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Abstract: Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition to forming a coherent description of the data‐generating process, probabilistic models enable parameter inference about given datasets. This procedure is well developed in the Bayesian perspective, in which one infers probability distributions describing to what extent various possible parameters agree with the data. In this paper, we motivate and review probabilistic modeling for adaptive immune receptor repertoire data then describe progress and prospects for future work, from germline haplotyping to adaptive immune system deployment across tissues. The relevant quantities in immune sequence analysis include not only continuous parameters such as gene use frequency but also discrete objects such as B‐cell clusters and lineages. Throughout this review, we unravel the many opportunities for probabilistic modeling in adaptive immune receptor analysis, including settings for which the Bayesian approach holds substantial promise (especially if one is optimistic about new computational methods). From our perspective, the greatest prospects for progress in probabilistic modeling for repertoires concern ancestral sequence estimation for B‐cell receptor lineages, including uncertainty from germline genotype, rearrangement, and lineage development. [ABSTRACT FROM AUTHOR]

Many of the reviews include discussion of diffusible molecules involved in cell-cell communication during the evolution of innate and adaptive responses (eg, interferons) and how these mediators influence the outcome of the dynamic processes visualized by optical methods. New data on tissue-resident T cells also fall in this category, as do recent observations of perivascular co-localization of effector lymphocytes and presenting cells at sites of effector function within tissues. Technologies are now emerging that will permit combining the protein and cell-based optical imaging methods used to date with recent advances in nucleic acid/genomic methods, especially single-cell sequencing. [Extracted from the article]

Summary: The diploë region of skull has recently been discovered to act as a myeloid cell reservoir to the underlying meninges. The presence of ossified vascular channels traversing the inner skull of cortex provides a passageway for the cells to traffic from the niche, and CNS‐derived antigens traveling through cerebrospinal fluid in a perivascular manner reaches the niche to signal myeloid cell egress. This review will highlight the recent findings establishing this burgeoning field along with the known role this niche plays in CNS aging and disease. It will further highlight the anatomical routes and physiological properties of the vascular structures these cells use for trafficking, spanning from skull to brain parenchyma. [ABSTRACT FROM AUTHOR]

Age‐associated B cells (ABCs) have emerged as critical components of immune responses. Their inappropriate expansion and differentiation have increasingly been linked to the pathogenesis of autoimmune disorders, aging‐associated diseases, and infections. ABCs exhibit a distinctive phenotype and, in addition to classical B cell markers, often express the transcription factor T‐bet and myeloid markers like CD11c; hence, these cells are also commonly known as CD11c+T‐bet+ B cells. Formation of ABCs is promoted by distinctive combinations of innate and adaptive signals. In addition to producing antibodies, these cells display antigen‐presenting and proinflammatory capabilities. It is becoming increasingly appreciated that the ABC compartment exhibits a high degree of heterogeneity, plasticity, and sex‐specific regulation and that ABCs can differentiate into effector progeny via several routes particularly in autoimmune settings. In this review, we will discuss the initial insights that have been obtained on the molecular machinery that controls ABCs and we will highlight some of the unique aspects of this control system that may enable ABCs to fulfill their distinctive role in immune responses. Given the expanding array of autoimmune disorders and pathophysiological settings in which ABCs are being implicated, a deeper understanding of this machinery could have important and broad therapeutic implications for the successful, albeit daunting, task of targeting these cells. [ABSTRACT FROM AUTHOR]

Humoral and cellular responses to viral infections coexist in a dynamic equilibrium that often results in efficient viral clearance. However, in some infections one of the two responses prevails, for instance when an overactivation of cytotoxic T cells is accompanied by weak and insufficient antibody responses. Although the cellular response is usually sufficient to control a primary viral infection, in some cases clearance is not complete and persistent infections ensue. In order to design effective therapeutic or vaccination strategies aiming at inducing early and potent neutralizing antibody responses, a deep knowledge of the cellular and molecular determinants of antiviral immune responses is needed. Here, we review our understanding on the spatiotemporal dynamics of antiviral humoral immune responses, with a particular focus on recent studies using intravital imaging approaches as an insightful complement to more traditional techniques. [ABSTRACT FROM AUTHOR]

Germinal centers (GCs) are the site of antibody affinity maturation, a fundamental immunological process that increases the potency of antibodies and thereby their ability to protect against infection. GC biology is highly dynamic in both time and space, making it ideally suited for intravital imaging. Using multiphoton laser scanning microscopy (MPLSM), the field has gained insight into the molecular, cellular, and structural changes and movements that coordinate affinity maturation in real time in their native environment. On the other hand, several limitations of MPLSM have had to be overcome to allow full appreciation of GC events taking place across different timescales. Here, we review the technical advances afforded by intravital imaging and their contributions to our understanding of GC biology. [ABSTRACT FROM AUTHOR]

