Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.

Protecting a bosonic qubit with autonomous quantum error correction.

To build a universal quantum computer from fragile physical qubits, effective implementation of quantum error correction (QEC)1 is an essential requirement and a central challenge. Existing demonstrations of QEC are based on an active schedule of error-syndrome measurements and adaptive recovery operations2,3,4,5,6,7 that are hardware intensive and prone to introducing and propagating errors. In principle, QEC can be realized autonomously and continuously by tailoring dissipation within the quantum system1,8,9,10,11,12,13,14, but so far it has remained challenging to achieve the specific form of dissipation required to counter the most prominent errors in a physical platform. Here we encode a logical qubit in Schrödinger cat-like multiphoton states15 of a superconducting cavity, and demonstrate a corrective dissipation process that stabilizes an error-syndrome operator: the photon number parity. Implemented with continuous-wave control fields only, this passive protocol protects the quantum information by autonomously correcting single-photon-loss errors and boosts the coherence time of the bosonic qubit by over a factor of two. Notably, QEC is realized in a modest hardware setup with neither high-fidelity readout nor fast digital feedback, in contrast to the technological sophistication required for prior QEC demonstrations. Compatible with additional phase-stabilization and fault-tolerant techniques16,17,18, our experiment suggests quantum dissipation engineering as a resource-efficient alternative or supplement to active QEC in future quantum computing architectures.

Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes.

Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.

The Energetic Landscape of Catch Bonds in TCR Interfaces.

Recognition of peptide/MHC complexes by αß TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.

CD8+ T Cell-Dependent Antitumor Activity In Vivo of a Mass Spectrometry-Identified Neoepitope despite Undetectable CD8+ Immunogenicity In Vitro.

Identification of neoepitopes that can control tumor growth in vivo remains a challenge even 10 y after the first genomics-defined cancer neoepitopes were identified. In this study, we identify a neoepitope, resulting from a mutation in the junction plakoglobin (Jup) gene (chromosome 11), from the mouse colon cancer line MC38-FABF (C57BL/6). This neoepitope, Jup mutant (JupMUT), was detected during mass spectrometry of MHC class I-eluted peptides from the tumor. JupMUT has a predicted binding affinity of 564 nM for the Kb molecule and a higher predicted affinity of 82 nM for Db. However, whereas structural modeling of JupMUT and its unmutated counterpart Jup wild-type indicates that there are little conformational differences between the two epitopes bound to Db, large structural divergences are predicted between the two epitopes bound to Kb. Together with in vitro binding data with RMA-S cells, these data suggest that Kb rather than Db is the relevant MHC class I molecule of JupMUT. Immunization of naive C57BL/6 mice with JupMUT elicits CD8-dependent tumor control of a MC38-FABF challenge. Despite the CD8 dependence of JupMUT-mediated tumor control in vivo, CD8+ T cells from JupMUT-immunized mice do not produce higher levels of IFN-γ than do naive mice. The structural and immunological characteristics of JupMUT are substantially different from those of many other neoepitopes that have been shown to mediate tumor control.

Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner.

Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.

Simultaneous spectral differentiation of multiple fluorophores in super-resolution imaging using a glass phase plate.

By engineering the point-spread function (PSF) of single molecules, different fluorophore species can be imaged simultaneously and distinguished by their unique PSF patterns. Here, we insert a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to produce distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrate that the resulting PSFs can be localized spatially and spectrally using a maximum-likelihood estimation algorithm and can be utilized for hyper-spectral super-resolution microscopy of biological samples. We produced superresolution images of fixed U2OS cells using X-PSFs for dSTORM imaging with simultaneous illumination of up to three fluorophore species. The species were distinguished only by the PSF pattern. We achieved ∼21-nm lateral localization precision (FWHM) and ∼17-nm axial precision (FWHM) with an average of 1,800 - 3,500 photons per PSF and a background as high as 130 - 400 photons per pixel. The modified PSF distinguished fluorescent probes with ∼80 nm separation between spectral peaks.

SARS-CoV-2 Infection Presenting as Acute Chest Syndrome in a Child With Hemoglobin SD-Los Angeles Disease: A Case Report and Review of Literature.

