convalescent and post-immunisation sera contain specific antibodies to Ea1, and to a lesser extent, to Sap. To determine if these proteins are capable of modifying the protective immune response to PA, A/J mice were immunised with equivalent amounts of recombinant PA and S-layer proteins in the presence of alhydrogel. IgG isotype profiles were determined and the animals were subsequently challenged with spores of B. anthracis STI. The results suggest that there was no significant shift in IgG isotype profile and that the presence of the S-layer proteins did not adversely affect the protective immune response induced by PA.     

Characterization of the human immune response to the UK anthrax vaccine

The anthrax bipartite lethal toxin (protective antigen (PA) and lethal factor (LF))-specific antibody responses of humans receiving the UK licensed anthrax vaccine were determined. The PA-specific IgG response peaked two weeks post immunization and fell back to pre-boost levels by week 12. The heterogeneity of the host population modulated the extent of the PA-specific antibody response. Significantly lower levels of LF-specific antibodies were also detected. Vaccinated individuals recognized the same PA epitope as the protective mouse lethal toxin neutralizing monoclonal 2D3 suggesting that this may also be a target for human protection.     

Travelling-wave analysis of a model of the immune response to cancer

In this paper we present a travelling-wave analysis of a mathematical model describing the growth of a solid tumour in the presence of an immune system response. From a modelling perspective, attention is focused upon the attack of tumour cells by tumour infiltrating cytotoxic lymphocytes (TICLs), in a small multicellular tumour, without necrosis and at some stage prior to (tumour-induced) angiogenesis. As we have shown in previous work, for a particular choice of parameters, the underlying reaction-diffusion-chemotaxis system of partial differential equations is able to simulate the well-documented phenomenon of cancer dormancy by depicting spatially heterogeneous tumour cell distributions that are characterized by a relatively small total number of tumour cells. This behaviour is consistent with several immunomorphological investigations. Moreover, the alteration of certain parameters of the model is enough to induce bifurcations into the system, which in turn result in tumour invasion in the form of a standard travelling wave. The work presented in this paper complements the bifurcation analysis undertaken by Matzavinos et al. [Math. Med. Biol. IMA 21 (2004) 1-34] and establishes the existence of travelling-wave solutions for the system under discussion by promoting the understanding of the geometry of an appropriate phase space.     

Mathematical model for the cancer stem cell hypothesis

Recent research on the origin of brain cancer has implicated a subpopulation of self-renewing brain cancer stem cells for malignant tumour growth. Various genes that regulate self-renewal in normal stem cells are also found in cancer stem cells. This implies that cancers can occur because of mutations in normal stem cells and early progenitor cells. A predictive mathematical model based on the cell compartment method is presented here to pose and validate non-intuitive scenarios proposed through the neural cancer stem cell hypothesis. The growths of abnormal (stem and early progenitor) cells from their normal counterparts are ascribed with separate mutation probabilities. Stem cell mutations are found to be more significant for the development of cancer than a similar mutation in the early progenitor cells. The model also predicts that, as previously hypothesized, repeated insult to mature cells increases the formation of abnormal progeny, and hence the risk of cancer.