The number of regulatory B cell "followers" has increased steadily in the last few years confirming the rising interest in understanding the relevance of this subset of B cells in controlling immune responses in a variety of immune-related diseases. Multiple sclerosis (MS) has been historically considered a T cell-driven disease; however, the recent undeniable success of B cell-depletion therapy in the amelioration of MS clearly shows the involvement of B cells in the pathology of this disease.22,23 Wang et al24 provide a balanced resume of recent findings showing the complex interplay of both pathogenic and protective effects that B cells have in this disease. Increased intensity and prolonged DTH reactions were observed in B cell-depleted DNFB-sensitized guinea pigs.3 Later studies showed that adoptive transfer of lymphocytes or total splenocytes suppressed the intensity of the DTH response.4,5 These cells were dubbed "suppressor B cells." This issue also provides several insights into the mechanisms of action of B cell depletion and how novel therapies targeting the interaction between B cells and cells of the innate immune system are currently used to inform drug development. [Extracted from the article]

Humoral immunity is a critical component of the coordinated response required to resolve viral infections and mediate protection following pathogen clearance or vaccination. A better understanding of factors shaping the memory B cell response will allow tailored development of efficient preventative vaccines against emerging acute viral infections, therapeutic vaccines, and immunotherapies for chronic viral infections. Here, we use recent data obtained by profiling antigen‐specific B cell responses in hepatitis B as a framework to explore lessons that can be learnt from different viral infections about the diverse influences on humoral immunity. Hepatitis B provides a paradigm where successful B cell responses in resolved or vaccinated individuals can be contrasted to the failed response in chronic infection, while also exemplifying the degree to which B cell responses within infected individuals can differ to two antigens from the same virus. Drawing on studies in other human and murine infections, including emerging data from COVID‐19, we consider the influence of antigen quantity and structure on the quality of the B cell response, the role of differential CD4 help, the importance of germinal center vs extrafollicular responses and the emerging concept that responses residing in non‐lymphoid organs can participate in B cell memory. [ABSTRACT FROM AUTHOR]

B cells have classically been recognized for their unique and indispensable role in the production of antibodies. Their potential as immunoregulatory cells with anti‐inflammatory functions has received increasing attention during the last two decades. Herein, we highlight pioneering studies in the field of regulatory B cell (Breg) research. We will review the literature on Bregs with a particular focus on their role in the regulation of allergic inflammation. [ABSTRACT FROM AUTHOR]

Memory B cells (Bmem) provide an active second layer of defense against re‐infection by pathogens that have bypassed the passive first layer provided by neutralizing antibodies. Here, we review recent progress in our understanding of Bmem heterogeneity in terms of their origin (germinal center‐dependent vs center‐independent), phenotype (canonical vs atypical vs age‐associated B cells), trafficking (recirculating vs tissue‐resident), and fate (plasma cell vs germinal center differentiation). The development of transgenic models and intravital imaging technologies has made it possible to track the cellular dynamics of Bmem reactivation by antigen, their interactions with follicular memory T cells, and differentiation into plasma cells in subcapsular proliferative foci in the lymph nodes of immune animals. Such in situ studies have reinforced the importance of geography in shaping the outcome of the secondary antibody response. We also review the evidence for Bmem reactivation and differentiation into short‐lived plasma cells in the pathogenesis of disease flares in relapsing‐remitting autoimmune diseases. Elucidating the mechanisms that control the Bmem fate decision to differentiate into plasma cells or germinal center B cells will aid future efforts to more precisely engineer fit‐for‐purpose vaccines as well as to treat antibody‐mediated autoimmune diseases. [ABSTRACT FROM AUTHOR]

The current concepts for development of autoreactive B cells in SLE (systemic lupus erythematosus) focus on extrinsic stimuli and factors that provoke B cells into tolerance loss. Traditionally, major tolerance loss pathways are thought to be regulated by factors outside the B cell including autoantigen engagement of the B‐cell receptor (BCR) with simultaneous type I interferon (IFN) produced by dendritic cells, especially plasmacytoid dendritic cells (pDCs). Later, in autoreactive follicles, B‐cells encounter T‐follicular helper cells (Tfh) that produce interleukin (IL)‐21, IL‐4 and pathogenic cytokines, IL‐17 and IFN gamma (IFNɣ). This review discusses these mechanisms and also highlights recent advances pointing to the peripheral transitional B‐cell stage as a major juncture where transient autocrine IFNβ expression by developing B‐cells imprints a heightened susceptibility to external factors favoring differentiation into autoantibody‐producing plasmablasts. Recent studies highlight transitional B‐cell heterogeneity as a determinant of intrinsic resistance or susceptibility to tolerance loss through the shaping of B‐cell responsiveness to cytokines and other environment factors. [ABSTRACT FROM AUTHOR]

