Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein.

Adenovirus vaccines, particularly the COVID-19 Ad5-nCoV adenovirus vaccine, have emerged as promising tools in the fight against infectious diseases. In this study, we investigated the structure of the T cell response to the Spike protein of the SARS-CoV-2 virus used in the COVID-19 Ad5-nCoV adenoviral vaccine in a phase 3 clinical trial (NCT04540419). In 69 participants, we collected peripheral blood samples at four time points after vaccination or placebo injection. Sequencing of T cell receptor repertoires from Spike-stimulated T cell cultures at day 14 from 17 vaccinated revealed a more diverse CD4+ T cell repertoire compared to CD8+. Nevertheless, CD8+ clonotypes accounted for more than half of the Spike-specific repertoire. Our longitudinal analysis showed a peak T cell response at day 14, followed by a decline until month 6. Remarkably, multiple T cell clonotypes persisted for at least 6 months after vaccination, as demonstrated by ex vivo stimulation. Examination of CDR3 regions revealed homologous sequences in both CD4+ and CD8+ clonotypes, with major CD8+ clonotypes sharing high similarity with annotated sequences specific for the NYNYLYRLF peptide, suggesting potential immunodominance. In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases.

Pyrazolate vs. phenylethynide: direct exchange of the anionic bridging ligand in a cyclic trinuclear silver complex.

Cyclic trinuclear Ag(I) pyrazolate interacts with phenylacetylene forming a mix-ligand complex in which one pyrazolate ligand is changed to phenylethynide. The CC- fragment coordinates only to two silver(I) atoms via one carbon atom demonstrating unique µ2-η1 σ-coordination with close Ag-C bond lengths and Ag-C-C angles. The complex exhibits blue emission under UV irradiation.

Tetranuclear Copper(I) and Silver(I) Pyrazolate Adducts with 1,1'-Dimethyl-2,2'-bibenzimidazole: Influence of Structure on Photophysics.

A reaction of a cyclic trinuclear copper(I) or silver(I) pyrazolate complex ([MPz]3, M = Cu, Ag) with 1,1'-dimethyl-2,2'-bibenzimidazole (L) leads to the formation of tetranuclear adducts decorated by one or two molecules of a diimine ligand, depending on the amount of the ligand added (0.75 or 1.5 equivalents). The coordination of two L molecules stabilizes the formation of a practically idealized tetrahedral four-metal core in the case of a copper-containing complex and a distorted tetrahedron in the case of a Ag analog. In contrast, complexes containing one molecule of diimine possess two types of metals, two- and three-coordinated, forming the significantly distorted central M4 cores. The diimine ligands are twisted in these complexes with dihedral angles of ca. 50-60°. A TD-DFT analysis demonstrated the preference of a triplet state for the twisted 1,1'-dimethyl-2,2'-bibenzimidazole and a singlet state for the planar geometry. All obtained complexes demonstrated, in a solution, the blue fluorescence of the ligand-centered (LC) nature typical for free diimine. In contrast, a temperature decrease to 77 K stabilized the structure close to that observed in the solid state and activated the triplet states, leading to green phosphorescence at ca. 500 nm. The silver-containing complex Ag4Pz4L exhibited dual emission from both the singlet and triplet states, even at room temperature.

HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire.

In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the diminishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunoprevalent epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides.

Clonal diversity predicts persistence of SARS-CoV-2 epitope-specific T-cell response.

T cells play a pivotal role in reducing disease severity during SARS-CoV-2 infection and formation of long-term immune memory. We studied 50 COVID-19 convalescent patients and found that T cell response was induced more frequently and persisted longer than circulating antibodies. We identified 756 clonotypes specific to nine CD8+ T cell epitopes. Some epitopes were recognized by highly similar public clonotypes. Receptors for other epitopes were extremely diverse, suggesting alternative modes of recognition. We tracked persistence of epitope-specific response and individual clonotypes for a median of eight months after infection. The number of recognized epitopes per patient and quantity of epitope-specific clonotypes decreased over time, but the studied epitopes were characterized by uneven decline in the number of specific T cells. Epitopes with more clonally diverse TCR repertoires induced more pronounced and durable responses. In contrast, the abundance of specific clonotypes in peripheral circulation had no influence on their persistence.

Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2.

The ongoing COVID-19 pandemic calls for more effective diagnostic tools. T cell response assessment serves as an independent indicator of prior COVID-19 exposure while also contributing to a more comprehensive characterization of SARS-CoV-2 immunity. In this study, we systematically assessed the immunogenicity of 118 epitopes with immune cells collected from multiple cohorts of vaccinated, convalescent, healthy unexposed, and SARS-CoV-2-exposed donors. We identified 75 immunogenic epitopes, 24 of which were immunodominant. We further confirmed HLA restriction for 49 epitopes and described association with more than 1 HLA allele for 14 of these. Exclusion of 2 cross-reactive epitopes that generated a response in prepandemic samples left us with a 73-epitope set that offered excellent diagnostic specificity without losing sensitivity compared with full-length antigens, and this evoked a robust cross-reactive response. We subsequently incorporated this set of epitopes into an in vitro diagnostic Corona-T-test, which achieved a diagnostic accuracy of 95% in a clinical trial. In a cohort of asymptomatic seronegative individuals with a history of prolonged SARS-CoV-2 exposure, we observed a complete absence of T cell response to our epitope panel. In combination with strong reactivity to full-length antigens, this suggests that a cross-reactive response might protect these individuals.

Quantification of DAS VSP Quality: SNR vs. Log-Based Metrics.

The initial quantification of data quality is an important step in seismic data acquisition design, including the choice of sensing strategy. The signal-to-noise ratio (SNR) often drives the choice of distributed acoustic sensing (DAS) parameters in vertical seismic profiling (VSP). We compare this established approach for data quality assessment with metrics comparing DAS data products to available well logs. First, we create kinematic and dynamic data products derived from original seismic data, such as the interval velocity and amplitude of P-wave arrivals. Next, we quantify the quality of derived data products using well log data by calculating various statistical metrics. Using a large dataset of 220 different VSP experiments with a fixed source location and various DAS acquisition parameters, such as gauge length (GL), conveyance type, and lead-in length, we analyzed the statistical distribution of various metrics. The results indicate the decoupling between seismic-based and log-based metrics as well as between the quality of dynamic and kinematic data-products for the same record. Therefore, we propose using fit-for-purpose metrics to optimize the acquisition cost. In particular, for ray-based tomographic processing, it is sufficient to use traveltime-based metrics. On the other hand, for advanced dynamic analysis, amplitude-based metrics define the quality of final processing products. Hence, it is crucial to use fit-for-purpose metrics to optimize DAS VSP acquisition.

Distributed Acoustic Sensing (DAS) Response of Rising Taylor Bubbles in Slug Flow.

Slug flow is one of the most common flow types encountered in surface facilities, pipelines, and wellbores. The intermittent gas phase, in the form of a Taylor bubble, followed by the liquid phase can be destructive to equipment. However, commonly used point flow sensors have significant limitations for flow analysis. Distributed acoustic sensing (DAS) can turn optical fibers into an array of distributed strain rate sensors and provide substantial insights into flow characterization. We built a 10 m vertical laboratory flow loop equipped with wrapped fiber optic cables to study the DAS response of rising Taylor bubbles. Low-passed DAS data allow for velocity tracking of Taylor bubbles of different sizes and water velocities. Moreover, we measured the velocity of the wake region following the Taylor bubble and explored the process of Taylor bubbles merging. The amplitude analysis of DAS data allows for the estimation of Taylor bubble size. We conclude that DAS is a promising tool for understanding Taylor bubble properties in a laboratory environment and monitoring destructive flow in facilities across different industries to ensure operations are safe and cost-effective.

Knowns and Unknowns about CAR-T Cell Dysfunction.