Hemoglobin D-Los Angeles is a variant of hemoglobin that can polymerize in the deoxygenated state. When co-inherited with Hemoglobin S (HbSD-Los Angeles disease) a severe sickling syndrome similar to HbSS can result. Corona virus infectious disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome-corona virus-2. It has been associated with acute chest syndrome (ACS) in individuals with sickle cell disease (SCD), but this complication has not previously been reported in patients with HbSD-Los Angeles. Dexamethasone has been shown to improve outcomes in non-SCD patients with severe acute respiratory syndrome-corona virus-2 pneumonia or acute respiratory distress syndrome; however, its use in SCD patients with ACS is controversial due to a reported increased risk of complications including vaso-occlusive painful episodes. Herein, we reported a patient with HbSD-Los Angeles and COVID-19-associated ACS whom we treated with dexamethasone without transfusion. The patient experienced a rapid recovery without sequelae from steroid use. To further evaluate the use of steroids, we conducted a literature review focusing on the management of pediatric SCD patients with COVID-19-associated ACS. We identified a total of 39 pediatric patients with SCD and COVID-19, of whom 21 (54%) had ACS. Packed red blood cell transfusion (n=11), exchange transfusion (n=4), or a combination of exchange transfusion and packed red blood cell transfusion (n=4) were the most frequently reported treatment, with hydroxychloroquine (n=5), remdesivir (n=1), and tocilizumab (n=1) also being reported. Three patients were treated with dexamethasone. All patients recovered and no adverse outcomes from steroid use were reported. Even though transfusion is considered the standard of care for children with ACS and steroids are not routinely recommended, our experience suggested that COVID-19-associated ACS may be an important exception, especially for patients who refuse transfusion or are in resource-poor nations where blood transfusions may not be readily available. Further studies are warranted to confirm these observations.

Assessment of Library Services in Pediatric Hospitals in the United States and Canada.

This study reports on a 2022 survey of pediatric hospital librarians in the U.S. and Canada to assess the status of staffing, resources, and services in their libraries. The report compares the data against the MLA Hospital Library Caucus Standards (2022) and the Canadian Hospital Library Association Standards (2020). The report also provides a comparison of the libraries' rankings using the Regional U.S. News & World Report Best Children's Hospitals and Magnet status. This approach is intended to determine how librarians and library services at hospitals that are recognized by the above programs differ from those that are not recognized.

Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor.

Using a variety of activating and inhibitory receptors, natural killer (NK) cells protect against disease by eliminating cells that have downregulated class I major histocompatibility complex (MHC) proteins, such as in response to cell transformation or viral infection. The inhibitory murine NK receptor Ly49C specifically recognizes the class I MHC protein H-2Kb. Unusual among NK receptors, Ly49C exhibits a peptide-dependent sensitivity to H-2Kb recognition, which has not been explained despite detailed structural studies. To gain further insight into Ly49C peptide sensitivity, we examined Ly49C recognition biochemically and through the lens of dynamic allostery. We found that the peptide sensitivity of Ly49C arises through small differences in H-2Kb-binding affinity. Although molecular dynamics simulations supported a role for peptide-dependent protein dynamics in producing these differences in binding affinity, calorimetric measurements indicated an enthalpically as opposed to entropically driven process. A quantitative linkage analysis showed that this emerges from peptide-dependent dynamic tuning of electrostatic interactions across the Ly49C-H-2Kb interface. We propose a model whereby different peptides alter the flexibility of H-2Kb, which in turn changes the strength of electrostatic interactions across the protein-protein interface. Our results provide a quantitative assessment of how peptides alter Ly49C-binding affinity, suggest the underlying mechanism, and demonstrate peptide-driven allostery at work in class I MHC proteins. Lastly, our model provides a solution for how dynamic allostery could impact binding of some, but not all, class I MHC partners depending on the structural and chemical composition of the interfaces.

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides.

MOTIVATION: The binding of T-cell receptors (TCRs) to their target peptide MHC (pMHC) ligands initializes the cell-mediated immune response. In autoimmune diseases such as multiple sclerosis, the TCR erroneously recognizes self-peptides as foreign and activates an immune response against healthy cells. Such responses can be triggered by cross-recognition of the autoreactive TCR with foreign peptides. Hence, it would be desirable to identify such foreign-antigen triggers to provide a mechanistic understanding of autoimmune diseases. However, the large sequence space of foreign antigens presents an obstacle in the identification of cross-reactive peptides. RESULTS: Here, we present an in silico modeling and scoring method which exploits the structural properties of TCR-pMHC complexes to predict the binding of cross-reactive peptides. We analyzed three mouse TCRs and one human TCR isolated from a patient with multiple sclerosis. Cross-reactive peptides for these TCRs were previously identified via yeast display coupled with deep sequencing, providing a robust dataset for evaluating our method. Modeling query peptides in their associated TCR-pMHC crystal structures, our method accurately selected the top binding peptides from sets containing more than a hundred thousand unique peptides. AVAILABILITY AND IMPLEMENTATION: Analyses were performed using custom Python and R scripts available at https://github.com/weng-lab/antigen-predict. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structural dissimilarity from self drives neoepitope escape from immune tolerance.

