Molecular characterization of HLA class II binding to the LAG-3 T cell co-inhibitory receptor.

Immune checkpoint inhibitors (antibodies that block the T cell co-inhibitory receptors PD-1/PD-L1 or CTLA-4) have revolutionized the treatment of some forms of cancer. Importantly, combination approaches using drugs that target both pathways have been shown to boost the efficacy of such treatments. Subsequently, several other T cell inhibitory receptors have been identified for the development of novel immune checkpoint inhibitors. Included in this list is the co-inhibitory receptor lymphocyte activation gene-3 (LAG-3), which is upregulated on T cells extracted from tumor sites that have suppressive or exhausted phenotypes. However, the molecular rules that govern the function of LAG-3 are still not understood. Using surface plasmon resonance combined with a novel bead-based assay (AlphaScreenTM ), we demonstrate that LAG-3 can directly and specifically interact with intact human leukocyte antigen class II (HLA-II) heterodimers. Unlike the homologue CD4, which has an immeasurably weak affinity using these biophysical approaches, LAG-3 binds with low micromolar affinity. We further validated the interaction at the cell surface by staining LAG-3+ cells with pHLA-II-multimers. These data provide new insights into the mechanism by which LAG-3 initiates T cell inhibition.

Heterocyclic Phosphenium Cations and Their Divergent Coordination Chemistry.

While they are often encountered as reaction intermediates, phosphenium cations are not commonly incorporated into π-conjugated systems. We report the synthesis and characterization of donor-stabilized phosphenium cations supported by pyridylhydrazonide ligands. The preparation of these cations relies on precise control of ligand E-Z isomerism. The heterocycles were treated with a variety of transition metals, with [Rh(COD)Cl]2 yielding the only well-defined organometallic products. The optoelectronic properties of the phosphenium heterocycles and their transition-metal complexes were examined using UV-vis absorption spectroscopy, cyclic voltammetry, and modeling by density functional theory (DFT). Computations support the description of these compounds as phosphenium cations and corroborate our observation of a weak P-Npyridine bond, which was manifested experimentally as the Rh adducts undergo selective insertion of Rh into the P-Npyridine bond, depending on the substituent at phosphorus. The reported compounds provide a framework for further study of π-conjugated, N,N'-chelated phosphenium cations and their transition-metal adducts.

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.

Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https://vdjdb.cdr3.net.

A Boron Difluoride Hydrazone (BODIHY) Polymer Exhibits Aggregation-Induced Emission.

Polymers that exhibit aggregation-induced emission (AIE) find use, for example, as cell-imaging agents and as fluorometric sensors due to their unique optical properties. However, the structural diversity of AIE-active polymers has not necessarily advanced at the same rate as their applications. In this work, ring-opening metathesis polymerization is used to synthesize the first example of a polymer (Mn  = 61,600 g mol-1 , D = 1.32) containing boron difluoride hydrazone (BODIHY) heterocycles in its repeating unit. The BODIHY monomer and polymer described absorb and emit in the visible region in solution (λabs  = 428 and 429 nm, λem  = 528 and 526 nm) and as thin films (λabs  = 443 and 440 nm, λem  = 535 and 534 nm). Monomer (ΦFilm  = 10%) and polymer (ΦFilm  = 6%) exhibit enhanced emission as thin films compared to solution (ΦSoln  ≤ 1%) as well as AIE upon the addition of water to DMF solutions as a result of restriction of intramolecular motion. Enhancement factors for the monomer and polymer are determined to be 58 and 15, respectively. The title BODIHY polymer exhibited an earlier onset of AIE and enhanced sensitivity to solution viscosity when compared to the parent monomer.

Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope.

CD4+ T-cells recognize peptide antigens, in the context of human leukocyte antigen (HLA) class II molecules (HLA-II), which through peptide-flanking residues (PFRs) can extend beyond the limits of the HLA binding. The role of the PFRs during antigen recognition is not fully understood; however, recent studies have indicated that these regions can influence T-cell receptor (TCR) affinity and pHLA-II stability. Here, using various biochemical approaches including peptide sensitivity ELISA and ELISpot assays, peptide-binding assays and HLA-II tetramer staining, we focused on CD4+ T-cell responses against a tumor antigen, 5T4 oncofetal trophoblast glycoprotein (5T4), which have been associated with improved control of colorectal cancer. Despite their weak TCR-binding affinity, we found that anti-5T4 CD4+ T-cells are polyfunctional and that their PFRs are essential for TCR recognition of the core bound nonamer. The high-resolution (1.95 Å) crystal structure of HLA-DR1 presenting the immunodominant 20-mer peptide 5T4111-130, combined with molecular dynamic simulations, revealed how PFRs explore the HLA-proximal space to contribute to antigen reactivity. These findings advance our understanding of what constitutes an HLA-II epitope and indicate that PFRs can tune weak affinity TCR-pHLA-II interactions.

