Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that escape convalescent and vaccine-induced antibody responses has renewed focus on the development of broadly protective T-cell-based vaccines. Here, we apply structure-based network analysis and assessments of HLA class I peptide stability to define mutationally constrained CD8+ T cell epitopes across the SARS-CoV-2 proteome. Highly networked residues are conserved temporally among circulating variants and sarbecoviruses and disproportionately impair spike pseudotyped lentivirus infectivity when mutated. Evaluation of HLA class I stabilizing activity for 18 globally prevalent alleles identifies CD8+ T cell epitopes within highly networked regions with limited mutational frequencies in circulating SARS-CoV-2 variants and deep-sequenced primary isolates. Moreover, these epitopes elicit demonstrable CD8+ T cell reactivity in convalescent individuals but reduced recognition in recipients of mRNA-based vaccines. These data thereby elucidate key mutationally constrained regions and immunogenic epitopes in the SARS-CoV-2 proteome for a global T-cell-based vaccine against emerging variants and SARS-like coronaviruses.

Loss of Bcl-6-Expressing T Follicular Helper Cells and Germinal Centers in COVID-19.

Humoral responses in coronavirus disease 2019 (COVID-19) are often of limited durability, as seen with other human coronavirus epidemics. To address the underlying etiology, we examined post mortem thoracic lymph nodes and spleens in acute SARS-CoV-2 infection and observed the absence of germinal centers and a striking reduction in Bcl-6+ germinal center B cells but preservation of AID+ B cells. Absence of germinal centers correlated with an early specific block in Bcl-6+ TFH cell differentiation together with an increase in T-bet+ TH1 cells and aberrant extra-follicular TNF-α accumulation. Parallel peripheral blood studies revealed loss of transitional and follicular B cells in severe disease and accumulation of SARS-CoV-2-specific "disease-related" B cell populations. These data identify defective Bcl-6+ TFH cell generation and dysregulated humoral immune induction early in COVID-19 disease, providing a mechanistic explanation for the limited durability of antibody responses in coronavirus infections, and suggest that achieving herd immunity through natural infection may be difficult.

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.

No Correlation Exists Between Tibial- and Femoral-Based Measurements of Patella Alta in a Population With Chronic Patellofemoral Pain or Instability Undergoing Patella Distalization.

PURPOSE: To investigate whether the patellotrochlear index (PTI) predicts patella alta as determined by tibial-based methods of Insall-Salvati (IS) and Caton-Deschamp (CDI) indexes in a pathological population (with patellofemoral pain and/or instability), in addition to determining whether PTI and sagittal patellofemoral engagement (SPE) correlate with trochlea length as determined by lateral condyle index (LCI). METHODS: Patients with confirmed patella alta (IS/CDI ratio >1.2) undergoing tibial tubercle osteotomy for patellofemoral pain/instability with an available magnetic resonance imaging (MRI) scans were included. Patients who had undergone previous soft-tissue realignment, previous surgery, or trauma to the extensor mechanism were excluded. Two raters measured the IS, CDI, PTI, SPE, LCI, and knee flexion angle (KFA) on MRI. Interobserver reliability and correlation between measurements were calculated. RESULTS: In total, 71 knees were included. PTI (0.73), SPE (0.836), LCI (0.701), and KFA (0.8) demonstrated good- to near-excellent interobserver reliability. IS (0.65) and CDI (0.66) demonstrated moderate interobserver reliability. PTI and SPE showed the strongest significant correlation (0.8112, P = 2.2 × 10-16). IS and CD (0.39, P = .0007) showed a moderate significant correlation. PTI and KFA (0.53, P = 1.685 × 10-6) and SPE and KFA (0.61, P = 1.991 × 10-8) had a significant moderate correlation. LCI and KFA (-0.37, P = .0017) showed a significant moderate negative correlation. All other measurement indices correlated poorly and were insignificant. A total of 94.4% of the knees were defined as having patella alta using IS, with the remaining 5.6% having a raised CDI. Only 14% of cases had an IS of >1.2, a CDI >1.2, and a PTI <0.125, which increased to 39% (28/71) when the threshold for PTI was increased to <0.28. CONCLUSIONS: There was no correlation between tibial (IS and CD) and femoral methods (PTI and SPE) of quantifying patella alta. PTI and SPE did not correlate with trochlea length as measured by LCI. PTI, SPE, and LCI are significantly affected by the KFA during MRI. LEVEL OF EVIDENCE: Level IV, retrospective diagnostic radiographic investigation.

