The development of highly accurate deep learning models for protein structure prediction has transformed the landscape of T-cell receptor (TCR) structure data, which can now be accessed at repertoire scale. We provide a perspective on the growing field of structural TCR immunoinformatics, summarizing core principles of TCR structural biology and highlighting existing resources and tools. We outline computational methods for TCR structure prediction, and discuss outstanding challenges faced by current tools, as well as potential avenues to address these. We expand on the research enabled by the availability of predicted TCR structures, exploring the utility of TCR structure predictions for computationally inferring TCR specificity, as well as summarizing opportunities emerging from the adjacent field of antibody research. Finally, we provide a forward-looking perspective on the advances in deep learning research which have recently enabled computational design of TCRs and TCR-like binders.
As B cells are activated and differentiate into plasma cells, they execute migration programs that allow them to traffic within secondary lymphoid tissues and reach the bone marrow, where they can mature as long-lived plasma cells. Recent studies have revealed mechanisms underlying not only affinity-driven but also isotype-driven plasma cell selection. In addition, the importance of migration programs in plasma cell longevity has become increasingly appreciated. This review focuses on mechanisms that regulate plasma cell numbers and their migration to the bone marrow, with emphasis on our findings and recent advances in related fields.
Autoimmune diseases arise from the breakdown of immune tolerance through complex interactions between genetic predisposition, environmental exposures, and adaptive immune responses. High-throughput T-cell receptor (TCR) repertoire sequencing has transformed our ability to characterize these responses, providing unprecedented insights into clonal dynamics, antigen-driven selection, and immune history. In this review, we summarize the major alterations of TCR repertoires reported across autoimmune diseases, including changes in diversity, clonal expansion, repertoire architecture, and tissue distribution. We discuss the principal biological and technical challenges that currently limit repertoire interpretation, with particular emphasis on the concept that bulk repertoires represent composite mixtures of biologically distinct T-cell populations. Finally, we highlight emerging approaches integrating single-cell profiling, computational modeling, and antigen-specificity inference that are reshaping the field. We propose that TCR repertoires should be viewed as dynamic molecular footprints of autoimmune disease, providing a systems-level framework to improve mechanistic understanding, biomarker discovery, and the development of precision immunotherapies.
Germinal centers (GCs) are specialized microenvironments in which B cells undergo affinity maturation through iterative cycles of somatic hypermutation, proliferation and selection, generating antibodies with improved antigen-binding properties. Although GC B cells do not themselves secrete antibody, they differentiate into memory B cells and plasma cells that provide long-term humoral immunity. GC selection has traditionally been viewed as a process that preferentially expands B cells expressing the highest-affinity B cell receptors. However, recent studies have revealed that physiological GC responses preserve substantial clonal and affinity diversity, and generate plasma cells spanning a broad range of antibody affinities. Here, we review current understanding of the mechanisms governing GC B cell selection and discuss an alternative framework in which T cell help quantitatively refuels GC B cells rather than acting as a binary gate for cyclic re-entry. We further explore how antigen organization, antibody feedback and the biophysical context of antigen recognition may reconcile the apparent discrepancy between affinity-based selection and the maintenance of clonal diversity. Finally, we consider how these concepts may alter our expectations for the plasma cell populations emerging from GCs and discuss their implications for rational vaccine design.
Shape space is a decades-old conceptual model of antibody-antigen interactions that underlies antigenic maps used to trace viral evolution. Here, we apply this concept to T cell receptors (TCRs) and the peptide-MHC complexes (pMHCs) that they recognize. We start by reviewing the history of shape space and its deep connections to concepts in statistical physics (energy landscapes) and computer science (complexity theory). Leveraging these connections, we propose a model in which TCR-pMHC binding relies on multiple, possibly conflicting, structural constraints-implying that pMHCs recognized by the same TCR occupy several disjoint, non-convex regions in shape space. Our model makes two central predictions: (1) even small pMHC structure alterations can have major effects on immunogenicity; (2) two pMHCs recognized by the same TCR can have very different structures. We show that published TCR-pMHC interaction data generated by mutagenesis assays lend some support for this idea. We conclude by discussing implications of a multispecific and non-convex T cell epitope shape space for the prediction of immune responses in cancer immunotherapy and other applications.
