Brian M. Baker

T cell receptor (TCR) restriction by highly polymorphic major histocompatibility complex (MHC) proteins is a foundation of cellular immunity. Although the effects of MHC polymorphisms on peptide binding and selection are well established, how micropolymorphisms within MHC supertypes impact immune recognition is poorly understood. Here, we identified a mechanism through which the micropolymorphisms in two closely related HLA-A3 superfamily members govern TCR specificity. We previously showed that TCRs specific for a public neoantigen arising from a PIK3CA oncogenic hotspot mutation restricted by HLA-A*03:01 were unable to recognize the same epitope in the context of HLA-A*03:02 despite equivalent processing and presentation by both alleles. We found here that the two micropolymorphisms distinguishing A*03:02 from A*03:01 prevent TCR binding not by altering peptide binding or static structures, but by altering the conformational ensemble of the neoantigen, preventing it from adopting a binding-permissive state. The effect is rooted in how the two polymorphic sites interact with other covarying, evolutionarily coupled polymorphisms, reflecting a cross-groove network of interactions that controls the conformational adaptability of the peptide/HLA complex. We suggest polymorphism-dependent adaptability reflects an evolved feature of class I MHC proteins, further diversifying epitopes and contributing to how TCRs and other immunoreceptors differentiate between antigens. Beyond this mechanistic insight, our findings emphasize the need for high-resolution HLA typing in efforts across immunology, including antigen-specific immunotherapy.

T cell receptor (TCR) recognition of peptide/MHC complexes is fundamental for adaptive immunity. Many studies have described the importance of peptide/MHC motion or dynamics in TCR recognition. A role for dynamics in recognition intersects with the concept of dynamic allostery, which describes how alterations to a protein's energy landscape and thus motions influence function, often in the absence of conformational changes. Tuning of MHC protein energy landscapes by different peptides has clearly been shown. Evidence is mounting, however, that MHC polymorphisms also alter the protein's energy landscape. Here, we address this concept, summarizing findings that suggest that, in addition to dictating peptide binding and selection, naturally occurring variations within MHC proteins promote differential peptide and protein dynamics, altering TCR recognition in an MHC allele‐dependent manner. We hypothesize that MHC polymorphisms have been selected evolutionarily in part to tune the protein's dynamic response, altering immune specificity and further diversifying immune responses across populations.

T cell receptor (TCR) restriction by highly polymorphic major histocompatibility complex (MHC) proteins is a foundation of cellular immunity. Although the effects of MHC polymorphisms on peptide binding and selection are well established, how micropolymorphisms within MHC supertypes impact immune recognition is poorly understood. Here, we identified a novel mechanism through which the micropolymorphisms in two closely related HLA-A3 superfamily members determine TCR specificity. We previously showed that TCRs specific for a public neoantigen from the PIK3CA oncogene presented by HLA-A*03:01 were unable to recognize the same epitope in the context of HLA-A*03:02. We found here that the micropolymorphisms distinguishing A*03:02 from A*03:01 exert their effect not by altering peptide binding or static structures, but by changing the conformational ensemble of the neoantigen in the groove, preventing it from adopting a conformation compatible with TCR binding. The effect is rooted in how the two polymorphic sites interact with other co-varying, evolutionarily coupled polymorphisms, reflecting a cross-groove network of interactions that controls the conformational adaptability of the peptide/HLA complex. We suggest polymorphism-dependent conformational adaptability reflects an evolved feature of class I MHC proteins that amplifies the impact of peptides in the groove, further diversifying epitopes and contributing to how TCRs and other immunoreceptors differentiate between antigens. Beyond this mechanistic insight, our findings emphasize the need for high-resolution HLA typing in efforts across immunology, including antigen-specific immunotherapy.

