Search

Mice with human hematopoietic system have become critical for research and preclinical studies. Mice with patient-derived xenografts of different tumors exist without human immune system. Answers can be addressed with the same immunodeficient mice that are chimeric for the human hemato-lymphoid system (humanized mice). The growing field of immune-oncology could benefit from preclinical studies with the humanized mice. Other fields will also benefit such as studies of infectious disease, regenerative medicine, organ transplant, and allergies. Here, we describe the method to humanize immune-deficient mice with human CD34 + hematopoietic cells.

Several computational methods have been proposed to infer the cellular composition from bulk RNA-seq data of a tumor biopsy sample. Elucidating interactions in the tumor microenvironment can yield unique insights into the status of the immune system. In immuno-oncology, this information can be crucial for deciding whether the immune system of a patient can be stimulated to target the tumor. Here, we shed a light on the working principles, capabilities, and limitations of the most commonly used methods for cell-type deconvolution in immuno-oncology and offer guidelines for method selection.

Neutrophils, also known as polymorphonuclear neutrophils (PMNs), have long been considered as the short-lived, nonspecific white cells that form pus-and also happen to kill invading microbes. Indeed, neutrophils were often neglected (and largely not considered) as immune cells. This historic view of neutrophils has changed considerably over the past several decades, and we now know that in addition to playing the predominant role in the clearance of bacteria and fungi, they have a major role in shaping the host response to infection and immune system homeostasis. The change in our view of the role of neutrophils in the immune system has been due in large part to the study of these cells in vitro. Such work has been made possible by new and/or improved methods and approaches used to investigate neutrophils. These methods are the focus of this volume.

Since the performance of in silico approaches for estimating immune-cell fractions from bulk RNA-seq data can vary, it is often advisable to compare results of several methods. Given numerous dependencies and differences in input and output format of the various computational methods, comparative analyses can become quite complex. This motivated us to develop immunedeconv, an R package providing uniform and user-friendly access to seven state-of-the-art computational methods for deconvolution of cell-type fractions from bulk RNA-seq data. Here, we show how immunedeconv can be installed and applied to a typical dataset. First, we give an example for obtaining cell-type fractions using quanTIseq. Second, we show how dimensionless scores produced by MCP-counter can be used for cross-sample comparisons. For each of these examples, we provide R code illustrating how immunedeconv results can be summarized graphically.

The immune system in a broad sense is a mechanism that allows a living organism to discriminate between "self" and "nonself." Examples of immune systems occur in multicellular organisms as simple and ancient as sea sponges. In fact, complex multicellular life would be impossible without the ability to exclude external life from the internal environment. This introduction to the immune system will explore the cell types and soluble factors involved in immune reactions, as well as their location in the body during development and maintenance. Additionally, a description of the immunological events during an innate and adaptive immune reaction to an infection will be discussed, as well as a brief introduction to autoimmunity, cancer immunity, vaccines, and immunotherapies.

The major reasons for developing human monoclonal antibodies were to be able to efficiently manipulate their effector functions while avoiding immunogenicity seen with rodent antibodies. Those effector functions involve interactions with the complement system and naturally occurring Fc receptors on diverse blood white cells. Antibody immunogenicity results from the degree to which the host immune system can recognize and react to these therapeutic agents. Thus far, there is still no generally applicable technology guaranteed to render therapeutic antibodies antigenically silent. This is not to say that the task is impossible, but rather that we need to train the immune system to help us. This can be achieved if we take advantage of natural mechanisms by which an individual can be rendered tolerant of "foreign" antigens, and as a corollary minimize the potential immunogenicity of any contaminating protein aggregates, or "aggregates" arising from antibodies complexing with their antigen. I here summarize our efforts to engineer antibodies to harness optimal effector functions, while also minimizing their immunogenicity. Potential avenues to achieve the latte are predicted from classical work showing that monomeric "foreign" immunoglobulins are good tolerogens, while aggregates of immunoglobulins ate intrinsically immunogenic. Consequently, I argue that one solution to the immunogenicity problem lies in ensuring a temporal quantitative advantage of tolerogenic non-cell-bound monomer over the cell-binding immunogenic form.