The nature of the human T cell response to the cancer antigen 5T4 is determined by the balance of regulatory and inflammatory T cells of the same antigen-specificity: implications for vaccine design.

The oncofoetal antigen 5T4 is a promising T cell target in the context of colorectal cancer, as demonstrated by a recent clinical study where 5T4-specific T cell responses, induced by vaccination or cyclophosphamide, were associated with a significantly prolonged survival of patients with metastatic disease. Whilst Th1-type (IFN-γ+) responses specific to 5T4, and other oncofoetal antigens, are often readily detectable in early stage CRC patients and healthy donors, their activity is suppressed as the cancer progresses by CD4+CD25hiFoxp3+ regulatory T cells (Treg) which contribute to the immunosuppressive environment conducive to tumour growth. This study mapped the fine specificity of Th1 and Treg cell responses to the 5T4 protein. Surprisingly, both immunogenic peptides and those recognised by Tregs clustered in the same HLA-DR transcending epitope-rich hotspots within the 5T4 protein. Similarly, regions of low Th1-cell immunogenicity also did not contain peptides capable of stimulating Tregs, further supporting the notion that Treg and Th1 cells recognise the same peptides. Understanding the rules which govern the balance of Th1 and Treg cells responding to a given peptide specificity is, therefore, of fundamental importance to designing strategies for manipulating the balance in favour of Th1 cells, and thus the most effective anti-cancer T cell responses.

Self-reported modifying effects of resilience factors on perceptions of workload, patient outcomes, and burnout in physician-attendees of an international emergency medicine conference.

Emergency medicine has one of the highest rates of burnout of all medical specialties. Recent research has identified putative sources of burnout in emergency medicine, including stress of overnight shifts, psychological demands of handling emergency patients, and perceived poor departmental support systems. This burnout is detrimental to the quality of patient care, and thus represents an important target to simultaneously improve both physician wellness and patient outcomes. We lack consensus on the best way to combat the impacts of physician burnout in part, because we do not know the protective factors that best enable individuals to manage their burnout and be resilient to its impacts on their patient care. The goal of this study was to identify the resilience factors that have the greatest influence on the relationship between physician burnout symptoms and perceptions of workload impact on patient outcomes. We conducted a cross-sectional web-based anonymous survey of full-time attending emergency medicine physicians and measured self-reported responses about perceived impacts of workload on patient care and symptoms of burnout. Additionally, we measured resilience factor-related items (such as shift length/type, spirituality, home life, etc.), stratified the responses by level of agreement with the statements, and assessed how each impacted the relationship between burnout domains and perceived workload/patient outcomes. The level of agreement with five resilience factor statements influenced the magnitude of correlation between workload's effects on patient outcomes and burnout. These factors included personal spirituality, utility of mindfulness techniques, sleep quality, perceptions of home life, and the presence of institutional debriefing procedures. This work identified five resilience factors that may enable emergency medicine physicians to mitigate the impact of their burnout on their work and patient care. Promoting these resilience factors represent targets for institutional-level interventions to improve both physician wellness and patient outcomes.

Impact of physician workload on burnout in the emergency department.

Emergency medicine is one of the medical fields with the highest rates of physician burnout. Research demonstrates hospitalists believe increasing workloads contribute to decreases in patient safety and satisfaction, and increases in morbidity and mortality. Our objective was to identify if emergency physicians who believe workload impacts patient care also experience worse rates of burnout symptoms. This two-phase study used an online survey with cross-sectional design distributed to emergency medicine physicians following the New Jersey American College of Emergency Physicians (NJ ACEP) Scientific Assembly in May 2016 and members of the ACEP Well-Being Committee and Wellness Section in December 2016. Respondents felt the greatest workload burdens by being '…unable to fully discuss treatment options or answer questions of a patient or family member' or leading to 'Delay in admitting or discharging patients.' Excessive workload also contributed to respondents having to 'Admit to hospital instead of discharge' and resulted in 'Worsened patient satisfaction.' The 'Emotional Exhaustion' domain of the Maslach Burnout Inventory was the most highly affected by the perceived effects of workload on patient outcomes and 'Personal Accomplishment' was least affected. This research highlights the perception that workload contributing to patient harm may be associated with emergency medicine burnout.

Large extinction ratio optical electrowetting shutter.

A large extinction ratio optical shutter has been demonstrated using electrowetting liquids. The device is based on switching between a liquid-liquid interface curvature that produces total internal reflection and one that does not. The interface radius of curvature can be tuned continuously from 9 mm at 0 V to -45 mm at 26 V. Extinction ratios from 55.8 to 66.5 dB were measured. The device shows promise for ultracold chip-scale atomic clocks.

Adaptive electrowetting lens-prism element.

