Information integration of protein–protein interactions as essential tools for immunomics

After a brief introduction to point out the necessity to advance for a global understanding of the macromolecular interactions occurring during the immune system development and responses, Section 2 will be devoted to analyse the current tools for an automatic location of information on these protein–protein interactions in the web. In the next section (Section 3), we will point out different action lines to improve these tools and, consequently, to increase the efficiency to establish (to understand) the “protein network skeleton” that controls our immune responses. Finally, we will briefly present our current strategy and work to advance towards this goal.     

Functional responses and scaling in predator-prey interactions of marine fishes: contemporary issues and emerging concepts

Predator-prey interactions are a primary structuring force vital to the resilience of marine communities and sustainability of the world's oceans. Human influences on marine ecosystems mediate changes in species interactions. This generality is evinced by the cascading effects of overharvesting top predators on the structure and function of marine ecosystems. It follows that ecological forecasting, ecosystem management, and marine spatial planning require a better understanding of food web relationships. Characterising and scaling predator-prey interactions for use in tactical and strategic tools (i.e. multi-species management and ecosystem models) are paramount in this effort. Here, we explore what issues are involved and must be considered to advance the use of predator-prey theory in the context of marine fisheries science. We address pertinent contemporary ecological issues including (1) the approaches and complexities of evaluating predator responses in marine systems; (2) the 'scaling up' of predator-prey interactions to the population, community, and ecosystem level; (3) the role of predator-prey theory in contemporary fisheries and ecosystem modelling approaches; and (4) directions for the future. Our intent is to point out needed research directions that will improve our understanding of predator-prey interactions in the context of the sustainable marine fisheries and ecosystem management.     

From cellular microbiology to bacteria‐based next generations of cancer immunotherapies

Pioneer work by Prof. Cossart among others, studying the interactions between pathogenic bacteria and host cells (this discipline was termed Cellular Microbiology), was fundamental to determine the bacterial infection processes and to improve our knowledge of different cellular mechanisms. The study of bacteria–host interactions also involves in vivo host immune responses, which can be manipulated by bacteria, being these last potent tools for different immunotherapies. During the last years, tumour immunotherapies, mainly the use of antibodies that target immune checkpoints [checkpoint inhibitors (CPI)], have been a revolution in oncology, allowing the treatment of tumours otherwise with very bad prognosis. In the same direction, bacteria inoculations have been used from long to treat some cancers; for example, non‐muscle‐invasive bladder cancer can be successfully treated with the bacterium Bacillus Calmette Guerin (BCG). More recently, it has been shown that microbiota could determine the success of CPI immunotherapies and intense research is being performed in order to use bacteria as immunotherapy tools due to their ability to activate the immune system. In this context, to expand the knowledge of the bacteria–immune system interactions will be fundamental to improve tumour immunotherapies.     

Combining oncolytic virotherapy and tumour vaccination

The interactions between the immune system, a malignant tumour and an oncolytic virus are complex and poorly understood. For oncolytic viruses to become successful therapeutics we need to better understand these interactions and identify strategies to take advantage of defects in the innate immune response within tumours and avoid cellular anti-viral responses while capitalizing on anti-tumoural immunity. In this review we will discuss the evidence for the induction of tumour-specific immune responses by oncolytic viruses as well as by cancer vaccines. We will then describe some of the barriers to successful cancer immunotherapy, and finally we will outline a strategy for enhancing anti-tumoural immunity while reducing anti-viral immunity by combining tumour vaccination with oncolytic viral therapy.     

Interplay between hepatitis B virus and the innate immune responses: implications for new therapeutic strategies

Hepatitis B virus (HBV) infection is still a worldwide health problem; however, the current antiviral therapies for chronic hepatitis B are limited in efficacy. The outcome of HBV infection is thought to be the result of complex interactions between the HBV and the host immune system. While the role of the adaptive immune responses in the resolution of HBV infection has been well characterized, the contribution of innate immune mechanisms remains elusive until recent evidence implicates that HBV appears to activate the innate immune response and this response is important for controlling HBV infection. Here, we review our current understanding of innate immune responses to HBV infection and the multifaceted evasion by the virus and discuss the potential strategies to combat chronic HBV infection via induction and restoration of host innate antiviral responses.     