The adaptive immune system is tasked with producing antibodies that recognize a wide scope of potential pathogens, including those never before encountered, and concurrently avoiding formation of antibodies binding host tissues. The diverse repertoire of antibodies produced by V(D)J recombination inevitably includes autoantibodies that bind to self‐antigens, estimated to be as much as 70% of nascent antibodies on immature B cells. Early theoretical models of tolerance hypothesized that such self‐reactive clones could not possibly be allowed to survive and mature. However from the first direct view of the fate of nascent B cells carrying a self‐binding antibody it was clear that many "forbidden clones" circulate to secondary lymphoid tissues, where they adopt an IgMlow IgD+ cell surface phenotype and are prevented from secreting autoantibodies by a series of tolerance checkpoints referred to as "clonal anergy." Since anergic B cells can be reactivated to secrete pathogenic autoantibodies in certain settings, the advantage of controlling self‐reactive antibodies by clonal anergy has until recently remained enigmatic. Here we review this topic and recent advances showing that anergic B cells are recruited into the germinal center to mutate away from self‐reactivity, undergoing "clonal redemption" into cells making antibodies with exquisite specificity for foreign immunogens. [ABSTRACT FROM AUTHOR]

Phosphatidylinositol 3 kinases (PI3K) are a family of lipid kinases that are activated by a variety of cell‐surface receptors, and regulate a wide range of downstream readouts affecting cellular metabolism, growth, survival, differentiation, adhesion, and migration. The importance of these lipid kinases in lymphocyte signaling has recently been highlighted by genetic analyses, including the recognition that both activating and inactivating mutations of the catalytic subunit of PI3Kδ, p110δ, lead to human primary immunodeficiencies. In this article, we discuss how studies on the human genetic disorder "Activated PI3K‐delta syndrome" and mouse models of this disease (Pik3cdE1020K/+ mice) have provided fundamental insight into pathways regulated by PI3Kδ in T and B cells and their contribution to lymphocyte function and disease, including responses to commensal bacteria and the development of autoimmunity and tumors. We highlight critical roles of PI3Kδ in T follicular helper cells and the orchestration of the germinal center reaction, as well as in CD8+ T‐cell function. We further  present data demonstrating the ability of the AKT‐resistant FOXO1AAA mutant to rescue IgG1 class switching defects in Pik3cdE1020K/+ B cells, as well as data supporting a role for PI3Kδ in promoting multiple T‐helper effector cell lineages. [ABSTRACT FROM AUTHOR]

Although calcium signaling and the important role of calcium release–activated calcium channels is well recognized in the context of immune cell signaling, there is a vast diversity of ion channels and transporters that regulate the entry of ions beyond calcium, including magnesium, zinc, potassium, sodium, and chloride. These ions play a critical role in numerous metabolic and cellular processes. The importance of ions in human health and disease is illustrated by the identification of primary immunodeficiencies in patients with mutations in genes encoding ion channels and transporters, as well as the immunological defects observed in individuals with nutritional ion deficiencies. Despite progress in identifying the important role of ions in immune cell development and activation, we are still in the early stages of exploring the diversity of ion channels and transporters and mechanistically understanding the role of these ions in immune cell biology. Here, we review the biology of ion signaling in B cells and the identification of critical ion channels and transporters in B‐cell development, activation, and differentiation into effector cells. Elucidating the role of ion channels and transporters in immune cell signaling is critical for expanding the repertoire of potential therapeutics for the treatment of immune disorders. Moreover, increased understanding of the role of ions in immune cell function will enhance our understanding of the potentially serious consequences of ion deficiencies in human health and disease. [ABSTRACT FROM AUTHOR]