Type 1 diabetes (T1D) is characterized by T cell-mediated destruction of insulin producing pancreatic β cells. However, stressed β cells are increasingly recognized as active contributors to disease pathogenesis rather than passive targets of immune attack. In this context, oxidative stress in β cells may promote oxidative post-translational modifications (oxPTMs) of insulin, generating modified insulin forms that have emerged as potential drivers of neoantigen formation and autoimmune responses. Due to their exceptionally high insulin biosynthetic load, limited antioxidant defenses, and susceptibility to endoplasmic reticulum and mitochondrial stress, β cells operate in an environment permissive to oxidative protein modification. Multiple studies have demonstrated that insulin is susceptible to several oxidative and nonenzymatic modifications, including oxidation, chlorination, nitration, and glycation, generating structurally distinct proteoforms with altered biological and immunological properties. Importantly, oxidatively modified insulin species (oxPTM-insulin) are recognized by both autoantibodies and autoreactive T cells in individuals with T1D, supporting their role as neoantigens. In this review, we discuss the mechanisms leading to oxPTM-insulin generation, summarize the biochemical and immunological evidence supporting their relevance in T1D, and examine the methodological challenges and controversies surrounding their identification. Finally, we explore the potential of oxPTM-insulin as a biomarker and therapeutic target in T1D.
Citrullination and deamidation are post-translational modifications (PTMs) increasingly recognized as important contributors to neoepitope formation in type 1 diabetes (T1D). Under inflammatory and endoplasmic reticulum stress conditions, beta cells activate calcium-dependent peptidylarginine deiminase and transglutaminase enzymes, leading to self-protein modification, altered peptide charge and HLA-binding properties, thereby generating neoepitopes that can be recognized by autoreactive CD4+ and CD8+ T cells. Accumulating evidence from both murine and human studies demonstrates that immune responses against citrullinated and deamidated beta cell proteins are present and increase with disease progression, supporting a role in epitope spreading rather than disease initiation. Although both PTMs are biochemically analogous, their kinetics and regulation are distinct: citrullination appears as an earlier and partly intrinsic response of stressed beta cells, whereas deamidation is more closely associated with sustained inflammation and later disease stages. In parallel, reduced PTM-generating enzyme expression in the thymus may limit central tolerance to modified epitopes, facilitating escape of autoreactive T cells. In this review, we summarize current insights into the biochemical and immunological roles of citrullination and deamidation in T1D, with emphasis on their temporal regulation, contribution to neoepitope formation, and potential as therapeutic targets, highlighting key findings from our own work in the field.
Age-associated B cells (ABCs) are a distinct B cell population characterized by coexpression of T-bet and CD11c. First described in aged female mice and autoimmune-prone strains, ABCs are now recognized to be associated with multiple human autoimmune diseases, including systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis, where their frequency correlates with disease activity. Their differentiation requires toll-like receptor (TLR) signaling, IFN-γ, IL-21, BCR engagement, with ZEB2 emerging as the nonredundant transcriptional master regulator of ABC identity. Here we review requirements for ABC differentiation, their defining phenotypic and functional features, and their tissue-specific distribution and pathogenic contributions in diverse inflammatory settings. A central theme is that ABCs are tissue-homing cells whose contribution extends beyond blood and lymphoid organs. In kidney, inflamed synovium, salivary glands, and adipose tissue, ABCs drive pathology through locally differentiated autoantibody-secreting cells, stromal activation, antigen presentation, and cytokine production. We further discuss roles for ABCs in neurological diseases, including their enrichment in the cerebrospinal fluid in multiple sclerosis (MS) and their contribution to neuroinflammation in Alzheimer's disease, and highlight the EBV-ABC axis as a mechanism linking viral infection to autoimmunity. In summary, ABCs are multi-functional, tissue-adaptable pathogenic effectors whose contributions to human disease extend beyond classical autoimmunity into metabolic dysfunction and neurodegeneration.