Mosquito immune responses and malaria transmission: lessons from insect model systems and implications for vertebrate innate immunity and vaccine development

The introduction of novel biochemical, genetic, molecular and cell biology tools to the study of insect immunity has generated an information explosion in recent years. Due to the biodiversity of insects, complementary model systems have been developed. The conceptual framework built based on these systems is used to discuss our current understanding of mosquito immune responses and their implications for malaria transmission. The areas of insect and vertebrate innate immunity are merging as new information confirms the remarkable extent of the evolutionary conservation, at a molecular level, in the signaling pathways mediating these responses in such distant species. Our current understanding of the molecular language that allows the vertebrate innate immune system to identify parasites, such as malaria, and direct the acquired immune system to mount a protective immune response is very limited. Insect vectors of parasitic diseases, such as mosquitoes, could represent excellent models to understand the molecular responses of epithelial cells to parasite invasion. This information could broaden our understanding of vertebrate responses to parasitic infection and could have extensive implications for anti-malarial vaccine development.     

The role of connexins in controlling cell growth and gene expression

The purpose of this paper is to provide a brief overview of current thinking on the role of connexins, in particular Cx43, in growth regulation, and a more detailed discussion as to potential mechanisms involved with an emphasis on gene expression. While the precise molecular mechanism by which connexins can affect the growth of normal or tumor cells remains elusive, a number of exciting reports have expanded our understanding and are presented in some detail. Thus, we will discuss (Section 2): the role of protein-protein interactions in integrating connexins into multiple signal transduction pathways; phosphorylation at specific sites and reversal of growth inhibition; the role of the carboxy-terminal regulatory domain as a signaling molecule. Some of our latest work on the potential functions of endogenously produced carboxy-terminal fragments of Cx43 are also presented (Section 3). Finally, Section 4 will pay tribute to the rapidly emerging realization that connexins such as Cx43 and Cx32 exert important and extensive effects on gene expression, particularly those genes linked to growth regulation.     

Interplay between hepatitis B virus and the innate immune responses:implications for new therapeutic strategies

Hepatitis B virus(HBV) infection is still a worldwide health problem;however,the current antiviral therapies for chronic hepatitis B are limited in efficacy.The outcome of HBV infection is thought to be the result of complex interactions between the HBV and the host immune system.While the role of the adaptive immune responses in the resolution of HBV infection has been well characterized,the contribution of innate immune mechanisms remains elusive until recent evidence implicates that HBV appears to activate the innate immune response and this response is important for controlling HBV infection.Here,we review our current understanding of innate immune responses to HBV infection and the multifaceted evasion by the virus and discuss the potential strategies to combat chronic HBV infection via induction and restoration of host innate antiviral responses.     

Dissecting p53-dependent apoptosis

The complexity of the p53 protein, coupled with the vast cellular responses to p53, is simply astonishing. As new isoforms, functional domains and protein-protein interactions are described; each morsel of information forces us to think (and re-think) about how it 'fits' into the current p53 paradigm. One aspect of p53 signaling that is under refinement is the mechanism(s) leading to apoptosis. Here we discuss what is known about p53-induced apoptosis, what proteins and protein-protein interactions are responsible for regulating apoptosis, how can this cascade be genetically dissected, and what pharmacological tools are available to modulate p53-dependent apoptosis. While everything may not comfortably fit into our understanding of p53, all of these data will certainly broaden our viewpoint on the complexity and significance of the p53-induced apoptotic pathway. Here, our discussion is primarily focused on the works presented at the 12th International p53 Workshop, except where appropriate background is required.     