The inherent antigen cross-reactivity of the T cell receptor (TCR) is balanced by high specificity. Surprisingly, TCR specificity often manifests in ways not easily interpreted from static structures. Here we show that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen and its wild-type (WT) counterpart emerges from distinct motions within the HLA-A3 peptide binding groove that vary with the identity of the peptide’s first primary anchor. These motions create a dynamic gate that, in the presence of the WT peptide, impedes a large conformational change required for TCR binding. The neoantigen is insusceptible to this limiting dynamic, and, with the gate open, upon TCR binding the central tryptophan can transit underneath the peptide backbone to the opposing side of the HLA-A3 peptide binding groove. Our findings thus reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I binding grooves, with implications for resolving long-standing and often confounding questions about T cell specificity.

αβ T cell receptor (TCR) recognition of peptide–MHC complexes lies at the core of adaptive immunity, balancing specificity and cross‐reactivity to facilitate effective antigen discrimination. Early structural studies established basic frameworks helpful for understanding and contextualizing TCR recognition and features such as peptide specificity and MHC restriction. However, the growing TCR structural database and studies launched from structural work continue to reveal exceptions to common assumptions and simplifications derived from earlier work. Here we explore our evolving understanding of TCR recognition, illustrating how structural and biophysical investigations regularly uncover complex phenomena that push against paradigms and expand our understanding of how TCRs bind to and discriminate between peptide/MHC complexes. We discuss the implications of these findings for basic, translational, and predictive immunology, including the challenges in accounting for the inherent adaptability, flexibility, and occasional biophysical sloppiness that characterize TCR recognition.