T-cell recognition of peptides incorporating nonsynonymous mutations, or neoepitopes, is a cornerstone of tumor immunity and forms the basis of new immunotherapy approaches including personalized cancer vaccines. Yet as they are derived from self-peptides, the means through which immunogenic neoepitopes overcome immune self-tolerance are often unclear. Here we show that a point mutation in a non-major histocompatibility complex anchor position induces structural and dynamic changes in an immunologically active ovarian cancer neoepitope. The changes pre-organize the peptide into a conformation optimal for recognition by a neoepitope-specific T-cell receptor, allowing the receptor to bind the neoepitope with high affinity and deliver potent T-cell signals. Our results emphasize the importance of structural and physical changes relative to self in neoepitope immunogenicity. Considered broadly, these findings can help explain some of the difficulties in identifying immunogenic neoepitopes from sequence alone and provide guidance for developing novel, neoepitope-based personalized therapies.

Monolithic all-silicon flat lens for broadband LWIR imaging.

We designed, fabricated, and characterized a flat multi-level diffractive lens comprised of only silicon with diameter=15.2mm, focal length=19mm, numerical aperture of 0.371, and operating over the long-wave infrared (LWIR) spectrum=8µm to 14 µm. We experimentally demonstrated a field of view of 46°, depth of focus >5mm, and wavelength-averaged Strehl ratio of 0.46. All of these metrics were comparable to those of a conventional refractive lens. The active device thickness is only 8 µm, and its weight (including the silicon substrate) is less than 0.2 g.

Measurement of Endotracheal Tube Positioning on Chest X-Ray Using Object Detection.

Patients who are intubated with endotracheal tubes often receive chest x-ray (CXR) imaging to determine whether the tube is correctly positioned. When these CXRs are interpreted by a radiologist, they evaluate whether the tube needs to be repositioned and typically provide a measurement in centimeters between the endotracheal tube tip and carina. In this project, a large dataset of endotracheal tube and carina bounding boxes was annotated on CXRs, and a machine-learning model was trained to generate these boxes on new CXRs and to calculate a distance measurement between the tube and carina. This model was applied to a gold standard annotated dataset, as well as to all prospective data passing through our radiology system for two weeks. Inter-radiologist variability was also measured on a test dataset. The distance measurements for both the gold standard dataset (mean error = 0.70 cm) and prospective dataset (mean error = 0.68 cm) were noninferior to inter-radiologist variability (mean error = 0.70 cm) within an equivalence bound of 0.1 cm. This suggests that this model performs at an accuracy similar to human measurements, and these distance calculations can be used for clinical report auto-population and/or worklist prioritization of severely malpositioned tubes.

The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics.

The role of the αß T cell receptor (TCR) in identifying immunological targets and signaling appropriate responses provides for exciting translational opportunities. Yet TCRs mediate one of the most complex protein-protein interactions in biology, with intricate signaling and selection mechanisms adding additional layers of sophistication. In this review, we discuss how these complexities influence the development and optimization of TCR-based therapeutics, focusing on the intersection between structure, affinity, and specificity. We highlight similarities between TCRs and germline antibodies in molecular recognition, but emphasize that engineering TCRs by mimicking antibody maturation may not translate into improved biological outcomes. A key point is the need to distinguish TCR biochemical recognition from T cell functional recognition and the complications this distinction has for efforts in TCR engineering. We suggest learning from natural immunity and taking advantage of structural features and state-of-the-art protein design principles as a means to optimize TCRs for therapeutic use.

An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes.

T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.

Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen.