Host pathogen protein interactions predicted by comparative modeling

Pathogens have evolved numerous strategies to infect their hosts, while hosts have evolved immune responses and other defenses to these foreign challenges. The vast majority of host-pathogen interactions involve protein-protein recognition, yet our current understanding of these interactions is limited. Here, we present and apply a computational whole-genome protocol that generates testable predictions of host-pathogen protein interactions. The protocol first scans the host and pathogen genomes for proteins with similarity to known protein complexes, then assesses these putative interactions, using structure if available, and, finally, filters the remaining interactions using biological context, such as the stage-specific expression of pathogen proteins and tissue expression of host proteins. The technique was applied to 10 pathogens, including species of Mycobacterium, apicomplexa, and kinetoplastida, responsible for "neglected" human diseases. The method was assessed by (1) comparison to a set of known host-pathogen interactions, (2) comparison to gene expression and essentiality data describing host and pathogen genes involved in infection, and (3) analysis of the functional properties of the human proteins predicted to interact with pathogen proteins, demonstrating an enrichment for functionally relevant host-pathogen interactions. We present several specific predictions that warrant experimental follow-up, including interactions from previously characterized mechanisms, such as cytoadhesion and protease inhibition, as well as suspected interactions in hypothesized networks, such as apoptotic pathways. Our computational method provides a means to mine whole-genome data and is complementary to experimental efforts in elucidating networks of host-pathogen protein interactions.     

Translating innate immunity into immunological memory: implications for vaccine development

Vaccination is the most effective means of preventing infectious diseases. Despite the success of many vaccines, there is presently little knowledge of the immunological mechanisms that mediate their efficacy. Such information will be critical in the design of future vaccines against old and new infectious diseases. Recent advances in immunology are beginning to provide an intellectual framework with which to address fundamental questions about how the innate immune system shapes adaptive immunity. In this review, we summarize current knowledge about how the innate immune system modulates the quantity and quality of long-term T and B cell memory and protective immune responses to pathogens. In addition, we point out unanswered questions and identify critical challenges, the solution of which, we believe, will greatly facilitate the rational design of novel vaccines against a multitude of emerging infections.     

Structural aspects of nucleic acid-sensing Toll-like receptors

Invading pathogens elicit potent immune responses in cells through interactions between structurally conserved molecules derived from the pathogens and specialized innate immune receptors such as the Toll-like receptors (TLRs). Nucleic acid is one of the principal TLR ligands. Nucleic acid-sensing TLRs recognize an array of nucleic acids, including double-stranded RNA, single-stranded RNA, and DNAs with specific sequence motifs. Although ligand-induced dimerization is commonly observed followed by TLR activation, both the specific recognition mechanisms and the ligand–receptor interactions vary among different TLRs. In this review, we highlight our current understanding of how these receptors recognize their cognate ligands based on the recent advances in structural biology.     

Dendritic cells as a conduit to improve HIV vaccines

Many potential HIV vaccine strategies are being explored in both animal model and human settings. The success of any vaccine relies on relevant antigenic determinants being presented to the immune system for the activation of broad and long-lasting immunity. Effective immunity against HIV infection will likely require both the cellular and humoral arms of the immune system, where HIV-specific killer cells eradicate infected targets and neutralizing antibody responses contribute by preventing the initial infection of host cells. As the most potent antigen presenting cell of the immune system, the dendritic cell (DC) orchestrates the activation of adaptive immune responses as well as contributing to the early innate responses to a pathogen, which may also aid in the initial control of infection. It follows therefore, that the efficiency of a vaccine antigen would be greatly enhanced if targeted to the appropriate DCs to ensure optimal presentation to and subsequently activation of the immune system. This review will discuss (i) the current status of DC biology, covering distinct DC subsets and stages of activation and how these influence the types of immune responses that are induced, (ii) how DCs can be exploited to improve the efficacy of HIV vaccine strategies currently under investigation, (iii) what has been learned from in vivo model systems using DCs, and (iv) future considerations to advance HIV vaccinology.     

Can immunological principles and cross-disciplinary science illuminate the path to vaccines for HIV and other global health challenges?

Vaccines are one of the most impactful and cost-effective public health measures of the twentieth century. However, there remain great unmet needs to develop vaccines for globally burdensome infectious diseases and to allow more timely responses to emerging infectious disease threats. Recent advances in the understanding of immunological principles operative not just in model systems but in humans in concert with the development and application of powerful new tools for profiling human immune responses, in our understanding of pathogen variation and evolution, and in the elucidation of the structural aspects of antibody–pathogen interactions, have illuminated pathways by which these unmet needs might be addressed. Using these advances as foundation, we herein present a conceptual framework by which the discovery, development and iterative improvement of effective vaccines for HIV, malaria and other globally important infectious diseases might be accelerated.     