Post-translational modifications (PTMs) can generate neo-epitopes, modified peptides that evade immune tolerance and trigger immune responses. This review focuses on the TG2/LRP1 pathway as a new paradigm for coupling the formation of post-translationally modified peptides with their effective presentation as T-cell antigens by dendritic cells. Transglutaminase 2 (TG2) catalyzes the Gln → Glu conversion of specific residues in peptides derived from dietary gluten thereby enhancing their affinity for HLA-DQ2, the principal genetic determinant of celiac disease. However, because such modified peptides are scarce in intestinal mucosa, an effective mechanism for lysosomal uptake by antigen-presenting cells (APCs) is necessary. Protein-protein interaction between certain peptide-bound TG2 complexes and the low-density lipoprotein receptor-related protein 1 (LRP1) results in efficient endocytosis of these antigenic peptides along with their concomitant release in the endo-lysosomal compartment as deamidated products. An analogous PTM-driven mechanism for antigen presentation may also operate in autoimmune conditions associated with peptidylarginine deiminase (PADI) activity, such as rheumatoid arthritis (RA). The exquisite cellular selectivity of the TG2/LRP1 pathway has implications not only for understanding its role in autoimmunity but also for its potential exploitation in vaccine design.
In vertebrate adaptive immune systems, somatically diversified antigen receptors assume a central role in self/nonself discrimination. Attesting to the presence of a unique but unknown selective environment at early stages of vertebrate evolution, this facility emerged twice, in the ancestors of jawless and jawed vertebrates. Thus, the molecular structure of incomplete antigen receptor genes and their mode of assembly into functional genes are different in the two sister groups of vertebrates. It appears that adaptive immunity evolved in steps, trading immunologically favorable diversity of antigen receptor repertoires against the inherent risks of potentially destructive self recognition. Initially, the associated quality control mechanisms were largely cell-autonomous and grounded in the evolutionarily selected sequence composition of individual components available for assembly. At later stages, diversity increased in lock-step with emerging cell-nonautonomous quality control strategies: primary lymphoid organs spatially and temporally coupled repertoire development and assessment for self reactivity; regulatory cell types emerged to keep self reactive clones in check in the periphery. In this review, we discuss how comparative studies of vertebrate species situated at key positions in the phylogenetic tree have revealed traces of the evolutionary past of adaptive immune systems.
Type 1 diabetes (T1D) arises when autoreactive lymphocytes target pancreatic β-cells, yet the mechanisms that convert β-cell self-proteins into disease-relevant antigens remain incompletely defined. β-cells are uniquely positioned to generate neoantigens because they devote extraordinary protein synthesis capacity to insulin production and maintain thousands of dense-core insulin granules. While a small fraction of granules undergoes glucose-stimulated exocytosis, excess, aged, or immature granules can be degraded through crinophagy, a lysosomal pathway in which secretory granules fuse with lysosomes to form crinosomes. Recent immunopeptidomic studies suggest that crinosomes are not merely disposal compartments but antigen-editing organelles that remodel insulin granule cargo into pathogenic epitopes. These include free insulin B-chain peptides, hybrid insulin peptides, post-translationally modified insulin and C-peptide epitopes, and stress-induced insulin sequence variants such as insulin B-peptide C19S. Because several crinosome-associated epitopes are poorly represented in the thymus, crinophagy may create a peripheral antigen repertoire that permits escape from central tolerance and activation of autoreactive T cells in islets and draining lymphoid tissues. This review discusses the physiology of β-cell granule turnover, the mechanisms of crinosome-associated neoantigen generation, and their implications for T1D pathogenesis, biomarkers, and therapeutic targeting.
In this review, we cover the discovery of hybrid insulin peptides (HIPs) as antigens for CD4 T cells involved in pathogenesis and regulation of autoimmune diabetes. HIPs represent a unique posttranslational modification in autoimmunity and consist of peptide sequences from two beta-cell proteins, one being proinsulin, covalently joined to form new nongenomic peptides. Using the nonobese diabetic (NOD) mouse model, we showed that HIPs are target antigens for a panel of diabetogenic CD4 T-cell clones. The prototype clone of this panel is BDC-2.5, and the first HIP identified was the peptide ligand for BDC-2.5, the 2.5HIP, consisting of an insulin C-peptide fragment combined with a natural cleavage product of chromogranin A. T cells with different TCRs, all specific for the 2.5HIP, were shown to be a dominant population among the T cells infiltrating the islets of NOD mice. T cells reactive to HIPs are significantly elevated in the PBMC of newly diagnosed patients with type 1 diabetes (T1D) and in at-risk subjects, an important finding from a clinical standpoint. When coupled to biodegradable nanoparticles (NPs), HIPs can serve as epitopes to induce antigen-specific tolerance. 2.5HIP NPs not only prevent transfer of disease by BDC-2.5 T cells but also prolong islet graft survival in diabetic NOD mice. Investigation of the mechanisms underlying 2.5HIP NP-induced tolerance revealed that protection occurs through an IL-10-dependent process in which regulatory T cells in the graft tissue are increased, limiting dendritic cell licensing and the subsequent terminal differentiation of both CD4 and CD8 islet-specific T cells.