The link between systemic autoimmunity, brain pathology, and aberrant behavior is still a largely unexplored field of biomedical science. Accumulating evidence points to causal relationships between immune factors, neurodegeneration, and neuropsychiatric manifestations. By documenting autoimmunity-associated neuronal degeneration and cytotoxicity of the cerebrospinal fluid from disease-affected subjects, the murine MRL model had shown high validity in revealing principal pathogenic circuits. In addition, unlike any other autoimmune strain, MRL mice produce antibodies commonly found in patients suffering from lupus and other autoimmune disorders. This review highlights importance of the MRL model as a useful preparation in understanding the links between immune system and brain function.

Mass cytometry has emerged as a new state-of-the-art technology that enables in-depth characterization of cellular populations and functions at a single cell resolution. We describe the application of this technology to deeply phenotype the blood and bone marrow components of multiple myeloma patients in a clinical setting. This technology allows for simultaneous quantification of more than 40 markers, overcoming the challenges of traditional fluorescence-based flow cytometry.

Tumor development is closely related to chronic inflammation and to evasion of immune defense mechanisms by neoplastic cells. The mediators of the inflammatory process as well as proteins involved in immune response or immune response evasion can be subject to various epigenetic changes such as methylation, acetylation, or phosphorylation. Some of these, such as cytokine suppressors, are undergoing repression through epigenetic changes, and others such as cytokines or chemokines are undergoing activation through epigenetic changes, both modifications having as a result tumor progression. The activating changes can affect the receptor molecules involved in immune response and these promote inflammation and subsequently tumor development while the inactivating changes seem to be related to the tumor regression process. The proteins involved in antigen presentation, and, therefore in immune response escape, such as classical HLA proteins and related APM (antigen presentation machinery) with their epigenetic changes contribute to the tumor development process, either to tumor progression or regression, depending on the immune effector cells that are in play.

There is considerable research interest overlap between biological anthropology and psychoneuroimmunology (PNI), particularly given recent anthropological interest in endocrine and immune system functioning over the life span and in different environmental contexts. In this chapter, I argue that conducting research on non-WEIRD populations and applying an anthropological, evolutionary approach to PNI can greatly strengthen our understanding of immune-endocrine-behavior connections. This chapter reviews population-level variation in the human immune and endocrine systems, as well as genetic and environmental contributions to this variation. The effects of culture on shaping health outcomes and stress responses are also considered. Finally, this chapter discusses some noninvasive sampling methodologies appropriate to field research and alternatives to laboratory-based research designs. By confronting variable social and environmental contexts, PNI can greatly expand on its existing contributions to the treatment and understanding of depression, mood disorders, stress, and other aspects of health and well-being.

Peyer's patches (PPs) are secondary lymphoid organs that coordinate the immunoglobulin A (IgA) response against commensal and pathogenic bacteria. In contrast to the immune dynamics in peripheral lymph nodes, the dynamics of immune response in PP have not been extensively characterized in vivo by two-photon microscopy, mainly due to the PP location on the anti-mesenteric side of the small intestine and the associated peristaltic movement.Here, we describe an approach based on a custom-made spring-loaded platform to immobilize PPs and allow for two-photon microscopy imaging in vivo. We also list different strategies based on fluorescent dyes, as well as Cre/Lox and Reporter-based system, that can be used to image specific immune cell populations in distinct areas of PPs.

Recent developments in mouse models that harbor part of a human immune system have proved extremely valuable to study the in vivo immune response to human specific pathogens such as Epstein-Barr virus. Over the last decades, advances in immunodeficient mouse strains that can be used as recipients for human immune cells have greatly enhanced the use of these models. Here, we describe the generation of mice with reconstituted human immune system (HIS mice) using immunocompromised mice transplanted with human CD34 + hematopoietic stem cells. We will also describe how such mice, in which human immune cells are generated de novo, can be used to study EBV infection.

The recent development of severely immunodeficient mouse strains enabled the production of new-generation humanized mice, in which major components of the human immune system are reconstituted. These new-generation humanized mice can be infected with human pathogenic viruses that do not infect regular mice and target cells of the hematoimmune system. Here we describe the method for preparing humanized mice, infecting them with EBV, and for their virological and immunological analyses. The results obtained from our own mouse models are briefly described.