Mast cell responses to helminth infection

Mast cells have been suggested to be major effector cells in the immune response to infection with helminths. It is now clear, however, that mast cells are heterogeneous and have a diversity of important functions. In this review, Timothy Lee, Mark Swieter and Dean Befus point out that much of the confusion about the role of mast cells in immunity stems from methods and interpretations which are inadequate for the diversity of roles played by these cells in host responses to parasites. Classical histochemistry may fail to reveal active mast cells, and studies using chemical antagonists are difficult to interpret until we know more about the action of the drugs. The authors show that current research is extending our knowledge of mast cell heterogeneity, and helping to define the powerful array of mediators that they can use to orchestrate the immune response to helminth infections.     

Facing Inward from Compartment Shores: How Many Pathways were we Looking For?

Protein toxins of the Shiga family have become potent tools in studying a number of intracellular transport events such as endocytosis, the communication between endosomes and the biosynthetic/secretory pathway, and retrograde transport from the Golgi apparatus to the endoplasmic reticulum. It seems clear today that most of these transport events can be explained from the toxins' interactions with cellular factors. This review will primarily focus on the discussion of recent data obtained on Shiga toxin and related toxins. We will point out to what extent the study of these proteins has opened new avenues for the development of intracellular targeting tools.     

Structural immunology of costimualtory and coinhibitory molecules

The T cell costimulatory pathways are central to regulating immune responses, and targeting these pathways represents one of the most promising approaches for achieving immunotherapy. The molecular structures of costimulation revealed invaluable mechanistic insights underlying costimulatory receptor/ligand specificity, affinity, oligomeric state, and valency, which provided the bases for better manipulation of these signaling pathways. The incredible growth of this field led to identification of new members and unexpected interactions, revealing a complicated regulatory network of immune responses. The advances in structural biology of costimulation will promise unprecedented opportunities for furthering our understanding and therapeutic application of T cell costimulatory pathways.     

Danger signals and nonself entity of tumor antigen are both required for eliciting effective immune responses against HER-2/neu positive mammary carcinoma: implications for vaccine design

Using parental FVB mice and their neu transgenic counterparts, FVBN202, we showed for the first time that dangerous hyperplasia of mammary epithelial cells coincided with breaking immunological tolerance to the neu "self" tumor antigen, though such immune responses failed to prevent formation of spontaneous neu-overexpressing mammary carcinoma (MMC) or reject transplanted MMC in FVBN202 mice. On the other hand, neu-specific immune responses appeared to be effective against MMC in parental FVB mice because of the fact that rat neu protein was seen as "nonself" antigen in these animals and the protein was dangerously overexpressed in MMC. Interestingly, low/intermediate expression of the neu "nonself" protein in tumors induced immune responses but such immune responses failed to reject the tumor in FVB mice. Our results showed that self-nonself (SNS) entity of a tumor antigen or danger signal alone, while may equally induce an antigen-specific immune response, will not warrant the efficacy of immune responses against tumors. On the other hand, entity of antigen in the context of dangerous conditions, i.e. abnormal/dangerous overexpression of the neu nonself protein, will warrant effective anti-tumor immune responses in FVB mice. This unified "danger-SNS" model suggests focusing on identification of naturally processed cryptic or mutated epitopes, which are considered semi-nonself by the host immune system, along with novel dangerous adjuvant in vaccine design.     

Mechanisms of cellular communication through intercellular protein transfer

In a multicellular system, cellular communication is a must for orchestration and coordination of cellular events. Advent of the latest analytical and imaging tools has allowed us to enhance our understanding of the intercellular communication. An intercellular exchange of proteins or intact membrane patches is a ubiquitous phenomenon, and has been the subject of renewed interest, particularly in the context of immune cells. Recent evidence implicates that intercellular protein transfers, including trogocytosis is an important mechanism of the immune system to modulate immune responses and transferred proteins can also contribute to pathology. It has been demonstrated that intercellular protein transfer can be through the internalization/pathway, dissociation-associated pathway, uptake of exosomes and membrane nanotube formations. Exchange of membrane molecules/antigens between immune cells has been observed for a long time, but the mechanisms and functional consequences of these transfers remain unclear. In this review, we will discuss the important findings concerning intercellular protein transfers, possible mechanisms and highlight their physiological relevance to the immune system, with special reference to T cells such as the stimulatory or suppressive immune responses derived from T cells with acquired dendritic cell membrane molecules.