T cells are central to adaptive immunity, recognizing antigenic peptides, called epitopes, via the T cell receptor (TCR). The immense diversity and cross-reactivity of the TCR repertoire makes direct interpretation of antigen specificity from repertoire sequencing challenging. High-throughput sequencing enables large-scale profiling of TCRs but does not directly reveal their target epitopes, requiring computational approaches to bridge this gap. This review outlines two complementary strategies, bottom-up and top-down approaches, to annotate TCR specificity. Bottom-up methods predict TCR-epitope specificity from curated TCR-epitope databases, identifying recurring patterns through distance-based, feature-based, or deep learning models. While effective for well-characterized epitopes, they are limited by biased training data, absence of negative data, and weak generalization to unseen epitopes. Top-down approaches instead infer antigen-driven responses from repertoire-level signals such as sequence similarity, enrichment, and TCR convergence. These methods enable discovery of disease- or exposure-associated TCR signatures without prior epitope knowledge but are sensitive to technical noise and biological confounding. Both approaches are complementary as bottom-up provides mechanistic specificity, while top-down enables discovery in complex datasets. Their integration, alongside multimodal modeling and improved benchmarking, is key to advancing TCR-epitope annotation and understanding adaptive immune responses.
The naïve T cell receptor (TCR) repertoire forms the immunological background from which adaptive cellular immune responses emerge. We examine the fundamental properties of the human naïve TCR repertoire through the perspective of Diversity, Equality, and Inclusion. We first consider the richness of the repertoire. A combination of experimental and computational approaches has been used to estimate that the human repertoire contains at least 100 million distinct naïve clonotypes. This estimate suggests an average size of each clonotype of 1000 T cells. However, evidence from both mathematical modeling and large-scale single-cell sequencing indicates that clonotype family sizes are very unequal, with a small subset of naïve TCRs present at substantially higher frequencies. Somatic recombination itself does not contribute significantly to this inequality, as the probability of generating an identical clonotype multiple times in an individual is very small. Instead, clonotype size is likely to be largely driven by thymic or post-thymic expansion, but the mechanisms driving heterogeneity remain poorly understood. Finally, despite clonal deletion being a cornerstone of immunological dogma, experimental evidence for functional "holes" in the naïve repertoire caused by negative thymic selection is surprisingly limited. Alternative tolerance mechanisms, including regulatory T cells and T cell quorum sensing, are likely to play important roles. This review highlights the need for further research to identify the mechanisms that shape the frequency distribution of naïve TCR clone sizes and to define its impact on primary immune responses. Further research is also needed to understand the role of quorum sensing in maintaining T cell tolerance, while avoiding potential vulnerabilities arising from extensive 'holes' in the TCR repertoire.
Macrophages, as central effectors of innate immunity, play context-specific and time-dependent roles in myocardial infarction (MI) and in the pathogenesis of ischemic heart failure (HF). Their plasticity, heterogeneity, and interactions with other cardiac and immune cells determine whether inflammation resolves and repair ensues, or maladaptive remodeling culminates in ventricular dysfunction. In this review, we synthesize findings from lineage-tracing studies, single-cell transcriptomic atlases, and clinical trials to highlight macrophage ontogeny, recruitment, reparative programs, and pathogenic functions in chronic remodeling. We discuss embryonically-derived cardiac resident macrophages, recruitment of monocyte-derived macrophages and their respective roles after ischemic injury, and how efferocytotic clearance of cellular and mitochondrial debris is a key component of the reparative response. We highlight macrophage interactions with cardiomyocytes, fibroblasts, neutrophils, T cells, and conduction system cells, and outline translational strategies involving chemokine pathway inhibition and specialized pro-resolving mediators. Mechanistic insight into macrophage ontogeny, heterogeneity, and intercellular interactions has uncovered novel therapeutic possibilities. Targeted, temporally staged macrophage therapies, using biomarkers and imaging for patient stratification, may improve post-MI healing and prevent progression toward ischemic HF.