The signaling pathway of the evolutionary old transcription factor AhR is inducible by a number of small molecular weight chemicals, including toxicants such as polycyclic aromatic hydrocarbons, bacterial toxic pigments, and physiological compounds such as tryptophan derivatives or dietary indoles. AhR activation is of immunological importance, but at the same time mediates toxicity of environmental pollutants, such as immunosuppression by dioxins. Measuring AhR activity and identification of ligands is thus of great interest for a variety of research fields. In this chapter, I briefly introduce the AhR signaling pathway, its role in immunology, and the tools and assays needed to analyze AhR signaling. Both are also needed when therapeutic applications are envisioned.

Animal models have been instrumental in our understanding of the mechanisms of rejection and the testing of novel treatment options in the context of transplantation. We have now entered an exciting era with research on humanized mice driving advances in translational studies and in our understanding of the function of human cells in response to pathogens and cancer as well as the recognition of human allogeneic tissues in vivo. In this chapter we provide a historical overview of humanized mouse models of transplantation to date, outlining the distinct strains and share our experiences in the study of human transplantation immunology.

Galectins are an evolutionarily ancient family of glycan-binding proteins (GBPs) and are found in all animals. Although they were discovered over 30 years ago, ideas about their biological functions continue to evolve. Current evidence indicates that galectins, which are the only known GBPs that occur free in the cytoplasm and extracellularly, are involved in a variety of intracellular and extracellular pathways contributing to homeostasis, cellular turnover, cell adhesion, and immunity. Here we review evolving insights into galectin biology from a historical perspective and explore current evidence regarding biological roles of galectins.

Understanding the interplay between metabolic and cellular signaling systems has emerged as a focus in the study of metabolic disorders, cancer, and immune responses. Immune system is active in the regulation of metabolism. Lymphocyte activation initiates a program of cell growth, proliferation, and differentiation that increase metabolic demand. Activated lymphocytes must alter their metabolism to support these increased synthetic activities. In this chapter, we describe how signaling via the immune system integrates with metabolic functions to control immune response and vice versa. It has been explained mainly in the context of T lymphocyte activation and, to a lesser detail, in other immune cell types.

The various cells and proteins responsible for immunity constitute the immune system, and their orchestrated response to defend foreign/non-self substances (antigen) is known as the immune response. When an antigen attacks the host system, two distinct, yet interrelated, branches of the immune system are active-the nonspecific/innate and specific/adaptive immune response. Both of these systems have certain physiological mechanisms, which enable the host to recognize foreign materials to itself and to neutralize, eliminate, or metabolize them. Innate immunity represents the earliest development of protection against antigens. Adaptive immunity has again two branches-humoral and cell mediated. It should be noted that both innate and adaptive immunities do not work independently. Moreover, most of the immune responses involve the activity and interplay of both the humoral and the cell-mediated immune branches of the immune system. We have described these branches in detail along with the mechanism of antigen recognition. This chapter also describes the disorders of immune system in brief.

A large volume of data relevant to immunology research has accumulated due to sequencing of genomes of the human and other model organisms. At the same time, huge amounts of clinical and epidemiologic data are being deposited in various scientific literature and clinical records. This accumulation of the information is like a goldmine for researchers looking for mechanisms of immune function and disease pathogenesis. Thus the need to handle this rapidly growing immunological resource has given rise to the field known as immunoinformatics. Immunoinformatics, otherwise known as computational immunology, is the interface between computer science and experimental immunology. It represents the use of computational methods and resources for the understanding of immunological information. It not only helps in dealing with huge amount of data but also plays a great role in defining new hypotheses related to immune responses. This chapter reviews classical immunology, different databases, and prediction tool. Further, it briefly describes applications of immunoinformatics in reverse vaccinology, immune system modeling, and cancer diagnosis and therapy. It also explores the idea of integrating immunoinformatics with systems biology for the development of personalized medicine. All these efforts save time and cost to a great extent.