Summary: The purpose of this article is to review the role of extrafollicular and T‐cell independent antibody responses in humoral immunity. We consider two interrelated questions: (a) do T‐cell independent antibody responses dominated by IgM and/or IgA play unique functions in immunity and homeostasis; and (b) is it typical for these responses to result in lifelong protection? In addressing these questions, we consider the established advantages of T‐cell driven responses including the unique role played by germinal center reactions in these responses, and contrast the processes and outcomes of germinal center‐centric responses with germinal center‐ and T‐cell independent antibodies. We suggest that T‐independent and other extrafollicular responses contribute substantially to highly stable antibody repertoires in both the serum and the intestine, providing relatively constitutive humoral barriers with the collective dual function of protecting against invading pathogens and regulating the composition of non‐pathogenic microbial communities. [ABSTRACT FROM AUTHOR]

Summary: Despite the extreme diversity of T‐cell repertoires, many identical T‐cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely shared sequences, often referred to as “public,” have been suggested to be over‐represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here, we show that even for large cohorts, the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations, we propose a public/private sequence classifier, “PUBLIC” (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes. [ABSTRACT FROM AUTHOR]

Summary: The vast majority of vaccines exploit antibody memory to induce lasting immunity. Memory B cells are generated during the initial response to infection, but persist long after the infection has cleared. Immune memory success relies on its adaptability: in response to different pathogens, variants of a single pathogen, and in balancing persistence with reactivation and plasma cell differentiation. This is likely achieved by producing a B cell memory population that is highly diverse, and recent work has highlighted the importance of memory B cell subsets in mediating the dichotomous roles of the population. This review will detail the characterization, function and both intrinsic and extrinsic regulation of different memory B cell subsets: memory B cell precursors within the germinal center, phenotypic, and functional heterogeneity of the memory B cell population, and memory B cell subsets that reside in tissues. In particular, understanding the genetic and epigenetic regulation of memory B diversity may be critical for gaining insight into B cell memory responses to pathogens that have evaded effective vaccine design. Therefore, there is a vital need to understand the mechanisms underlying the origin, function and translational potential of the heterogeneity within the memory B cell population. [ABSTRACT FROM AUTHOR]

Summary: The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self‐reactive B cells removed. Later antigen‐dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen‐specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub‐speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action. [ABSTRACT FROM AUTHOR]

Summary: Vaccines or early childhood exposure to infection mediate immunity, that is, improved resistance against disease and death caused by a second infection with the same agent. This has been explained by and equaled to immunological memory, that is, an “altered immune system behavior” that is maintained in a presumably antigen‐independent fashion. This review summarizes epidemiological and experimental data, that largely falsify this idea and that show that periodic re‐exposure to antigen either, artificially as vaccines or naturally as low‐level persisting antigens or infections, or immune complexes on follicular dendritic cells or endemic re‐exposure is necessary for protection. Both, the huge success of vaccines in controlling childhood infections, the reduction in clinical disease and the chance of endemically re‐exposure, have gradually reduced periodical re‐exposure to infections and thereby endangered protective herd immunity. In parallel, vaccine deniers have created susceptibility islands even in an otherwise well vaccinated population, thereby creating a very new situation when compared to the later parts of the 20th century. If protective Immunity is—as emphasized here—antigen driven, then increasingly frequent revaccinations will be necessary (even more so with too much attenuated vaccines) to maintain both herd immunity and individual resistance to acute infections. Of course, this rule also applies to tumor vaccines. [ABSTRACT FROM AUTHOR]

HIV-1 and its surface envelope glycoproteins (Env), gp120 and gp41, have evolved immune evasion strategies that render the elicitation of effective antibody responses to the functional Env entry unit extremely difficult. HIV-1 establishes chronic infection and stimulates vigorous immune responses in the human host; forcing selection of viral variants that escape cellular and antibody (Ab)-mediated immune pressure, yet possess contemporary fitness. Successful survival of fit variants through the gauntlet of the human immune system make this virus and these glycoproteins a formidable challenge to target by vaccination, requiring a systematic approach to Env mimetic immunogen design and evaluation of elicited responses. Here, we review key aspects of HIV-1 Env immunogenicity and immunogen re-design, based on experimental data generated by us and others over the past decade or more. We further provide rationale and details regarding the use of newly evolving tools to analyze B cell responses, including approaches to use next generation sequencing for antibody lineage tracing and B cell fate mapping. Together, these developments offer opportunities to address long-standing questions about the establishment of effective B cell immunity elicited by vaccination, not just against HIV-1. [ABSTRACT FROM AUTHOR]