Immunotherapy using chimeric antigen receptor (CAR) T cells is a promising option for cancer treatment. However, T cells and CAR-T cells frequently become dysfunctional in cancer, where numerous evasion mechanisms impair antitumor immunity. Cancer frequently exploits intrinsic T cell dysfunction mechanisms that evolved for the purpose of defending against autoimmunity. T cell exhaustion is the most studied type of T cell dysfunction. It is characterized by impaired proliferation and cytokine secretion and is often misdefined solely by the expression of the inhibitory receptors. Another type of dysfunction is T cell senescence, which occurs when T cells permanently arrest their cell cycle and proliferation while retaining cytotoxic capability. The first section of this review provides a broad overview of T cell dysfunctional states, including exhaustion and senescence; the second section is focused on the impact of T cell dysfunction on the CAR-T therapeutic potential. Finally, we discuss the recent efforts to mitigate CAR-T cell exhaustion, with an emphasis on epigenetic and transcriptional modulation.

Mononuclear Copper(I) 3-(2-pyridyl)pyrazole Complexes: The Crucial Role of Phosphine on Photoluminescence.

A series of emissive Cu(I) cationic complexes with 3-(2-pyridyl)-5-phenyl-pyrazole and various phosphines: dppbz (1), Xantphos (2), DPEPhos (3), PPh3 (4), and BINAP (5) were designed and characterized. Complexes obtained exhibit bright yellow-green emission (ca. 520-650 nm) in the solid state with a wide range of QYs (1-78%) and lifetimes (19-119 µs) at 298 K. The photoluminescence efficiency dramatically depends on the phosphine ligand type. The theoretical calculations of buried volumes and excited states explained the emission behavior for 1-5 as well as their lifetimes. The bulky and rigid phosphines promote emission efficiency through the stabilization of singlet and triplet excited states.

Cu6- and Cu8-Cage Sil- and Germsesquioxanes: Synthetic and Structural Features, Oxidative Rearrangements, and Catalytic Activity.

This study reports intriguing features in the self-assembly of cage copper(II) silsesquioxanes in the presence of air. Despite the wide variation of solvates used, a series of prismatic hexanuclear Cu6 cages (1-5) were assembled under mild conditions. In turn, syntheses at higher temperatures are accompanied by side reactions, leading to the oxidation of solvates (methanol, 1-butanol, and tetrahydrofuran). The oxidized solvent derivatives then specifically participate in the formation of copper silsesquioxane cages, allowing the isolation of several unusual Cu8-based (6 and 7) and Cu6-based (8) complexes. When 1,4-dioxane was applied as a reaction medium, deep rearrangements occurred (with a total elimination of silsesquioxane ligands), causing the formation of mononuclear copper(II) compounds bearing oxidized dioxane fragments (9 and 11) or a formate-driven 1D coordination polymer (10). Finally, a "directed" self-assembly of sil- and germsesquioxanes from copper acetate (or formate) resulted in the corresponding acetate (or formate) containing Cu6 cages (12 and 13) that were isolated in high yields. The structures of all of the products 1-13 were established by single-crystal X-ray diffraction, mainly based on the use of synchrotron radiation. Moreover, the catalytic activity of compounds 12 and 13 was evaluated toward the mild homogeneous oxidation of C5-C8 cycloalkanes with hydrogen peroxide to form a mixture of the corresponding cyclic alcohols and ketones.

Adoptive Immunotherapy beyond CAR T-Cells.

Adoptive cell immunotherapy (ACT) is a vibrant field of cancer treatment that began progressive development in the 1980s. One of the most prominent and promising examples is chimeric antigen receptor (CAR) T-cell immunotherapy for the treatment of B-cell hematologic malignancies. Despite success in the treatment of B-cell lymphomas and leukemia, CAR T-cell therapy remains mostly ineffective for solid tumors. This is due to several reasons, such as the heterogeneity of the cellular composition in solid tumors, the need for directed migration and penetration of CAR T-cells against the pressure gradient in the tumor stroma, and the immunosuppressive microenvironment. To substantially improve the clinical efficacy of ACT against solid tumors, researchers might need to look closer into recent developments in the other branches of adoptive immunotherapy, both traditional and innovative. In this review, we describe the variety of adoptive cell therapies beyond CAR T-cell technology, i.e., exploitation of alternative cell sources with a high therapeutic potential against solid tumors (e.g., CAR M-cells) or aiming to be universal allogeneic (e.g., CAR NK-cells, γδ T-cells), tumor-infiltrating lymphocytes (TILs), and transgenic T-cell receptor (TCR) T-cell immunotherapies. In addition, we discuss the strategies for selection and validation of neoantigens to achieve efficiency and safety. We provide an overview of non-conventional TCRs and CARs, and address the problem of mispairing between the cognate and transgenic TCRs. Finally, we summarize existing and emerging approaches for manufacturing of the therapeutic cell products in traditional, semi-automated and fully automated Point-of-Care (PoC) systems.