Immunodeficient mice engrafted with human immune systems provide an exciting model to study human immunobiology in an in vivo setting without placing patients at risk. The essential parameter for creation of these "humanized models" is engraftment of human hematopoietic stem cells (HSC) that will allow for optimal development of human immune systems. However, there are a number of strategies to generate humanized mice and specific protocols can vary significantly among different laboratories. Here we describe a protocol for the co-implantation of human HSC with autologous fetal liver and thymic tissues into immunodeficient mice to create a humanized model with optimal human T cell development. This model, often referred to as the Thy/Liv or BLT (bone marrow, liver, thymus) mouse, develops a functional human immune system, including HLA-restricted human T cells, B cells, and innate immune cells.

MicroRNAs (miRNAs) are tiny regulators of gene expression on the posttranscriptional level. Since the discovery of the first miRNA 20 years ago, thousands of them have been described. The discovered miRNAs have regulatory functions in biological and pathological processes. Biologically, miRNAs have been implicated in development, differentiation, proliferation, apoptosis, and immune responses. In this work, we summarize the role of miRNA in biological processes taking into account the various areas named above.

The immune system specifically recognizes and eliminates foreign antigens and, thus, protects integrity of the host. During maturation of the immune system, tolerance mechanisms develop that prevent or inhibit potentially harmful reactivities to self-antigens. Autoreactive B and T cells that are generated during immune responses are eliminated by apoptosis in the thymus, lymph nodes, or peripheral circulation or actively suppressed by regulatory T cells. However, autoreactive cells may survive due to failure of apoptosis or molecular mimicry, i.e., presentation and recognition of cryptic epitopes of self-antigens, or aberrant lymphokine production. Preservation of the host requires the development of immune responses to foreign antigen and tolerance to self-antigens. Autoimmunity results from a breakdown of tolerance to self-antigens through an interplay of genetic and environmental factors.One of the basic functions of the immune system is to specifically recognize and eliminate foreign antigens and, thus, protect integrity of the host. Through rearrangements and somatic mutations of various gene segments encoding T and B cell receptors and antibody molecules, the immune system acquires tremendous diversity. During maturation of the immune system, recognition of self-antigens plays an important role in shaping the repertoires of immune receptors. Tolerance mechanisms develop that prevent or inhibit potentially harmful reactivities to self-antigens. These self-defense mechanisms are mediated on the levels of central and peripheral tolerance, i.e., autoreactive T cells are either eliminated by apoptosis in the thymus, lymph nodes, or peripheral circulation or actively suppressed by regulatory T cells. Likewise, autoreactive B cells are eliminated in the bone marrow or peripheral lymphoid organs. However, immune responses triggered by foreign antigens may be sustained by molecular mimicry, i.e., presentation and recognition of cryptic epitopes of self-antigens. Further downstream, execution of immune responses depends on the functioning of intracellular signaling networks and the cooperation of many cell types communicating via surface receptors, cytokines, chemokines, and antibody molecules. Therefore, autoimmunity represents the end result of the breakdown of one or multiple basic mechanisms of immune tolerance (Table 1).

Although many studies have documented peripheral immune alterations in patients with psychiatric and neurological disorders, almost all these data in humans are correlative. The actions of IL-2 on neurodevelopment, function, and disease are the result of both IL-2's actions in the peripheral immune system and intrinsic actions in the CNS. Determining if, and under what conditions (e.g., development, acute injury) these different actions of IL-2 are operative in the brain is essential to make advances in understanding the multifaceted affects of IL-2 on CNS function and disease. Mouse models have provided ways to obtain new insights into how the complex biology of a cytokine such as IL-2 can have simultaneous, dynamic effects on multiple systems (e.g., regulating homeostasis in the brain and immune system, autoimmunity that can affect both systems). Here we describe some of the relevant literature and our research using different mouse models. This includes models such as congenic IL-2 knockout mice bred on immunodeficient backgrounds coupled with immune reconstitution strategies used to dissect neuroimmunological processes involved in the development of septohippocampal pathology, and test the hypothesis that dysregulation of the brain's endogenous neuroimmunological milieu may occur with the loss of brain IL-2 gene expression and be involved in initiating CNS autoimmunity. Use of animal models like these in the field of psychoneuroimmunology may lead to critical advances into our understanding of the role of brain cytokines and autoimmunity in neurodegenerative diseases (e.g., Alzheimer's disease), neurodevelopmental disorder (e.g., autism, schizophrenia), and autoimmune diseases including multiple sclerosis.