Recognition of antigenic peptides bound to major histocompatibility complex (MHC) proteins by αß T cell receptors (TCRs) is a hallmark of T cell mediated immunity. Recent data suggest that variations in TCR binding geometry may influence T cell signaling, which could help explain outliers in relationships between physical parameters such as TCR-pMHC binding affinity and T cell function. Traditionally, TCR binding geometry has been described with simple descriptors such as the crossing angle, which quantifies what has become known as the TCR's diagonal binding mode. However, these descriptors often fail to reveal distinctions in binding geometry that are apparent through visual inspection. To provide a better framework for relating TCR structure to T cell function, we developed a comprehensive system for quantifying the geometries of how TCRs bind peptide/MHC complexes. We show that our system can discern differences not clearly revealed by more common methods. As an example of its potential to impact biology, we used it to reveal differences in how TCRs bind class I and class II peptide/MHC complexes, which we show allow the TCR to maximize access to and "read out" the peptide antigen. We anticipate our system will be of use in not only exploring these and other details of TCR-peptide/MHC binding interactions, but also addressing questions about how TCR binding geometry relates to T cell function, as well as modeling structural properties of class I and class II TCR-peptide/MHC complexes from sequence information. The system is available at https://tcr3d.ibbr.umd.edu/tcr_com or for download as a script.

Pharmacologic Characterization of ALD403, a Potent Neutralizing Humanized Monoclonal Antibody Against the Calcitonin Gene-Related Peptide.

ALD403 is a genetically engineered, humanized immunoglobulin G1 monoclonal antibody that inhibits the action of human calcitonin gene-related peptide (CGRP). Clinical trial data indicate that ALD403 is effective as a preventive therapy for migraine and has an acceptable safety profile. For preclinical characterization of ALD403, rabbit antibodies targeting α-CGRP were humanized and modified to eliminate fragment crystallizable (Fc) γ receptor (FcγR) and complement interactions. The ability of ALD403 to inhibit CGRP-induced cAMP production was assessed using a cAMP bioassay (Meso Scale Discovery). The IC50 for inhibition of cAMP release was 434 and 288 pM with the rabbit-human chimera antibody and the humanized ALD403, respectively. ALD403 inhibited α-CGRP binding with an IC50 of 4.7 × 10-11 and 1.2 × 10-10 M for the α-CGRP and AMY1 receptors, respectively. ALD403 did not induce antibody-dependent cellular cytotoxicity or complement-dependent cytotoxicity and did not stably interact with any of the FcγR mediating these functions, exhibiting only weak binding to FcγRI. ALD403 significantly lowered capsaicin-induced blood flow responses in rodents at all time points starting at 5 minutes postapplication in a dose-dependent manner. In conclusion, ALD403 is a potent functional ligand inhibitor of α-CGRP‒driven pharmacology. SIGNIFICANCE STATEMENT: α-Calcitonin gene-related peptide blockade by ALD403 was assessed via radiolabeled ligand displacement, in vitro inhibition of cell signaling, and in vivo inhibition of capsaicin-induced vasodilation. Lack of engagement of fragment crystallizable-mediated immune-effector functions by ALD403 was shown.

MHC Bias by T Cell Receptors: Genetic Evidence for MHC and TCR Coevolution.

Major histocompatibility complex (MHC) restriction is a fundamental tenet of T cell biology, but the underlying mechanisms have remained controversial. The extent to which T cell receptors (TCRs) are biased towards MHC proteins in particular has been widely discussed. In a recent paper, Sharon et al. report direct evidence for coevolution between TCR and MHC genes, helping to explain how MHC compatibility and bias can be encoded within TCRs.

T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability.

T cell receptor cross-reactivity allows a fixed T cell repertoire to respond to a much larger universe of potential antigens. Recent work has emphasized the importance of peptide structural and chemical homology, as opposed to sequence similarity, in T cell receptor cross-reactivity. Surprisingly, though, T cell receptors can also cross-react between ligands with little physiochemical commonalities. Studying the clinically relevant receptor DMF5, we demonstrate that cross-recognition of such divergent antigens can occur through mechanisms that involve heretofore unanticipated rearrangements in the peptide and presenting MHC protein, including binding-induced peptide register shifts and extensions from MHC peptide binding grooves. Moreover, cross-reactivity can proceed even when such dramatic rearrangements do not translate into structural or chemical molecular mimicry. Beyond demonstrating new principles of T cell receptor cross-reactivity, our results have implications for efforts to predict and control T cell specificity and cross-reactivity and highlight challenges associated with predicting T cell reactivities.