An adaptive electrowetting-based element with focusing and steering capability has been demonstrated in a monolithic design. Curvature and tip-tilt variation have been demonstrated using low voltages. A steering range of up to 4.3° and lens tuning of 18 diopters have been measured at 30 V DC and 21 V DC, respectively.

Focus-tunable low-power electrowetting lenses with thin parylene films.

Electrowetting lenses with record low power consumption (microwatts) have been demonstrated using high-quality parylene AF-4 dielectric layers and large dodecyl sulfate ions. Water and propylene glycol are interchanged as the polar liquid to enable diverging and converging lens operation achievable with the application of 15 V. The optical quality of the lenses is comparable to conventional microlenses and the tuning exhibits very little (<0.5°) contact angle hysteresis.

Tightrope act: autophagy in stem cell renewal, differentiation, proliferation, and aging.

Autophagy is a constitutive lysosomal catabolic pathway that degrades damaged organelles and protein aggregates. Stem cells are characterized by self-renewal, pluripotency, and quiescence; their long life span, limited capacity to dilute cellular waste and spent organelles due to quiescence, along with their requirement for remodeling in order to differentiate, all suggest that they require autophagy more than other cell types. Here, we review the current literature on the role of autophagy in embryonic and adult stem cells, including hematopoietic, mesenchymal, and neuronal stem cells, highlighting the diverse and contrasting roles autophagy plays in their biology. Furthermore, we review the few studies on stem cells, lysosomal activity, and autophagy. Novel techniques to detect autophagy in primary cells are required to study autophagy in different stem cell types. These will help to elucidate the importance of autophagy in stem cells during transplantation, a promising therapeutic approach for many diseases.

Gender Harmony: A Case for Nursing Informatics.

The design of digital health information systems around a conflated gender/sex binary contributes to health inequities. Lack of specific information that supports affirming communication lead to inappropriate care, disrespectful encounters with healthcare staff, and avoidance of health services by clients who have been harmed by misgendering, deadnaming and being outed. The HL7 International Gender Harmony Model (HL7 GHM) supports the design, implementation and use of DHIS that enable affirming clinical interactions and care. This case study will demonstrate how applying the HL7 GHM can address the harms reported in a recently published account of one patient in Canada.

Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.

Deep learning models have been shown to accurately predict protein structure from sequence, allowing researchers to explore protein space from the structural viewpoint. In this paper we explore whether "novel" features, such as distinct loop conformations can arise from these predictions despite not being present in the training data. Here we have used ABodyBuilder2, a deep learning antibody structure predictor, to predict the structures of ~1.5M paired antibody sequences. We examined the predicted structures of the canonical CDR loops and found that most of these predictions fall into the already described CDR canonical form structural space. We also found a small number of "new" canonical clusters composed of heterogeneous sequences united by a common sequence motif and loop conformation. Analysis of these novel clusters showed their origins to be either shapes seen in the training data at very low frequency or shapes seen at high frequency but at a shorter sequence length. To evaluate explicitly the ability of ABodyBuilder2 to extrapolate, we retrained several models whilst withholding all antibody structures of a specific CDR loop length or canonical form. These "starved" models showed evidence of generalisation across CDRs of different lengths, but they did not extrapolate to loop conformations which were highly distinct from those present in the training data. However, the models were able to accurately predict a canonical form even if only a very small number of examples of that shape were in the training data. Our results suggest that deep learning protein structure prediction methods are unable to make completely out-of-domain predictions for CDR loops. However, in our analysis we also found that even minimal amounts of data of a structural shape allow the method to recover its original predictive abilities. We have made the ~1.5 M predicted structures used in this study available to download at https://doi.org/10.5281/zenodo.10280181.

Switchable Optical Properties of Dyes and Nanoparticles in Electrowetting Devices.

The optical properties of light-absorbing materials in optical shutter devices are critical to the use of such platforms for optical applications. We demonstrate switchable optical properties of dyes and nanoparticles in liquid-based electrowetting-on-dielectric (EWOD) devices. Our work uses narrow-band-absorbing dyes and nanoparticles, which are appealing for spectral-filtering applications targeting specific wavelengths while maintaining device transparency at other wavelengths. Low-voltage actuation of boron dipyromethene (BODIPY) dyes and nanoparticles (Ag and CdSe) was demonstrated without degradation of the light-absorbing materials. Three BODIPY dyes were used, namely Abs 503 nm, 535 nm and 560 nm for dye 1 (BODIPY-core), 2 (I2BODIPY) and 3 (BODIPY-TMS), respectively. Reversible and low-voltage (≤20 V) switching of dye optical properties was observed as a function of device pixel dimensions (300 × 900, 200 × 600 and 150 × 450 µm). Low-voltage and reversible switching was also demonstrated for plasmonic and semiconductor nanoparticles, such as CdSe nanotetrapods (abs 508 nm), CdSe nanoplatelets (Abs 461 and 432 nm) and Ag nanoparticles (Abs 430 nm). Nanoparticle-based devices showed minimal hysteresis as well as faster relaxation times. The study presented can thus be extended to a variety of nanomaterials and dyes having the desired optical properties.

