bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profound phenotype alteration and delayed regeneration of circulating antigen presenting cells in COVID-19
Authors: Winheim Elena , Rinke Linus , Lutz Konstantin , Reischer Anna , Münchhoff Maximilian , Hellmuth Johannes , Scherer Clemens , Subklewe Marion , Krug Anne B 
Published: February 2023

Abstract
Disease manifestations in COVID-19 range from mild symptoms to severe/critical illness with lung inflammation, hypercoagulation and cardiovascular complications, which may be caused by a dysregulated innate immune response. Antigen presenting cells may contribute to the inflammatory response and shape the adaptive immune response in COVID-19 patients. We therefore investigated the frequency and phenotype of circulating dendritic cells (DCs) and monocytes in hospitalized COVID-19 patients with mild/moderate or severe disease at different time points (n=65). We found an overall reduction of DCs and a shift towards the CD14+ DC3 population within the DCs in patients vs. controls.
In patients with more severe disease, we observed upregulation of CXCR3, CCR2, CD40 and PD-L1, but reduced expression of CD86 and HLADR in monocytes and conventional DCs (cDCs) within the first 3 weeks after diagnosis (n=26). Increased proliferation and expansion of precursor cells in the blood indicated an enhanced turnover that was observed even in convalescent patients. Proliferating cDC2 and DC3 showed a phenotype similar to that found in healthy controls suggesting that the phenotype alterations are induced in differentiated DCs by external factors. The observed changes were accompanied by increased inflammatory cytokine levels in the plasma and lymphopenia.
Thus, in more severe COVID-19 circulating cDCs and monocytes exhibited a profoundly altered expression of costimulatory molecules and were poised to exit the blood in response to inflammatory chemokines. Increased proliferation even after recovery indicated delayed regeneration of the mononuclear phagocyte system.
In Silico Assessment of SARS-CoV-2 Mutations with Relevancy to Prophylactic and Monoclonal-Based Treatment Strategies
Authors: Benoit Lora , Mikbel Deena , Vilela Mario , Alsalihi Yusur , Shakran Dina , Merino Edward , Mohseni Ali 
Published: February 2023

Abstract
The ongoing pandemic caused by SARS-CoV-2 has inflicted significant disease burden worldwide. Several vaccines are now in use that are based on the virus’s highly immunogenic spike “S” protein, which mediates infection of host cells. However, since the emergence of the reference strain in 2019, the virus has underdone &gt;40,000 nucleotide mutations, many of which have resulted in deletions or amino acid substitutions in the S protein. Most mutations appear to be random, while others deviate from expected outcomes. Indeed, some non-random mutations appear to confer resistance to either innate or adaptive immune functions while other enhance transmissibility. Although the consequences of these mutations are largely unknown, there is concern for the ability of select mutations to detract from the protection conferred by prophylaxis strategies and interventional therapies. We have therefore selected &gt;50 whole genome-length mutant strain from 3 relatively closed populations to compare against widely circulating strains of concern and the reference strain so that we could assess differences in mutation events within the context of distinct population immunogenetics. For each strain we have biochemically characterized potentially critical mutations, assessed the randomness of each mutation, and assessed key mutations occurring in the S, M, E and N proteins for their ability to influence innate or adaptive immune recognition using bioinformatic platforms. The results of this study further our understanding for how these mutations influence population-based immunity to the virus, including biomedical interventions, as well as help explain the selection pressures and external events that are driving this genetic diversification.
T-B lymphocyte interactions mediated by SLAM-associated protein (SAP) are essential for diabetes in transgenic anti-insulin VH125SD.NOD mice
Authors: McNitt Dudley H , Bonami Rachel H , Hulbert Chrys , Thomas James W 
Published: February 2023

Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by T cell-mediated destruction of insulin-producing beta cells. An essential role for B lymphocytes in the disease process and molecular signatures for T follicular helper cells (Tfhs) in T1D point to the importance of T-B lymphocyte interactions in the pathological process. To understand mechanisms that underpin these T-B interactions, we introduced deficiency of the signaling lymphocyte activation molecular (SLAM)-associated protein (SAP) into VH125SD.NOD mice. In VH125SD.NOD mice a targeted anti-insulin VH gene generates a small population of anti-insulin B lymphocytes that are highly diabetogenic yet are functionally silent for autoantibody production. We find that SAPko dramatically eliminates germinal centers in spleen, pancreatic draining lymph nodes and pancreas. However, insulitis was similar between SAP-sufficient and SAPko VH125SD.NOD mice early in T1D development (8–12 weeks old) but differed later in disease onset (13–17 weeks old). Strikingly, SAP is essential for T1D development, as SAPko VH125SD.NOD mice did not develop T1D. Despite elimination of germinal centers, the numbers of Tfh cells were largely unaffected in the absence of SAP. These findings suggest that prolonged T-B lymphocyte conjugates maintained by SAP are not required for retaining Tfhs; however, these interactions maybe essential for the genesis of pathogenic Tfhs when functionally silent B lymphocytes recognize a beta cell autoantigen.
CD8αα expression increases during demyelinating disease progression
Authors: Thyagarajan Hiran Maye , Cornwall Douglas H. , Evavold Brian D. 
Published: February 2023

Abstract
Experimental autoimmune encephalomyelitis (EAE) is a well-described mouse model for multiple sclerosis (MS), a demyelinating autoimmune disorder of the central nervous system (CNS). While the role of CD4 T cells is well established, other immune cell types, particularly CD8 T cells, are key contributors to disease pathogenesis. Our study aims to categorize the functional contributions of CD8 T cell subsets to EAE kinetics and disease outcomes. The use of myelin oligodendrocyte glycoprotein (MOG) 35–55 peptide alongside an adjuvant to inoculate mice, provides a reproducible disease model. Demyelinating disease severity was analyzed at defined timepoints including, onset (d10–14), peak (d17–21), early chronic (d28–35) and late chronic (d80–120) stages. The total number of CD3+ T cells in the CNS remained consistent during EAE. However, it goes from a CD4 T cell dominated response at peak EAE to an equalized 1:1 ratio of CD4 and CD8 T cells at late chronic stage. Furthermore, differentiation of CD8 T cell subsets based on CD8α and CD8β protein expression revealed that CD8αα T cells numbers increase to comprise ~40% of the CD8+ population at late chronic EAE. In addition, CD8βLO cells become a prominent subset during late chronic stage, with a concomitant decrease in CD8αβHI T cells. Moreover, CD8αα T cells are activated and exhibit a central memory phenotype along with downregulation of exhaustion markers by FACS analysis, and yet have significantly reduced cytokine expression. These results are consistent with single cell RNA sequencing data obtained at the peak and late chronic time points. Thus, CD8αα T cells constitute a phenotypically distinct class of CD8 T cell subsets, with a blunted effector role in demyelinating disease outcome.
Inhibition of cholesterol pathway intermediates attenuates IL-33 mediated mast cell cytokine production
Authors: Jackson Kaitlyn G. , Dailey Jordan , Kankaria Roma , Sebti Said , Ryan John J 
Published: February 2023

Abstract
Asthma is a growing problem in developed countries, affecting over 24 million individuals in the US alone. Allergic asthma is denoted by a Th2 response that supports IgE-mediated mast cell function and is enhanced by the cytokine IL-33. Although corticosteroids and other treatments are available to help control asthma, many patients have persistent symptoms. In order to meet this unmet need, we investigated the utility of repurposing statin drugs. Statins decrease serum cholesterol by inhibiting HMG-CoA reductase. These drugs have anti-inflammatory effects largely ascribed to loss of isoprenyl lipids downstream of HMGCR. We previously found that statins could decrease IgE-mediated mast cell function. Our current data demonstrate that HMGCR inhibition by simvastatin or isoprenylation blockade with the novel compound FGT-2734 attenuates IL-33 induced mast cell cytokine production in vitro. Statin efficacy for the treatment of allergic asthma has been inconsistent in clinical trials. However, our data suggest that inhibiting isoprenylated signaling molecules may provide a feasible therapeutic target in mast cell-driven disease, and supports the use of statins as a potential adjunct or alternative treatment for individuals with asthma.
Activation of human skin mast cells by vancomycin via MrgX2: Comparison to the effects of brimonidine
Authors: Fukuoka Yoshihiro , Schwartz Daniel L , Ward Brant R 
Published: February 2023