Complex Pathways Drive Pluripotent Fmoc-Leucine Self-Assemblies.

Nature uses complex self-assembly pathways to access distinct functional non-equilibrium self-assemblies. This remarkable ability to steer same set of biomolecules into different self-assembly states is done by avoiding thermodynamic pit. In synthetic systems, on demand control over 'Pathway Complexity' to access self-assemblies different from equilibrium structures remains challenging. Here we show versatile non-equilibrium assemblies of the same monomer via alternate assembly pathways. The assemblies nucleate using non-classical or classical nucleation routes into distinct metastable (transient hydrogels), kinetic (stable hydrogels) and thermodynamic structures [(poly)-crystals and 2D sheets]. Initial chemical and thermal inputs force the monomers to follow different assembly pathways and form soft-materials with distinct molecular arrangements than at equilibrium. In many cases, equilibrium structures act as thermodynamic sink which consume monomers from metastable structures giving transiently formed materials. This dynamics can be tuned chemically or thermally to slow down the dissolution of transient hydrogel, or skip the intermediate hydrogel altogether to reach final equilibrium assemblies. If required this metastable state can be kinetically trapped to give strong hydrogel stable over days. This method to control different self-assembly states can find potential use in similar biomimetic systems to access new materials for various applications.

Transcriptomics and Proteomics Approach for the Identification of Altered Blood microRNAs and Plasma Proteins in Parkinson's Disease.

Parkinson's disease (PD) is a neurodegenerative disorder caused by the selective destruction of dopaminergic neurons (DA-nergic). Clinically, PD is diagnosed based on developing signs and symptoms. A neurological and physical examination and sometimes medical and family history also help in the diagnosis of PD. However, most of these features are visible when more than 80% of the dopaminergic neurons have degenerated. An understanding of the selective degeneration process at the cellular and molecular level and the development of new biomarkers are required for effective PD management. Several studies have been carried out using a selected set of miRNAs/ mRNAs and proteins to develop biomarkers of PD; however, an unbiased and combined miRNA-protein profiling study was required to identify the markers of progressive and selected degeneration of dopaminergic neurons in PD patients. In the present study, we have carried out global protein profiling through LC-MS/MS and miRNA profiling by using a "brain-specific" miRNA array panel of 112 miRNAs in PD patients and healthy controls to find the unprejudiced group of proteins and miRNAs that are deregulating in PD. In the whole blood samples of PD patients compared to healthy controls, the expression of 23 miRNAs and 289 proteins was significantly increased, whereas the expression of 4 miRNAs and 132 proteins was considerably downregulated. Network analysis, functional enrichment, annotation, and analysis of miRNA-protein interactions were also performed as part of the bioinformatics investigation of the discovered miRNAs and proteins revealing several pathways that lead to PD development and pathogenesis. Based on the analysis of miRNA and protein profiling, we have identified four miRNAs (hsa-miR-186-5p, miR-29b, miR-139 & has-miR-150-5p) and four proteins (YWHAZ, PSMA4, HYOU1, & SERPINA1), which can be targeted for the development of new biomarkers of PD. In vitro studies have identified the role of miR-186-5p in regulating the levels of the YWHAZ/YWHAB & CALM2 gene, which has shown maximum downregulation in PD patients and is known for its role in neuroprotection from apoptotic cell death & calcium regulation. In conclusion, our research has identified a group of miRNA-proteins that can be developed as PD biomarkers; however, future studies on the release of these miRNAs and proteins in extracellular vesicles circulating in the blood of PD patients can further validate these as specific biomarkers of PD.

EgoActive: Integrated Wireless Wearable Sensors for Capturing Infant Egocentric Auditory-Visual Statistics and Autonomic Nervous System Function 'in the Wild'.