Our immune system is a complex network that enables an organism to differentiate between "self" and "non-self". This function maintains homeostasis and protects the body from pathogenic threats. While the systems in humans and other vertebrate animals are complex and multi-armed, even ancient organisms such as sea sponges, possess rudimentary immune systems. The capacity to differentiate between self and non-self is foundational to the viability of more complex multicellular life [1].In vertebrate animals, antigen presentation via the highly polymorphic major histocompatibility complex class I (MHC-I) and class II (MHC-II) proteins is a key component of adaptive immunity [2]. These proteins display peptide fragments on the cell membrane so that T cells may recognize them to initiate an immune response. For MHC-I, which is found on all nucleated cells, intracellular proteins act as sources of these peptides, allowing CD8 + cytotoxic T lymphocytes to identify and eliminate infected or malignant cells [3]. On the other hand, MHC-II proteins are expressed on specialized antigen-presenting cells (APCs), such as B lymphocytes, dendritic cells (DCs), and macrophages, and present peptides from exogenous proteins, allowing CD4 + helper T lymphocytes to coordinate broader immune responses [4]. For both CD8 + and CD4 + T cells, T cell receptors (TCRs) bind to specific peptide-MHC complexes, triggering a signaling cascade and leading to T cell activation and subsequent downstream responses (Figure 1).Dysregulation of MHC function is implicated in various human diseases [4]. Autoimmune disorders, for instance, can result from genetic polymorphisms in MHC genes that cause immune intolerance and thus erroneous targeting of self-tissues [5,6]. Altered MHC expression is also linked to the evasion of immune surveillance in viral infection and cancer which enables diseased cells to escape recognition and destruction by the immunocytes [7]. Additionally, specific MHC alleles are linked to enhanced vulnerability to some viral infections, including HIV, and hepatitis B and C [8]. The development of tailored immunological therapeutics for these conditions thus requires a thorough understanding of the molecular mechanisms driving T cell activation and MHC antigen presentation.A promising path for therapeutic innovation in a variety of diseases is provided by research on MHC polymorphismsresearch on the precise studies of MHCs, their presented peptides, and how they are recognized by T cells. Our research topic, "Specific Targeting of MHC Antigens for Tcells and Immune Cells in Human Disease" delves into novel and precise methods of peptide-MHC targeting and modulating their recognition. We seek to contribute to the development of personalized therapies that enhance immune responses against viral infections, autoimmune disorders, and cancer by focusing on the molecular mechanisms governing peptide-MHC presentation, recognition, and T cell activation. This collection features five seminal papers that contribute to the understanding of immune modulation by investigating how enhancing TCR specificity via framework engineering can result in more precise and focused immune responses [9]. It also examines exosomal membrane proteins for how they are composed, their physiological aspects, and therapeutic applications [10]. Additionally, our collection explores a key challenge in alloimmunity by explaining the use of IL-2 and TGF-β loaded nanoformulations to support transplantation tolerance [11]. The implications of the MHC-restricted immunopeptidome in transplantation are also explored, particularly its role in transplant rejection and tolerance [12]. Finally, the MHC-I/LILRB1 pathway is explored as a potential innate immune checkpoint in cancer which offers insights into cancer immunotherapy [13]. Together, this collection presents innovative approaches for modulating immune responses and advancing the treatment of human diseases.In their research, Rosenberg et al. explored tuning TCR specificity by introducing mutations in regions far from the binding surface [9]. Deep mutational scanning of the HIV-specific 868 TCR revealed ways to reduce recognition of SL9 escape variants without altering affinity towards the native epitope. Simulations suggest that this mutation restricts loop motions, limiting TCR binding to diverse ligands. This study offers a potential strategy to enhance TCR specificity for use in immunotherapy.proteins being key contributors to these functions [10]. These proteins facilitate various functions, for instance, communicating between cells, mediating recognition of target cells, and regulating immune responses. Notably, these surface proteins on cancer-derived exosomes have emerged as potential biomarkers for early cancer detection. This review delves into the composition and physiology of exosome-surface proteins and highlights their importance in various physiological and pathological contexts [10]. By exploring these proteins, the authors aim to lay the groundwork for the development of novel diagnostic tools and therapeutic strategies in biomedicine.Horwitz et al. have reported their groundbreaking findings in the form of a brief report in which they evaluated the potential of IL-2 and TGF-β loaded nanoformulations [11]. These nanoformulations have previously shown to induce polyclonal T regulatory lymphocytes (Tregs) to help prevent allograft rejection and protect against graft-versus-host disease. They used a murine model of alloimmunization and demonstrated that the treatment with tolerogenic nanoformulations significantly inhibited the mixed lymphocyte reaction to alloantigens from donors without affecting responses to third-party antigens. This reduction in alloreactivity was accompanied by a 4 to 5-fold augmentation in CD4 + and CD8 + Tregs and a shift of recipient DCs toward a tolerogenic phenotype [11]. Together these provide explanation of tolerogenic nanoformulations...

SARS-CoV-2 infection can induce multisystem inflammatory syndrome in children, which resembles superantigen-induced toxic shock syndrome. Recent work has suggested that the SARS-CoV-2 spike (S) protein could act as a superantigen by binding T cell receptors (TCRs) and inducing broad antigen-independent T cell responses. Structure-based computational modeling identified potential TCR-binding sites near the S receptor-binding domain, in addition to a site with homology to known neurotoxins. We experimentally examined the mechanism underpinning this theory—the direct interaction between the TCR and S protein. Surface plasmon resonance of recombinantly expressed S protein and TCR revealed no detectable binding. Orthogonally, we pseudotyped lentiviruses with SARS-CoV-2 S in both wild-type and prefusion-stabilized forms, demonstrated their functionality in a cell line assay, and observed no transduction, activation, or stimulation of proliferation of CD8 ⁺ T cells. We conclude that it is unlikely that the SARS-CoV-2 spike protein engages nonspecifically with TCRs or has superantigenic character.

The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant PIK3CA and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide’s first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding. The more rigid neoantigen is insusceptible to this limiting dynamic, and with the gate open, is able to transit its central tryptophan residue underneath the peptide backbone to the contralateral side of the HLA-A3 peptide binding groove, facilitating TCR binding. Our findings reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I complexes, with implications for resolving long-standing and often confounding questions about the determinants of T cell specificity.

Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.