Abstract
Vancomycin (VCM) is a glycopeptide antibiotic that inhibits bacterial peptidoglycan biosynthesis and is used for the treatment of certain Gram-positive bacterial infections of the eyes. However, the use of VCM is associated with several potential adverse reactions. We examined the mechanism of activation of human mast cells by vancomycin (VCM) and compared to brimonidine, an alpha2-adrenergic receptor agonist used to treat in glaucoma. VCM induced degranulation and cytokine secretion by SMCs, which were suppressed by pertussis toxin (PTX) (similar to MrgX2 ligands). Brimonidine induced less degranulation than VCM that was partially inhibited by PTX. MrgX2 expression on the surface of SMCs was detected by FACS analysis. VCM enhanced FceRI-mediated degranulation and cytokine secretion in a dose-dependent manner, whereas brimonidine failed to induce cytokine production and suppressed FceRI-mediated cytokine secretion. VCM induced maximal ERK-phosphorylation by 5 min similar to compound 48/80, an MrgX2 ligand and inhibited by PTX. VCM- but not brimonidine-induced degranulation of MCs was significantly inhibited by QWF, an MrgX2 antagonist. This study indicates that VCM but not brimonidine activates human SMCs via MrgX2 and that MCs become more responsive to VCM when co-stimulated by aggregating FceRI, which may occur when sensitive patients exposed to aeroallergen and VCM.
A history of microbial exposures has a temporally limited inhibitory effect on mouse lung ILC2 responses to a fungal allergen
Authors: Block Katharine E , Iijima Koji , Pierson Mark , Walsh Daniel A , Kita Hirohito , Jameson Stephen C 
Published: February 2023

Abstract
The ability of some microbes and their products to restrain the immune response to allergens has been extensively studied and is a key element of the hygiene hypothesis. However, it is unclear whether a modulated immune response relates to recent microbial exposure, or whether a diverse infectious history promotes sustained changes in reactivity to allergens. Thus, we explored how prior microbial experience in “dirty” mice affected innate immune responses to an airway fungal allergen. Dirty mice were generated by cohousing laboratory mice with pet store mice for at least 60 days to allow for physiological transmission of microbes. Despite changes induced in many immune cell populations, lung type 2 innate lymphoid cell (ILC2) numbers and phenotype were unaltered by cohousing. Short term (4.5 hour) production of the type 2 cytokines IL-5 and IL-13 in response to Alternaria alternata extract was consistently depressed in dirty mice relative to specific pathogen free (SPF) and germ-free animals. This correlated with diminished release of IL-33, an alarmin that activates ILC2, in dirty mice. Nevertheless, at a later timepoint (24 hours) or after repeated Alternaria exposure, the influx of eosinophils, neutrophils and T cells into the lungs was similar in dirty and SPF mice. Our data therefore indicate that a history of robust and diverse microbial exposure delays but ultimately does not restrain development of a type 2 response to airway allergens, in contrast to the established inhibitory effects of acute exposure to certain microbes and their products.
Engineering T cells with improved TCR-CD3 interaction for optimal tumor killing
Authors: Yogambigai Velmurugu , Natarajan Aswin , Ge Chenghao , Yuan Zhou , Li Kaitao , Kim Joseph , Shin Hye Won , Rookwood Richard , Beesam Saikiran , Nyovanie Samantha T. , Patskovsky Yury , Zhu Cheng , Krogsgaard Michelle 
Published: February 2023

Abstract
T cell activation requires extracellular stimulatory signals mainly mediated by T cell receptor complex (TCR/CD3). Obtaining detailed mechanistic knowledge of the TCR-mediated signaling pathway holds significant importance in understanding immune diseases, formulating new immunotherapies, and overcoming immunosuppression in current therapies. Here, we used a novel strategy to overcome ineffective anti-tumor responses by modifying the TCR interaction with CD3 subunits without affecting the binding affinity and/or specificity of the TCR-antigen interaction. Based on NMR and mutational studies, we introduced specific alanine mutations in the Cβ helix 3 and Cβ helix 4 – F strand of the TCR extracellular domain. We demonstrated varied functionality in terms of IL-2 production as well as altered bond lifetime measured by biomembrane force probe assay (BFP). Selected mutations retained or displayed enhanced CD3 binding ability in a CD3 tetramer assay. Based on these results we generated retroviral TCR libraries by random mutagenesis at specific extracellular TCR-CD3 interaction sites, expressed them in a T cell hybridoma system and selected TCRs with novel binding specificity using soluble CD3γɛ- and CD3δɛ-tetramers. We are currently determining the correlation between CD3 tetramer binding, bond lifetime, and functionality (kinase activity, IL-2 production, and tumor rejection) of selected TCR mutants. By integrating binding data, T cell signaling data, and functional outcomes, we expect to be able to manipulate the human immune system via the extracellular TCR-CD3 interaction site to be utilized in novel human T cell therapies.
Precise control of immune modulation using DNA scaffold-mediated biomaterial functionalization
Authors: Huang Xiao , Tang Qizhi , Lim Wendell A. , Desai Tejal A. 
Published: February 2023