The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling.

T cell activation is governed through T cell receptors (TCRs), heterodimers of two sequence-variable chains (often an α and ß chain) that synergistically recognize antigen fragments presented on cell surfaces. Despite this, there only exist repositories dedicated to collecting single-chain, not paired-chain, TCR sequence data. We addressed this gap by creating the Observed TCR Space (OTS) database, a source of consistently processed and annotated, full-length, paired-chain TCR sequences. Currently, OTS contains 5.35 million redundant (1.63 million non-redundant), predominantly human sequences from across 50 studies and at least 75 individuals. Using OTS, we identify pairing biases, public TCRs, and distinct chain coherence patterns relative to antibodies. We also release a paired-chain TCR language model, providing paired embedding representations and a method for residue in-filling conditional on the partner chain. OTS will be updated as a central community resource and is freely downloadable and available as a web application.

Tebentafusp Induces a T-Cell-Driven Rash in Melanocyte-Bearing Skin as an Adverse Event Consistent with the Mechanism of Action.

Tebentafusp is a gp100xCD3-bispecific ImmTAC designed to redirect polyclonal T cells against cells presenting the melanocyte lineage-specific antigen gp100 on HLA-A∗02:01. Skin-related adverse events, predominantly rash, are frequent and occur within a few hours after initial infusions; yet, the mechanisms are unknown. In this study, we analyzed clinical data from the randomized phase 3 trial (NCT03070392) of tebentafusp (n = 252) versus investigator's choice (n = 126). Translational analyses were performed on paired on-treatment skin samples from 19 patients collected in the phase 1 trial (NCT01211262). Our analyses showed that rash is a clinical manifestation of tebentafusp-induced recruitment of T cells to cutaneous melanocytes. Development of rash depended on baseline expression levels of gp100 and other melanin pathway genes in the skin. On treatment, melanocyte number was reduced, and expression of melanocytic genes decreased, whereas gene expression related to immunity and cytokine signaling increased. When adjusted for baseline prognostic features, patients with rash within the first week of tebentafusp treatment had the same overall survival as patients without a rash in the phase 3 randomized trial IMCgp100-202 (hazard ratio = 0.84, 95% confidence interval = 0.53-1.32). In summary, skin rash is an off-tumor, on-target effect of tebentafusp against gp100+ melanocytes, in line with the mechanism of action.

Electrowetting lenses for compensating phase and curvature distortion in arrayed laser systems.

We have demonstrated a one-dimensional array of individually addressable electrowetting tunable liquid lenses that compensate for more than one wave of phase distortion across a wavefront. We report a scheme for piston control using tunable liquid lens arrays in volume-bound cavities that alter the optical path length without affecting the wavefront curvature. Liquid lens arrays with separately tunable focus or phase control hold promise for laser communication systems and adaptive optics.

Coimmunization with Preerythrocytic Antigens alongside Circumsporozoite Protein Can Enhance Sterile Protection against Plasmodium Sporozoite Infection.

Malaria-causing Plasmodium parasites have a complex life cycle and present numerous antigen targets that may contribute to protective immune responses. The currently recommended vaccine-RTS,S-functions by targeting the Plasmodium falciparum circumsporozoite protein (CSP), which is the most abundant surface protein of the sporozoite form responsible for initiating infection of the human host. Despite showing only moderate efficacy, RTS,S has established a strong foundation for the development of next-generation subunit vaccines. Our previous work characterizing the sporozoite surface proteome identified additional non-CSP antigens that may be useful as immunogens individually or in combination with CSP. In this study, we examined eight such antigens using the rodent malaria parasite Plasmodium yoelii as a model system. We demonstrate that despite conferring weak protection individually, coimmunizing each of several of these antigens alongside CSP could significantly enhance the sterile protection achieved by CSP immunization alone. Thus, our work provides compelling evidence that a multiantigen preerythrocytic vaccine approach may enhance protection compared to CSP-only vaccines. This lays the groundwork for further studies aimed at testing the identified antigen combinations in human vaccination trials that assess efficacy with controlled human malaria infection. IMPORTANCE The currently approved malaria vaccine targets a single parasite protein (CSP) and results in only partial protection. We tested several additional vaccine targets in combination with CSP to identify those that could enhance protection from infection upon challenge in the mouse malaria model. In identifying several such enhancing vaccine targets, our work indicates that a multiprotein immunization approach may be a promising avenue to achieving higher levels of protection from infection. Our work identified several candidate leads for follow-up in the models relevant for human malaria and provides an experimental framework for efficiently carrying out such screens for other combinations of vaccine targets.