Autism spectrum disorders (ASD) are complex and heterogeneous with a spectrum of diverse symptoms. Mounting evidence from a number of disciplines suggests a link between immune function and ASD. Although the causes of ASD have yet to be identified, genetic studies have uncovered a host of candidate genes relating to immune regulation that are altered in ASD, while epidemiological studies have shown a relationship with maternal immune disturbances during pregnancy and ASD. Moreover, decades of research have identified numerous systemic and cellular immune abnormalities in individuals with ASD and their families. These include changes in immune cell number, differences in cytokine and chemokine production, and alterations of cellular function at rest and in response to immunological challenge. Many of these changes in immune responses are associated with increasing impairment in behaviors that are core features of ASD. Despite this evidence, much remains to be understood about the precise mechanism by which the immune system alters neurodevelopment and to what extent it is involved in the pathogenesis of ASD. With estimates of ASD as high as 1% of children, ASD is a major public health issue. Improvements in our understanding of the interactions between the nervous and immune system during early neurodevelopment and how this interaction is different in ASD will have important therapeutic implications with wide ranging benefits.

The purpose of this review was to provide current knowledge about the possible association between psychosocial job stress and immune parameters in blood, saliva, and urine. Using bibliographic databases (PubMed, PsychINFO, Web of Science, Medline) and the snowball method, 56 studies were found. In general, exposure to psychosocial job stress (high job demands, low job control, high job strain, job dissatisfaction, high effort-reward imbalance, overcommitment, burnout, unemployment, organizational downsizing, economic recession) had a measurable impact on immune parameters (reduced NK cell activity, NK and T cell subsets, CD4+/CD8+ ratio, and increased inflammatory markers). The evidence supports that psychosocial job stresses are related to disrupted immune responses but further research is needed to demonstrate cause-effect relationships.

The link between systemic autoimmunity, brain pathology, and aberrant behavior is still largely unexplored field of biomedical science. Accumulating evidence points to causal relationships between immune factors, neurodegeneration, and neuropsychiatric manifestations. By documenting autoimmunity-associated neuronal degeneration and cytotoxicity of the cerebrospinal fluid from disease-affected subjects, the murine MRL model had shown high validity in revealing principal pathogenic circuits. In addition, unlike any other autoimmune strain, MRL mice produce antibodies commonly found in patients suffering from lupus and other autoimmune disorders. This review highlights importance of the MRL model as an indispensible preparation in understanding the links between immune system and brain function.

Over the past three decades, the field of psychoneuroimmunology research has blossomed into a major field of study, gaining interests of researchers across all traditionally accepted disciplines of scientific research. This chapter provides an overview of our current understanding in defining neuroimmune interactions with a primary focus of discussing the neuroendocrine receptor activity by immune cells. This chapter highlights the necessity of neuroimmune responses as it relates to a better understanding of the pathophysiological mechanisms of health and disease.

RNA interference (RNAi) is an important pathway to combat virus infections in insects and plants. Hallmarks of antiviral RNAi in these organisms are: (1) an increase in virus replication after inactivation of major actors in the RNAi pathway, (2) production of virus-derived small interfering RNAs (v-siRNAs), and (3) suppression of RNAi by dedicated viral proteins. In this chapter, we will review the mechanism of RNAi in insects, its function as an antiviral immune system, viral small RNA profiles, and viral counterdefense strategies. We will also consider alternative, inducible antiviral immune responses.