Abstract
Synthetic materials displaying multi-modal ligands with exact chemiophysical properties for immune modulation are valuable research tools and a promising therapeutic platform. However, precise chemical conjugation of multiple proteins on biomaterial surfaces is challenging. Through DNA hybridization-mediated biomolecule loading, we achieved high density and precise ratiometric control of multiple ligands on nano-/micro-particles. We found increasing ratios of anti-CD3 to anti-CD28, 1:5, 1:3, 1:1, 3:1 to 5:1, on microparticles yielded a linear increase of ex vivo expansion of primary human CD4+ and CD8+ T cells until reaching a plateau at 3:1 ratio. For CD8+ T cells, the ratio of 3:1 resulted in the highest percentage of central memory cells, 51.4 ± 7.2% vs. 14.4 ± 7.6% for 1:5 ratio (n = 5 donors). Particle surface presentation of IL-2 using an anti-IL-2 antibody (in trans to CD3/28 particles) yielded ~3 fold more ex vivo expansion of CD4+ and CD8+ T cells in 14 days when compared to the equivalent dose of soluble IL-2. Using intratumoral injection of microparticles presenting a ligand for a synthetic Notch receptor, we locally induced chimeric antigen receptor (CAR) expression on systemically infused engineered T cells and observed CAR T cell killing of the injected tumors, while sparing the uninjected identical tumors in the contralateral flank. These results highlight the potential of this platform in achieving better control of therapeutic cell manufacture and local tuning of immunotherapies. Ongoing work is using DNA origami-mediated patterning to dissect spatial requirements of various T cell activating ligands to better understand critical parameters of T cell activation with the goal to improve the design of immunotherapies.
Single-cell analyses characterize circulating anti-tumor CD8+ T cells in mice and humans and identify markers for their enrichment
Authors: Pauken Kristen E , Shahid Osmaan , Lagattuta Kaitlyn A , Mahuron Kelly M , Luber Jacob M , Lowe Margaret M , Huang Linglin , Delaney Conor , Long Jaclyn , Fung Megan E , Newcomer Kathleen , Tsai Katy K , Chow Melissa , Guinn Samantha , Kuchroo Juhi R , Burke Kelly P , Schenkel Jason M , Rosenblum Michael D , Daud Adil I , Sharpe Arlene H , Singer Meromit 
Published: February 2023

Abstract
The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential, but is currently challenging due to the limited number of reagents to track antigen-specific T cells. Here, we used paired single-cell RNA sequencing and T cell receptor (TCR) sequencing to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of mice with MC38 tumors or melanoma patients using the TCR as a molecular barcode. TM cells showed increased activation compared to non-matching T cells in blood, and appeared less exhausted than matching counterparts in tumor. Importantly, PD-1, which has been used to identify putative circulating anti-tumor CD8+ T cells, showed poor sensitivity for identifying TM cells in both mice and humans. By leveraging the transcriptome, we identified candidate cell surface marker panels for TM cells in mice and melanoma patients, and validated CX3CR1, NKG2D, and CD39 proteins in mice. Combinations of markers performed better than single markers in identifying TM cells from non-TM cells in the blood, providing a platform to potentially track TM cells based on surface markers instead of the TCR. These data demonstrate that the TCR can be used to identify tumor-relevant populations for comprehensive characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.
Impact of neutrophil extracellular traps (NETs) in primary graft dysfunction following human lung transplantation
Authors: Bonneau Steven , Landry Caroline , Bégin Stéphanie , Adam Damien , Clavet-Lanthier Marie-Élaine , Dasilva Ariane , Charles Elcha , Dumont Benjamin , Menaouar Ahmed , Neagoe Paul-Eduard , Brochiero Emmanuelle , Stevens Louis-Mathieu , Nasir Basil , Ferraro Pasquale , Noiseux Nicolas , Sirois Martin 
Published: February 2023