There have been sustained efforts toward using naturalistic methods in developmental science to measure infant behaviors in the real world from an egocentric perspective because statistical regularities in the environment can shape and be shaped by the developing infant. However, there is no user-friendly and unobtrusive technology to densely and reliably sample life in the wild. To address this gap, we present the design, implementation and validation of the EgoActive platform, which addresses limitations of existing wearable technologies for developmental research. EgoActive records the active infants' egocentric perspective of the world via a miniature wireless head-mounted camera concurrently with their physiological responses to this input via a lightweight, wireless ECG/acceleration sensor. We also provide software tools to facilitate data analyses. Our validation studies showed that the cameras and body sensors performed well. Families also reported that the platform was comfortable, easy to use and operate, and did not interfere with daily activities. The synchronized multimodal data from the EgoActive platform can help tease apart complex processes that are important for child development to further our understanding of areas ranging from executive function to emotion processing and social learning.

Expression of miR-145 and miR-18b in Peripheral Blood Samples of Head and Neck Cancer Patients.

Head and neck squamous cell carcinomas (HNSCC) is one of the most prevalent type of cancer known in Indian population. Studies are needed to identify the early biomarkers for HNSCC. MicroRNAs (miRNAs) are non-coding RNA molecules, expression of which can be used as biomarker for early diagnosis of HNSCC. For miRNA profiling total RNA, which also contained small RNAs were isolated from ten HNSCC tissue samples and adjacent control. Purity and concentration of eluted RNA was assessed using the NanoDrop1000® spectrophotometer, Reverse Transcription reaction was carried out with megaplex RT primers of pool A and pool B and the expression of selected miRNAs (miR-143/145 and miR-18a/b) was measured using TaqMan primers specific for mature miRNAs. Our study showed dramatic downregulation in expression of two miRNAs, miR-18b and miR-145 in blood samples of HNSCC patients, which are inhibitor of tumorigenesis and can be targeted as biomarker of HNSCC pathogenesis therefore developing avenues for miRNA role in prognosis and therapeutics. Supplementary Information: The online version contains supplementary material available at 10.1007/s12291-023-01119-2.

Chemically Fueled Autonomous Sol→Gel→Sol→Gel→Sol Transitions.

Complex non-equilibrium phase behaviors are a hallmark of natural self-assembling systems. Here we show how intricate phase transitions can be achieved through a chemically fueled reaction cycle to yield autonomous sol→gel→sol→gel→sol transitions. A relay of chemical transformations based on thiazinane metathesis leads to two consecutive transient gelations in a closed system. Within seconds of fuel addition to deactivated thiazinane monomers, an imine-based hydrogel forms that consists of fibrillar microspheres. This gel quickly loses its mechanical strength and forms a solution, from which a second aldehyde-based gel nucleates and remains stable for over one day. Overall, our reaction cycle gives rise to two consecutive re-entrant phase transitions without any experimental intervention.

Chemically Fueled Self-Sorted Hydrogels.

Narcissistic self-sorting in supramolecular assemblies can help to construct materials with more complex hierarchies. Whereas controlled changes in pH or temperature have been used to this extent for two-component self-sorted gels, here we show that a chemically fueled approach can provide three-component materials with high precision. The latter materials have interesting mechanical properties, such as enhanced or suppressed stiffness, and intricate multistep gelation kinetics. In addition, we show that we can achieve supramolecular templating, where pre-existing supramolecular fibers first act as templates for growth of a second gelator, after which they can selectively be removed.

High wall-plug efficiency and narrow linewidth III-V-on-silicon C-band DFB laser diodes.

We present recent results on compact and power efficient C-band distributed feedback lasers through adhesive bonding of a III-V die onto a silicon-on-insulator circuit. A wall-plug efficiency up to 16% is achieved for bias currents below 40 mA. The laser cavity is 180 µm long and a single facet output power up to 11 mW is measured at 20 °C by incorporating a broadband reflector in the silicon waveguide at one side of the cavity. Single mode operation at 1567 nm with a side mode suppression ratio of around 55 dB is demonstrated. By controlling the phase of the external feedback, the laser linewidth is decreased to 28 kHz. Measurement result shows a low relative intensity noise below -150 dB/Hz at 60 mA up to 6 GHz. We also report 20 and 10 Gbps data transmission at a bias current of 50 mA at 20 °C and 40 °C, respectively.

Swift catalytic reduction of hazardous pollutants by new generation microgels.