Monoclonal antibodies are essential therapeutics and diagnostics in a large number of diseases. Moreover, they are essential tools in all sectors of life sciences. Although the great majority of monoclonal antibodies currently in use are of mouse origin, the use of human B cells to generate monoclonal antibodies is increasing as new techniques to tap the human B cell repertoire are rapidly emerging. Cloned lines of immortalized human B cells are ideal sources of monoclonal antibodies. In this review, we summarize our studies to the regulation of the replicative life span, differentiation, and maturation of B cells that led to the development of a platform that uses immortalization of human B cells by in vitro genetic modification for antibody development. We describe a number of human antibodies that were isolated using this platform and the application of the technique in other species. We also discuss the use of immortalized B cells as antigen-presenting cells for the discovery of tumor neoantigens. [ABSTRACT FROM AUTHOR]

Immunoglobulin D (IgD) has remained a mysterious antibody class for almost half a century. IgD was initially thought to be a recently evolved Ig isotype expressed only by some mammalian species, but recent discoveries in fishes and amphibians demonstrate that IgD was present in the ancestor of all jawed vertebrates and has important immunological functions. The structure of IgD has been very dynamic throughout evolution. Mammals can express IgD through alternative splicing and class switch recombination. Active cell-dependent and T-cell-independent IgM-to-IgD class switching takes place in a unique subset of human B cells from the upper aerodigestive mucosa, which provides a layer of mucosal protection by interacting with many pathogens and their virulence factors. Circulating IgD can bind to myeloid cells such as basophils and induce antimicrobial, inflammatory, and B-cell-stimulating factors upon cross-linking, which contributes to not only immune surveillance but also inflammation and tissue damage when this pathway is overactivated under pathological conditions. Recent research shows that IgD is an important immunomodulator that orchestrates an ancestral surveillance system at the interface between immunity and inflammation. [ABSTRACT FROM AUTHOR]

Memory antibody responses are typically seen to T-cell-dependent antigens and are characterized by the rapid production of high titers of high-affinity antigen-specific antibody. The hallmark of T-cell-dependent memory B cells is their expression of a somatically mutated, isotype-switched B-cell antigen receptor, features that are mainly generated in germinal centers. Classical studies have focused on isotype-switched memory B cells (mainly IgG isotype) and demonstrated their unique intrinsic properties in terms of localization and responsiveness to antigen re-exposure. However, recent advances in monitoring antigen-experienced B cells have revealed the considerable heterogeneity of memory B cells, which include unswitched IgM+ and/or unmutated memory B cells. The IgM and IgG type memory B cells reside in distinct locations and appear to possess distinct origins and effector functions, together orchestrating humoral memory responses. [ABSTRACT FROM AUTHOR]

Decades of high-titered antibody are sustained due to the persistence of memory B cells and long-lived plasma cells (PCs). The differentiation of each of these subsets is antigen- and T-cell driven and is dependent on signals acquired and integrated during the germinal center response. Inherent in the primary immune response must be the delivery of signals to B cells to create these populations, which have virtual immortality. Differences in biology and chemotactic behavior disperse memory B cells and long-lived PCs to a spectrum of anatomic sites. Each subset must rely on survival factors that can support their longevity. This review focuses on the generation of each of these subsets, their survival, and renewal, which must occur to sustain serological memory. In this context, we discuss the role of antigen, bystander inflammation, and cellular niches. The contribution of BAFF (B-cell activating factor belonging to the tumor necrosis factor family) and APRIL (a proliferation-inducing ligand) to the persistence of memory B cells and PCs are also detailed. Insights that have been provided over the past few years in the regulation of long-lived B-cell responses will have profound impact on vaccine development, the treatment of pre-sensitized patients for organ transplantation, and therapeutic interventions in both antibody- and T-cell-mediated autoimmunity. [ABSTRACT FROM AUTHOR]

The U1 small nuclear ribonucleoprotein particle (snRNP) is a target of autoreactive B cells and T cells in several rheumatic diseases including systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD). We propose that inherent structural properties of this autoantigen complex, including common RNA-binding motifs, B and T-cell epitopes, and a unique stimulatory RNA molecule, underlie its susceptibility as a target of the autoimmune response. Immune mechanisms that may contribute to overall U1-snRNP immunogenicity include epitope spreading through B and T-cell interactions, apoptosis-induced modifications, and Toll-like receptor (TLR) activation through stimulation by U1-snRNA. We conclude that understanding the interactions between U1-snRNP and the immune system will provide insights into why certain patients develop anti-U1-snRNP autoimmunity, and more importantly how to effectively target therapies against this autoimmune response. [ABSTRACT FROM AUTHOR]