Abstract

Background:
Primary graft dysfunction (PGD), the major complication associated with lung transplantation in the peri-operative period, is characterized by vascular and alveolar inflammation and results in hypoxemia and lung edema. Up to 30% of recipients develop the most severe form of PGD (Grade 3; PGD3), leading to 50% mortality. Animal studies suggest that neutrophils can contribute to the inflammatory process through the release of neutrophil extracellular traps(NETs). NETs are composed of DNA filaments decorated with granular proteins, which can contribute to vascular occlusion associated with PGD. Our main objective is to correlate NETosis with recipient outcomes.

Methods:
Clinical data and blood samples were prospectively collected from donors and recipients (n=32) pre-, intra- and post-operatively (up to 72hrs). Inflammatory markers inducing NETs’ synthesis (CRP, IL6, IL8) and markers of NETs (myeloperoxidase [MPO], MPO-DNA complexes, cell-free DNA) were quantified by ELISA. When available, histology and immunochemistry techniques were used on donor lung samples collected before transplantation to evaluate the presence of activated neutrophils and NETs.

Results:
In lung samples from which PGD3 developed in recipients, there was a marked increase of vascular occlusion composed of activated neutrophils and NETs before transplantation. Also, in donors and recipients pre- and intra-operatively, circulating levels of inflammatory (CRP, IL6, IL8) and NETosis biomarkers (MPO-DNA, MPO, cfDNA) were up to 4-fold higher in PGD3 recipients compared to non-PGD3.

Conclusion:
Elevation of these NETosis biomarkers might serve to elaborate an algorithm to better delineate the recipients at risk of developing severe PGD.
SARS-CoV-2 vaccines induce potent immune responses in infant rhesus macaques
Authors: Curtis Alan D , Garrido Carolina , Dennis Maria , Gao Hongmei , Montefiori David , Van Rompay Koen KA , Tomai Mark A , Fox Christopher , Edwards Darin , Carfi Andrea , Corbett Kizzmekia , Graham Barney S , Permar Sallie , De Paris Kristina 
Published: February 2023

Abstract
SARS-CoV-2 has caused &gt; 100 million infections, &gt; 2 million deaths and disproportionally affects older and comorbid patients. Given authorized adult vaccines against SARS-CoV-2 together with the success of childhood vaccine programs for infectious diseases such as polio, early life vaccination has the potential to decrease transmissibility and mitigate ongoing public health and socioeconomic impacts of SARS-CoV-2.
Two groups of 8 infant monkeys were immunized at week (W) 0 & W4 with 15 μg prefusion SARS-CoV-2 S-2P spike protein (S) formulated with 3M-052 adjuvant, a TLR7/8 agonist, as a stable emulsion (Protein) or 30 μg mRNA encoding S in lipid nanoparticles (mRNA-LNP). Dosage decisions were made in the context of infant immunogenicity and safety. Both regimens were well tolerated.
Protein group IgG binding for RBD, NTD, S1 & S2 peaked at W6. ACE2 to RBD blocking (1:10 dilution) was 100% and D614G pseudovirus neutralizing antibody geometric mean titer (GMT) was 9,792 at W6. These responses were stable through W14. S-specific memory B cells were detected by W4. Vaccine-elicited S-specific T cell responses were dominated by IL-17 or IFNγ at W14. CD8 responses were variable.
mRNA-LNP-induced RBD, NTD, S1 & S2 binding responses peaked at W6. Plasma (1:10 dilution) blocked 100% of ACE2-RBD interactions and D614G neutralizing antibody GMT was &gt; 103 at W6. Blocking and neutralization responses persisted through W14. S-specific memory B cells were detected at W4. By W14, 100% of mRNA-LNP monkeys had S-specific CD4 T cells that expressed IL-2, IL-17, IFNγ or TNFα. CD8 responses were highly varied. This study is a proof-of concept for SARS-CoV-2 vaccine-induced immune responses in a pediatric setting and provides evidence that immunity may persist.