Advances in high-throughput sequencing, single-cell profiling, and genome engineering have transformed the study of T cell receptors (TCRs), enabling the identification and functional interrogation of antigen-specific repertoires at an unprecedented scale. This review discusses how recent methodological developments-including high-dimensional TCR discovery strategies, physiological receptor engineering, and longitudinal in vivo analyses-have reshaped our understanding of TCR-driven immune responses. Recruitment into immune responses originates from diverse naïve precursor pools and results in polyclonal populations in which multiple clonotypes contribute to antigen recognition. Within such populations, receptor properties, such as TCR avidity, influence the likelihood of recruitment, expansion, and persistence. However, the impact of these parameters depends strongly on biological context, including antigen availability, cellular competition, and tissue environment. Physiological engineering approaches, such as orthotopic TCR replacement, now enable causal interrogation of receptor function while preserving endogenous regulatory control. Together with advances in spatial and longitudinal profiling of human immune responses, these approaches allow increasingly precise analyses of connections between TCR identity and T cell fate. Integrating insights across antigen discovery, receptor engineering, and in vivo dynamics suggests that TCR biology is shaped by the interplay of receptor sequence, regulatory context, and tissue environment across time. Understanding these relationships will be essential for interpreting immune responses and for guiding the rational design of T cell-based immunotherapies.
T lymphocytes are increasingly recognized as central regulators of cardiac inflammation, contributing to both tissue repair and disease progression across conditions such as myocardial infarction, heart failure, and myocarditis. While traditionally viewed as transient responders to injury, emerging evidence indicates that cardiac T cell responses are often antigen-driven, clonally expanded, and sustained over time. In particular, α-myosin heavy chain (α-MyHC, encoded by MYH6) has emerged as a dominant cardiac autoantigen capable of eliciting pathogenic T cell responses in both experimental models and human disease. In parallel, tissue-resident memory T cells (Trm) have been established as a distinct population of memory T cells that persist within non-lymphoid tissues and provide rapid, localized responses upon antigen re-exposure. Although extensively studied in non-lymphoid and barrier tissues, Trm are now increasingly implicated in chronic inflammatory and autoimmune diseases, where they can act as long-lived reservoirs of antigen-experienced T cells. Here, we propose that cardiac injury seeds antigen-specific T cell populations that acquire tissue-resident phenotypes within the myocardium, thereby linking acute immune activation to chronic, relapsing inflammation. We first review the role of T cells in cardiac homeostasis, aging, and disease, highlighting features of antigen specificity, persistence, and local adaptation. We then outline the defining characteristics and developmental pathways of Trm and integrate emerging evidence for their presence and function in the heart. Particular emphasis is placed on α-MyHC-specific Trm as potential drivers of cardiac autoimmunity and immune-related adverse events of cancer immunotherapies, including immune checkpoint inhibitor-associated myocarditis. Finally, we discuss the implications of this framework for understanding chronic cardiac inflammation and for developing therapeutic strategies targeting tissue-resident immune populations.
Atherosclerotic cardiovascular disease (ASCVD) is increasingly recognized not just as a lipid-driven disease, but as a complex interplay between vascular cells and the immune system. Accumulating evidence highlights a central, yet heterogeneous role for B cells in atherogenesis, with distinct subsets displaying opposing roles. In this review, we provide an in-depth overview of the contributions of B cell subsets to ASCVD, including emerging insights into the roles and pathways of atheroprotective innate B cells producing IgM against oxidation-specific epitopes (IgMOSE) and newly appreciated age-associated B cells (ABCs), a distinct subset that accumulates with aging and potentially exacerbates atherosclerosis. By integrating insights from preclinical models and human studies, we describe the mechanisms through which B cell subsets influence ASCVD, including antigen presentation and immune checkpoint-mediated communication, secretion of cytokines and chemokines, and we highlight that humoral immunity in atherosclerosis reflects a context-dependent interplay between antibody effector properties and antigenic targets rather than antibody class alone. Finally, we explore how the advances in our understanding of B cells may guide the development of more targeted immunomodulatory therapies that enhance atheroprotective B cell functions while limiting atherogenic responses.