The immune system plays an important role in the development of personalized medicine for a variety of diseases including cancer, autoimmune diseases, and infectious diseases. Immunoinformatics, or computational immunology, is an emerging area that provides fundamental methodologies in the study of immunomics, that is, immune-related genomics and proteomics. The integration of immunoinformatics with systems biology approaches may lead to a better understanding of immune-related diseases at various systems levels. Such methods can contribute to translational studies that bring scientific discoveries of the immune system into better clinical practice. One of the most intensely studied areas of the immune system is immune epitopes. Epitopes are important for disease understanding, host-pathogen interaction analyses, antimicrobial target discovery, and vaccine design. The information about genetic diversity of the immune system may help define patient subgroups for individualized vaccine or drug development. Cellular pathways and host immune-pathogen interactions have a crucial impact on disease pathogenesis and immunogen design. Epigenetic studies may help understand how environmental changes influence complex immune diseases such as allergy. High-throughput technologies enable the measurements and catalogs of genes, proteins, interactions, and behavior. Such perception may contribute to the understanding of the interaction network among humans, vaccines, and drugs, to enable new insights of diseases and therapeutic responses. The integration of immunomics information may ultimately lead to the development of optimized vaccines and drugs tailored to personalized prevention and treatment. An immunoinformatics portal containing relevant resources is available at http://immune.pharmtao.com.

Developmental immunotoxicity (DIT) has emerged as a serious health consideration given the increases in the prevalence of many immune-based childhood diseases and conditions, including allergic diseases and asthma, recurrent otitis media, pediatric celiac disease, and type 1 diabetes. As a result, the use of DIT testing to identify potential environmental risk factors contributing to these and other diseases has become a higher priority. This introductory chapter considers: (1) the basis for an increased and earlier use of DIT testing in safety evaluations and (2) the general features of DIT testing strategies designed to reduce health risks.

Central to the evaluation of potential immunotoxicants is the concept that measurement of multiple parameters is required for the determination of toxicity toward the immune system. A carefully considered integration of endpoints involved in the immune response should be used to determine an immunotoxic effect. A functional evaluation, specifically the rodent T-cell-dependent antibody response (TDAR) model developed for regulated immunotoxicity evaluations, has been established to detect potential immunotoxicity, especially immunosuppression, caused by chemicals and novel pharmaceuticals in development. This chapter provides an overview and detailed procedures involved in the TDAR assay that measures the immune response (i.e., antibody production) to an introduced antigen (i.e., keyhole limpet hemocyanin (KLH)) in rats or mice treated with a chemical (e.g., a known immunotoxicant and/or a new drug candidate). The TDAR model of competent immune function requires the participation of multiple effector cells such as antigen presenting cells, T lymphocytes, and B lymphocytes to produce the final product, the antigen-specific antibody response. Thus, alterations in the level of antibody production to the specific antigen may reflect effects on any or all of the cell populations involved in TDAR.

Small interfering RNAs (siRNAs) are routinely used as a genetic tool and hold promise for a range of therapeutic applications. However, one of the hurdles of making these agents a real therapeutic modality includes the activation of innate immunity and off-target effects. Therefore, the use of siRNAs in functional genomics and therapies depends on the development of new strategies to overcome these unwanted effects. It appears that the major innate immune response to chemically synthesized siRNAs is mediated by TLR7 and/or TLR8 in immune cells. Importantly, it has also been shown that the replacement of uridines with their 2'-modified counterparts can prevent immune activation. Similarly, 2'-modifications, particularly at the seed sequence reduced the number of unwanted off-target genes without interfering with siRNA silencing potency of the anticipated target gene. This chapter describes how to separate gene silencing from immunostimulation. Also, it discusses the impact of these findings on the design of effective cancer vaccines.

Since the late 1980s, the study of the function and development of the human immune system has made intensive use of humanized animal models, among which mouse models have been proven extremely efficient and handy. Recent advances have lead to the establishment of new models with improved characteristics, both in terms of engraftment efficiency and in situ multilineage human hematopoietic development. In particular, the use of newborn BALB/c Rag2-/-gamma c-/- mice as recipients for human hematopoietic stem cells has proven particularly efficient. We describe here how to produce and monitor such "human immune system" (HIS) (BALB-Rag/gamma) mice, which offer large prospects for experimental study of the human immune system and as a preclinical screening tool.

Transgenic technology, the introduction of genetic information into the germ line of an animal to alter its genetic constitution stably, provides a powerful tool for studying the development, functions, and malfunctions of complex biological systems. The main advantage has been that it is possible to study the gene functioning in its natural milieu. This is particularly informative when the genes have been manipulated such that the regulation and tissue specificity of expression are altered. Although transgenic animals bear the introduced gene in every tissue, expression of that gene may be widespread or directed to particular cell lineages, depending on the regulatory sequences chosen.