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection.

COVID-19 is a global pandemic caused by the SARS-CoV-2 coronavirus. T cells play a key role in the adaptive antiviral immune response by killing infected cells and facilitating the selection of virus-specific antibodies. However, neither the dynamics and cross-reactivity of the SARS-CoV-2-specific T-cell response nor the diversity of resulting immune memory is well understood. In this study, we use longitudinal high-throughput T-cell receptor (TCR) sequencing to track changes in the T-cell repertoire following two mild cases of COVID-19. In both donors, we identified CD4+ and CD8+ T-cell clones with transient clonal expansion after infection. We describe characteristic motifs in TCR sequences of COVID-19-reactive clones and show preferential occurrence of these motifs in publicly available large dataset of repertoires from COVID-19 patients. We show that in both donors, the majority of infection-reactive clonotypes acquire memory phenotypes. Certain T-cell clones were detected in the memory fraction at the pre-infection time point, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2.

SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors.

Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID-19 patients and healthy donors sampled both prior to and during the pandemic. Healthy donors examined during the pandemic exhibited increased numbers of SARS-CoV-2-specific T cells, but no humoral response. Their probable exposure to the virus resulted in either asymptomatic infection without antibody secretion or activation of preexisting immunity. In convalescent patients, we observed a public and diverse T cell response to SARS-CoV-2 epitopes, revealing T cell receptor (TCR) motifs with germline-encoded features. Bulk CD4+ and CD8+ T cell responses to the spike protein were mediated by groups of homologous TCRs, some of them shared across multiple donors. Overall, our results demonstrate that the T cell response to SARS-CoV-2, including the identified set of TCRs, can serve as a useful biomarker for surveying antiviral immunity.

Advancing CAR T-Cell Therapy for Solid Tumors: Lessons Learned from Lymphoma Treatment.

Chimeric antigen receptor (CAR) immunotherapy is one of the most promising modern approaches for the treatment of cancer. To date only two CAR T-cell products, Kymriah® and Yescarta®, have been approved by the Food and Drug Administration (FDA) for the treatment of lymphoblastic leukemia and B-cell lymphoma. Administration of CAR T-cells to control solid tumors has long been envisaged as one of the most difficult therapeutic tasks. The first two clinical trials conducted in sarcoma and neuroblastoma patients showed clinical benefits of CAR T-cells, yet multiple obstacles still hold us back from having accessible and efficient therapy. Why did such an effective treatment for relapsed and refractory hematological malignancies demonstrate only relatively modest efficiency in the context of solid tumors? Is it due to the lucky selection of the "magic" CD19 antigen, which might be one of a kind? Or do lymphomas lack the immunosuppressive features of solid tumors? Here we review the existing knowledge in the field of CAR T-cell therapy and address the heterogeneity of solid tumors and their diverse strategies of immunoevasion. We also provide an insight into prospective developments of CAR T-cell technologies against solid tumors.

Synthesis, structures and luminescence of multinuclear silver(i) pyrazolate adducts with 1,10-phenanthroline derivatives.