The series of events leading to T-cell activation following antigen recognition has been extensively investigated. Although the exact mechanisms of ligand binding and transmission of this extracellular interaction into a productive intracellular signaling sequence remains incomplete, it has been known for many years that the immunoreceptor tyrosine activation motifs (ITAMs) of the T-cell receptor (TCR):CD3 complex are required for initiation of this signaling cascade because of the recruitment and activation of multiple protein tyrosine kinases, signaling intermediates, and adapter molecules. It however remains unclear why the TCR:CD3 complex requires 10 ITAMs, while many other ITAM-containing immune receptors, such as Fc receptors (FcRs) and the B cell receptor (BCR), contain far fewer ITAMs. We have recently demonstrated that various parameters of T cell development and activation are influenced by the number, as well as location and type, of ITAMs within the TCR:CD3 complex and hence propose that the TCR is capable of ‘scalable signaling’ that facilitates the initiation and orchestration of diverse T-cell functions. While many of the underlying mechanisms remain hypothetical, this review intends to amalgamate what we have learned from conventional biochemical analyses regarding initiation and diversification of T-cell signaling, with more recent evidence from molecular and fluorescent microscopic analyses, to propose a broader purpose for the TCR:CD3 ITAMs. Rather than simply signal initiation, individual ITAMs may also be responsible for the differential recruitment of signaling and regulatory molecules which ultimately affects T-cell development, activation and differentiation. [ABSTRACT FROM AUTHOR]

Notch signaling is required for the development of all T cells and marginal zone (MZ) B cells. Specific roles in T- and B-cell differentiation have been identified for different Notch receptors, the canonical Delta-like (Dll) and Jagged (Jag) Notch ligands, and downstream effectors of Notch signaling. Notch receptors and ligands are post-translationally modified by the addition of glycans to extracellular domain epidermal growth factor-like (EGF) repeats. The O-fucose glycans of Notch cell-autonomously modulate Notch–ligand interactions and the strength of Notch signaling. These glycans are initiated by protein O-fucosyltransferase 1 (Pofut1), and elongated by the transfer of N-acetylglucosamine (GlcNAc) to the fucose by β1,3GlcNAc-transferases termed lunatic, manic, or radical fringe. This review discusses T- and B-cell development from progenitors deficient in O-fucose glycans. The combined data show that Lfng and Mfng regulate T-cell development by enhancing the interactions of Notch1 in T-cell progenitors with Dll4 on thymic epithelial cells. In the spleen, Lfng and Mfng cooperate to modify Notch2 in MZ B progenitors, enhancing their interaction with Dll1 on endothelial cells and regulating MZ B-cell production. Removal of O-fucose affects Notch signaling in myelopoiesis and lymphopoiesis, and the O-fucose glycan in the Notch1 ligand-binding domain is required for optimal T-cell development. [ABSTRACT FROM AUTHOR]

The phosphoinositide 3-kinase (PI3K) family of lipid kinases regulates diverse aspects of lymphocyte behavior. This review discusses how genetic and pharmacological tools have yielded an increasingly detailed understanding of how PI3K enzymes function at different stages of lymphocyte development and activation. Following antigen receptor engagement, activated PI3K generates 3-phosphorylated inositol lipid products that serve as membrane targeting signals for numerous proteins involved in the assembly of multiprotein complexes, termed signalosomes, and immune synapse formation. In B cells, class IA PI3K is the dominant subgroup whose loss causes profound defects in development and antigen responsiveness. In T cells, both class IA and IB PI3K contribute to development and immune function. PI3K also regulates both chemokine responsiveness and antigen-driven changes in lymphocyte trafficking. PI3K modulates the function not only of effector T cells, but also regulatory T cells; these disparate functions culminate in unexpected autoimmune phenotypes in mice with PI3K-deficient T cells. Thus, PI3K signaling is not a simple switch to promote cellular activation, but rather an intricate web of interactions that must be properly balanced to ensure appropriate cellular responses and maintain immune homeostasis. Defining these complexities remains a challenge for pharmaceutical development of PI3K inhibitors to combat inflammation and autoimmunity. [ABSTRACT FROM AUTHOR]

A central characteristic of the immune system is the constantly changing location of most of its constituent cells. Lymphoid and myeloid cells circulate in the blood, and subsets of these cells enter, move, and interact within, then leave organized lymphoid tissues. When inflammation is present, various hematopoietic cells also exit the vasculature and migrate within non-lymphoid tissues, where they carry out effector functions that support host defense or result in autoimmune pathology. Effective innate and adaptive immune responses involve not only the action of these individual cells but also productive communication among them, often requiring direct membrane contact between rare antigen-specific or antigen-bearing cells. Here, we describe our ongoing studies using two-photon intravital microscopy to probe the in situ behavior of the cells of the immune system and their interactions with non-hematopoietic stromal elements. We emphasize the importance of non-random cell migration within lymphoid tissues and detail newly established mechanisms of traffic control that operate at multiple organizational scales to facilitate critical cell contacts. We also describe how the methods we have developed for imaging within lymphoid sites are being applied to other tissues and organs, revealing dynamic details of host-pathogen interactions previously inaccessible to direct observation. [ABSTRACT FROM AUTHOR]