In this manuscript, we report for the first time a new generation microgel synthesis without using any divinyl functionalized cross-linker. A new generation less crosslinked microgel structure has been achieved by optimizing the amount of N-hydroxy methyl acrylamide (NHMA) and using a fixed amount of styrene (St), acrylic acid (AA) and N-vinyl pyrrolidone (NVP) via a free radical emulsion solution polymerization technique. Poly(NHMA) works as a hydrophilic as well as a crosslinking agent. Furthermore, microgels have been upgraded into a composite by incorporation of Ag nanoparticles for catalytic reduction applications. Microgels and their composites have been characterized by EDAX, FT-IR, particle size analyzer, SEM, TEM, TGA, UV-vis spectroscopy and XRD. Methylene blue (MB) dye and p-nitrophenol (PNP) were chosen as model hazardous pollutants for catalytic reduction applications. Microgels efficiently adsorb both pollutants over the surface and microgel_Ag composites dramatically reduced both pollutants in the non-toxic form at room temperature by using smaller doses of NaBH4.

Role of the uS9/yS16 C-terminal tail in translation initiation and elongation in Saccharomyces cerevisiae.

The small ribosomal subunit protein uS9 (formerly called rpS16 in Saccharomyces cerevisiae), has a long protruding C-terminal tail (CTT) that extends towards the mRNA cleft of the ribosome. The last C-terminal residue of uS9 is an invariably conserved, positively charged Arg that is believed to enhance interaction of the negatively charged initiator tRNA with the ribosome when the tRNA is base-paired to the AUG codon in the P-site. In order to more fully characterize the role of the uS9 CTT in eukaryotic translation, we tested how truncations, extensions and substitutions within the CTT affect initiation and elongation processes in Saccharomyces cerevisiae. We found that uS9 C-terminal residues are critical for efficient recruitment of the eIF2•GTP•Met-tRNAiMet ternary complex to the ribosome and for its proper response to the presence of an AUG codon in the P-site during the scanning phase of initiation. These residues also regulate hydrolysis of the GTP in the eIF2•GTP•Met-tRNAiMet complex to GDP and Pi. In addition, our data show that uS9 CTT modulates elongation fidelity. Therefore, we propose that uS9 CTT is critical for proper control of the complex interplay of events surrounding accommodation of initiator and elongator tRNAs in the P- and A-sites of the ribosome.

Human Cytomegalovirus miR-UL70-3p Downregulates the H2O2-Induced Apoptosis by Targeting the Modulator of Apoptosis-1 (MOAP1).

Human Cytomegalovirus (HCMV) is a prototypic beta herpesvirus, causing persistent infections in humans. There are medications that are used to treat the symptoms; however, there is no cure yet. Thus, understanding the molecular mechanisms of HCMV replication and its persistence may reveal new prevention strategies. HCMV evasive strategies on the antiviral responses of the human host largely rely on its significant portion of genome. Numerous studies have highlighted the importance of miRNA-mediated regulation of apoptosis, which is an innate immune mechanism that eradicates virus-infected cells. In this study, we explore the antiapoptotic role of hcmv-miR-UL70-3p in HEK293T cells. We establish that hcmv-miR-UL70-3p targets the proapoptotic gene Modulator of Apoptosis-1 (MOAP1) through interaction with its 3'UTR region of mRNA. The ectopic expression of hcmv-miR-UL70-3p mimic significantly downregulates the H2O2-induced apoptosis through the translational repression of MOAP1. Silencing of MOAP1 through siRNA also inhibits the H2O2-induced apoptosis, which further supports the hcmv-miR-UL70-3p mediated antiapoptotic effect by regulating MOAP1 expression. These results uncover a role for hcmv-miR-UL70-3p and its target MOAP1 in regulating apoptosis.

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.

Re-programming Hydrogel Properties Using a Fuel-Driven Reaction Cycle.

Nature uses catalysis as an indispensable tool to control assembly and reaction cycles in vital non-equilibrium supramolecular processes. For instance, enzymatic methionine oxidation regulates actin (dis-)assembly, and catalytic guanosine triphosphate hydrolysis is found in tubulin (dis-)assembly. Here we present a completely artificial reaction cycle which is driven by a chemical fuel that is catalytically obtained from a "pre-fuel". The reaction cycle controls the dis-assembly and re-assembly of a hydrogel, where the rate of pre-fuel turnover dictates the morphology as well as the mechanical properties. By addition of additional fresh aliquots of fuel and removal of waste, the hydrogels can be re-programmed time after time. Overall, we show how catalytic fuel generation can control reaction/assembly kinetics and materials' properties in life-like non-equilibrium systems.