A set of silver(i) 3,5-bis(trifluoromethyl) pyrazolate adducts with 1,10-phenanthroline (L2), 2,9-dimethyl-1,10-phenanthroline (neocuproine, L3) and 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (bathocuproine, L4) was synthesized starting from trimeric silver pyrazolate Ag3Pz3. Reactions with sterically hindered L3 and L4 cause the destruction of the original trimeric core, yielding a dinuclear Ag2Pz2 cycle with an unprecedented chair configuration for L3, while bathocuproine L4 leads to the drastic rearrangement of the silver pyrazolate core into cationic Ag(L4)2 and anionic Ag5Pz6 subunits. All complexes obtained exhibit phosphorescence in the solid state. Time-dependent density functional theory calculations demonstrate their different possible emission processes, explaining their emission behavior as well as their lifetimes.

Interaction of a trinuclear copper(i) pyrazolate with alkynes and carbon-carbon triple bond activation.

The trinuclear copper(i) pyrazolate {[3,5-(CF3)2Pz]Cu}3 forms η2-copper/alkyne triple bond coordinated structures in the presence of acetylenes. There is no coordination of copper atoms to the phenyl ring of phenylacetylene and copper(i) acetylide formation during the interaction. It was observed that the complexes formed are the active catalytic species in click reactions.

The biological basis and clinical symptoms of CAR-T therapy-associated toxicites.

Currently, immunotherapy is attracting a lot of attention and may potentially become a leading approach in the treatment of cancer. One emerging therapeutic, the chimeric-antigen receptor T-cell adoptive immunotherapy (CAR-T) is showing remarkable efficacy in the treatment of several B-cell malignancies. The popularity of CAR-T has been founded on two CAR T-cell products recently approved by FDA (during 2017) in the treatment of relapsed/refractory B-cell acute lymphoblastic leukemia and B-cell lymphoma. However, their toxicities observed in clinical trials were extremely significant and in some cases even fatal with no approved algorithms for toxicity prediction being available to date. A deeper understanding of the biological basis of such complications is the key to prompt and comprehensive clinical management. Here we review the wide spectrum of effects associated with CAR T cell therapy with a major focus on the pathogenesis of cytokine release syndrome and neurotoxicity as the most common, potentially life-threatening effects of this treatment. We discuss the basis of clinical management and the existing models that predict the severity of toxicity, as well as the key factors that modulate this event. Finally, we will summarize the literature detailing universal allogenic CAR T-cells and their toxicity profile.

The Role of Weak Interactions in Strong Intermolecular M···Cl Complexes of Coinage Metal Pyrazolates: Spectroscopic and DFT Study.

The nondestructive reversible complexation of the macrocyclic group 11 metal pyrazolates {[3,5-(CF3)2Pz]M}3 (M = Cu(I), Ag(I)) to the halogen atom X = Cl, Br of η(3)-allyliron tricarbonyl halides (η(3)-2-R-C3H4)Fe(CO)3X is revealed by the variable-temperature spectroscopic (IR, NMR) study combined with density functional theory calculations. The composition of all complexes at room temperature is determined as 1:1. In the case of the [AgL]3 macrocycle, complexes 1:2 are observed at low temperature (<260 K). The complex's stability depends on the substituents in the allyl fragment and halide ligand as well as on the metal atom (Ag(I), Cu(I)) in the macrocycle. For bulky substituents (Me and Ph) the endo/exo equilibrium of the parent (η(3)-2-R-C3H4)Fe(CO)3X shifts upon the complex formation in favor of the exo isomer due to additional noncovalent interactions of the substituent with macrocycle.

Remarkable Structural and Electronic Features of the Complex Formed by Trimeric Copper Pyrazolate with Pentaphosphaferrocene.

According to spectroscopic (NMR, IR, UV/Vis) study, the interaction of pentaphosphaferrocene [Cp*Fe(η(5) -P5 )] with trimeric copper pyrazolate [(Cu{3,5-(CF3 )2 Pz})3 ] yields a new compound that is astonishingly stable in solution. Single-crystal X-ray analysis reveals unprecedented structural changes in the interacting molecules and the unique type of coordination [Cp*Fe(µ3 -η(5) :η(2) ,η(2) -P5 ){Cu(3,5-(CF3 )2 Pz)}3 ]. As a result of the 90° macrocycle folding, the copper atoms are able to behave both as a Lewis acid and as a Lewis base in the interaction with the cyclo-P5 ligand.