At least three types of B lymphocytes are important for providing memory in a humoral immune response: ‘classical’ memory cells that do not secrete immunoglobulin (Ig), long-lived plasma cells (LLPCs) in the bone marrow, and ‘innate-like’ B-1 cells. In this review, our work on B-lymphocyte-induced maturation protein-1 (Blimp-1), a critical regulator of terminal B-cell differentiation, is discussed in the context of current knowledge of all transcriptional controls that regulate these three types of B cells. Blimp-1 is not required for formation of memory cells, but it is required for them to progress toward becoming plasma cells. Blimp-1 is required for Ig secretion in plasma cells and in B-1 cells. Induction of the activator X-box-binding protein-1 and formation of µ-secreted mRNA depend on Blimp-1 in both cell types. Finally, even after their formation, LLPCs in the bone marrow continue to require Blimp-1 for their maintenance. [ABSTRACT FROM AUTHOR]

Genomics has provided a lever to pry open lymphoid cells and examine their regulatory biology. The large body of available gene expression data has also allowed us to define the of coordinately expressed genes, termed gene expression signatures, which characterize the states of cellular physiology that reflect cellular differentiation, activation of signaling pathways, and the action of transcription factors. Gene expression signatures that reflect the action of individual transcription factors can be defined by perturbing transcription factor function using RNA interference (RNAi), small-molecule inhibition, and dominant-negative approaches. We have used this methodology to define gene expression signatures of various transcription factors controlling B-cell differentiation and activation, including BCL-6, B lymphocyte-induced maturation protein-1 (Blimp-1), X-box binding protein-1 (XBP1), nuclear factor-κB (NF-κB), and c-myc. We have also curated a wide variety of gene expression signatures from the literature and assembled these into a signature database. Statistical methods can define whether any signature in this database is differentially expressed in independent biological samples, an approach we have used to gain mechanistic insights into the origin and clinical behavior of B-cell lymphomas. We also discuss the use of genomic-scale RNAi libraries to identify genes and pathways that may serve as therapeutic targets in B-cell malignancies. [ABSTRACT FROM AUTHOR]

Intestinal epithelium contains several specialized cell types including M cells, which can be found in the follicle-associated epithelium (FAE) or occasionally on the villi. M cells are critical for sampling of intestinal flora and for transferring pathogens across the epithelial barrier for recognition by the immune system. Development of M cells on the villi (Mv) is independent of the presence of lymphocytes, while development of the FAE and M cells within the FAE (Mf) is dependent on B lymphocytes. Here, the concept is discussed that B cells are not required for induction of Mf differentiation but are required for transition to and maintenance of the mature Mf phenotype. Signaling pathways possibly involved in the B-cell-independent stages of M-cell development are also discussed. [ABSTRACT FROM AUTHOR]

Approximately 85% of patients with defects in early B-cell development have X-linked agammaglobulinemia (XLA), a disorder caused by mutations in the cytoplasmic Bruton's tyrosine kinase (Btk). Although Btk is activated by cross-linking of a variety of cell-surface receptors, the most critical signal transduction pathway is the one initiated by the pre-B cell and B-cell antigen receptor complex. Mutations in Btk are highly diverse, and no single mutation accounts for more than 3% of patients. Although there is no strong genotype/phenotype correlation in XLA, the specific mutation in Btk is one of the factors that influences the severity of disease. Mutations in the components of the pre-B cell and B-cell antigen receptor complex account for an additional 5–7% of patients with defects in early B-cell development. Patients with defects in these proteins are clinically indistinguishable from those with XLA. However, they tend to be younger at the time of diagnosis, and whereas most patients with XLA have a small number of B cells in the peripheral circulation, these cells are not found in patients with defects inµ heavy chain or Igα. Polymorphic variants in the components of the pre-B cell and B-cell receptor complex, particularlyµ heavy chain andλ5, may contribute to the severity of XLA. [ABSTRACT FROM AUTHOR]