Virtual measurements of paracellular permeability and chronic inflammation via color coded pixel-wise T1 mapping.

To assess whether quantitative T1 relaxometry can measure permeability, chronic inflammation and mural thickening of mouse bladder wall. Adult female C57BL6 mice unexposed to radiation (controls) or 40 wk postirradiation of 10 Gy were scanned at 9.4 T before and after instillation (0.1 mL) of aqueous, novel contrast mixture (NCM) containing 4 mM gadobutrol and 5 mM ferumoxytol. Rapid acquisition with refocused echo (RARE) sequence was used with variable repetition times (TR). Pixel-wise maps of T1 relaxation times for the segmented bladder wall layers were generated from voxel-wise, nonlinear least square data fitting of TR-dependent signal intensity acquired with TR array of 0.4-10 s followed by the histology of harvested bladder. Significant differences between precontrast and postcontrast T1 (ΔT1) were noted in urothelium and lamina propria of both groups but only in detrusor of irradiated group (P < 0.001; 2-way ANOVA). Nearly twofold higher gadobutrol permeability (550 ± 73 vs. 294 ± 160 µM; P < 0.01) derived as per 1/ΔT1 = r1. [C] in urothelium of irradiated group. Inflammation and bladder wall thickening (0.75 ± 0. vs. 0.44 ± 0.08 mm; P < 0.001) predicted by MRI was subsequently confirmed by histology and altered expression of CD45 and zonula occludens-1 (ZO-1) relative to controls. NCM enhanced MRI relies on the retention of large molecular weight ferumoxytol in lumen for negative contrast, while permeation of the non-ionic, small molecular weight gadobutrol through ZO-1 generates positive contrast in bladder wall for virtual measurement of paracellular permeability and assessment of chronic inflammation in thin and distensible bladder wall, which is also defined by its variable shape and location within pelvis.

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.

T cell receptors (TCRs) have emerged as a new class of immunological therapeutics. However, though antigen specificity is a hallmark of adaptive immunity, TCRs themselves do not possess the high specificity of monoclonal antibodies. Although a necessary function of T cell biology, the resulting cross-reactivity presents a significant challenge for TCR-based therapeutic development, as it creates the potential for off-target recognition and immune toxicity. Efforts to enhance TCR specificity by mimicking the antibody maturation process and enhancing affinity can inadvertently exacerbate TCR cross-reactivity. Here we demonstrate this concern by showing that even peptide-targeted mutations in the TCR can introduce new reactivities against peptides that bear similarity to the original target. To counteract this, we explored a novel structure-guided approach for enhancing TCR specificity independent of affinity. Tested with the MART-1-specific TCR DMF5, our approach had a small but discernible impact on cross-reactivity toward MART-1 homologs yet was able to eliminate DMF5 cross-recognition of more divergent, unrelated epitopes. Our study provides a proof of principle for the use of advanced structure-guided design techniques for improving TCR specificity, and it suggests new ways forward for enhancing TCRs for therapeutic use.

How an alloreactive T-cell receptor achieves peptide and MHC specificity.

T-cell receptor (TCR) allorecognition is often presumed to be relatively nonspecific, attributable to either a TCR focus on exposed major histocompatibility complex (MHC) polymorphisms or the degenerate recognition of allopeptides. However, paradoxically, alloreactivity can proceed with high peptide and MHC specificity. Although the underlying mechanisms remain unclear, the existence of highly specific alloreactive TCRs has led to their use as immunotherapeutics that can circumvent central tolerance and limit graft-versus-host disease. Here, we show how an alloreactive TCR achieves peptide and MHC specificity. The HCV1406 TCR was cloned from T cells that expanded when a hepatitis C virus (HCV)-infected HLA-A2- individual received an HLA-A2+ liver allograft. HCV1406 was subsequently shown to recognize the HCV nonstructural protein 3 (NS3):1406-1415 epitope with high specificity when presented by HLA-A2. We show that NS3/HLA-A2 recognition by the HCV1406 TCR is critically dependent on features unique to both the allo-MHC and the NS3 epitope. We also find cooperativity between structural mimicry and a crucial peptide "hot spot" and demonstrate its role, along with the MHC, in directing the specificity of allorecognition. Our results help explain the paradox of specificity in alloreactive TCRs and have implications for their use in immunotherapy and related efforts to manipulate TCR recognition, as well as alloreactivity in general.