Immunologists have typically viewed alloreactivity schematically as a function of antigen presentation, expansion of alloreactive T and B cells within regional lymphoid tissues, and cellular infiltration and destruction of an allograft. Actual details of the steps between immune activation and accumulation of effector cells within a graft typically have not received much attention. However, just how cells ‘know’ to move to and migrate within a graft or not is proving to be of increasing interest, as the chemokine-dependent mechanisms underlying leukocyte recruitment to a transplant are dissected. Experimentally, chemokine receptor targeting can prolong or induce permanent allograft survival, despite preservation of alloresponses within secondary lymphoid tissues, whereas current immunosuppressive protocols have only modest effects on chemokine production and leukocyte homing. Recent knowledge of the chemokine-dependent nature of allograft rejection, acceptance, and tolerance induction are presented as a basis for understanding the rationale for preclinical trials of chemokine receptor-targeted therapies currently underway in primate recipients of solid organ allografts. [ABSTRACT FROM AUTHOR]

This essay seeks to summarize one scientist's pilgrim's progress through the world on antibody formation, attempting to capture the flavor of problems as encountered within their times. It seeks to portray a world where the direct template hypothesis ruled the day,where the function of lymphocytes was unknown, let alone the difference between T and B cells, and where antibody genes were but a dream. Struggles to establish the credential of the clonal selection hypothesis are presented in some detail, as are the implications which followed the 'one cell--one antibody' discovery. The other two main preoccupations of the author are presented more briefly, namely the essential features of the germinal center and the cellular basis of immunological tolerance within the B lymphocyte compartment. Naturally, the experiments become more sophisticated as both knowledge and technology mature. A continuing thread within the unfolding story is that one must not shy away from developing new techniques when problems demand them. [ABSTRACT FROM AUTHOR]

The development of mature B lymphocytes from multipotent progenitor cells requires the co-ordinated activities of a number of transcriptional regulatory proteins. The transcription factors encoded by the E2A gene are required for the development of committed B-lineage cells and regulate the expression of essential B-lineage genes at multiple stages of differentiation and activation. In this review we discuss the evidence that the E2A gene products function in the regulation of 1) transcription factors required for B-lineage determination, 2) accessibility and recombination of the IgH and IgL chain loci, and 4) isotype switching in activated, mature B lymphocytes. [ABSTRACT FROM AUTHOR]

Dendritic cells (DC) are usually thought of as antigen-presenting cells for T cells. However, recent studies from our laboratory and those of others have shown that they have important roles in B-cell activation and regulation of antibody synthesis. Rat DC make short term interactions with resting B cells and these interactions can be simulated by cross-linking molecules on either cell surface. These DC can retain antigen in native form for at least 36 h in vivo an in vitro and can subsequently release it for recognition by B cells. In vivo antibody responses induced by antigen-pulsed DC are skewed towards IgG. In vitro, naive B cells incubated with antigen-pulsed DC subsequently secrete IgM and IgG when cultured with an antigen-specific CD4[sup+] T-cell line, whereas if B cells are incubated with antigen without DC, only IgM is produced. These observations show that DC play an important role in the initiation of and regulaiton of antibody synthesis. [ABSTRACT FROM AUTHOR]

A hallmark of adaptive immune responses is the generation of long-lived protection after primary exposure to a pathogen. In humoral responses, this protection stems from a combination of sustained antibody titers and long-lived memory B cells (MBCs), with the former deriving from long-lived plasma cells (PCs). Both types of cell are thought to primarily derive from the germinal center (GC), a unique structure that forms during the immune response to many types of antigenic stimuli. GCs are seeded by antigen-specific B and T cells that were previously activated in the early stages of the response. The GC does not directly or immediately generate effector function; rather, it is a site of intense B-cell proliferation and cell death. GC B cells undergo both somatic hypermutation and isotype switch, and a Darwinian process very efficiently selects B cells with higher fitness for survival and expansion. GC B cells adopt a unique activation and transcriptional state, and the cells become poised to differentiate to either MBCs or PCs. Despite this general understanding of the events in the GC, the mechanisms that control both affinity selection as well as differentiation have not been well worked out. In this review, we address what is known about what determines whether GC B cells become MBCs or PCs. This is discussed in the broader context of the origins of both cell types, whether from the GC or potentially other sources. We present a model encompassing recent data from several laboratories including our own that suggests that the GC undergoes a temporal switch that alters the nature of its output from MBCs to PCs as the response progresses. We will discuss B-cell receptor signaling in the GC as it relates to potential mechanisms for affinity-based selection during the reaction. [ABSTRACT FROM AUTHOR]