bluuebunny/crossref_metadata_2025_split huggingface dataset:
mRNA delivery of epitope-specific monoclonal antibodies for treatment of viral infection
Authors: Hazell Nicholas , Hu Haitao , Bonam Srinivasa Reddy , Hajnik Renee , Nguyen Tina 
Published: November 2024

Abstract
The mRNA-lipid nanoparticle (mRNA-LNP) platform is versatile for development of vaccines and therapeutics, specifically for monoclonal antibody (mAb) treatment of viral disease. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 760 million worldwide and contributes to nearly 7 million associated fatalities. As vaccines protect those immune-competent, the elderly and immune-compromised share increased risk for development of severe lung disease. In addition, virus evolution leads to novel variants that pose an enhanced threat to the aforementioned subpopulations, highlighting a need for therapeutics that can rapidly be developed to prevent severe disease in these high-risk populations. mAbs that neutralize are effective for treating SARS-CoV-2 infections with a number of mAbs targeting SARS-CoV-2 identified. We generated mRNAs expressing two different mAbs, LY-CoV1404 (mRNA-1404) and 76E1 (mRNA-76E1), that target different SARS-CoV-2 epitopes and formulated them in LNPs. In vitro analysis support both mRNAs can produce and secrete mAbs with epitope specificity in cells following transfection and in vivo studies exhibit durable antibody expression. Following single mRNA-LNP administration (5ug and 15ug dose via intramuscular or subcutaneous route), serum antibodies remained detectable 5 weeks out. Our data indicate that mRNA is a promising platform for the delivery of therapeutic mAbs to treat human disease such as viral infections.
A combination of TLR9 and STING agonists favors antigen cross-presentation and promotes Th1 immune response against influenza virus
Authors: Thomas Sanya , Pak Jensen , Doss-Gollin Simon , Ryff Kevin , Beijnen Elizabeth , Pedersen Gabriel , Christensen Dennis , Levy Ofer , van Haren Simon 
Published: November 2024

Abstract
Adjuvants can boost the type, magnitude, breadth, and durability of vaccine responses. We have previously demonstrated that combining adjuvants through rational design can overcome age-specific impairments in inducing Th1 immunity, trigger antigen cross-presentation, and enable CD8-driven protective immunity of protein-based vaccine formulations. Here, we screened 78 adjuvant combinations to explore their molecular mechanism of action through human in vitro modeling and identified combinations that synergistically promote the expansion of antigen-specific CD4+ cells, induce cross-presentation on MHC class I resulting in activation of antigen-specific CD8+ cells, and redirect the type of immune response to favor the production of Th1-promoting cytokines. The combination of CpG (TLR9 agonist) and 2,3-cGAMP (STING agonist) promoted influenza-specific CD4+ and CD8+ T cell activation and selectively favored the secretion of Th1-polarizing cytokines TNF and IL-12p70. Activation of T-bet-expressing Th1 cells was also observed with this adjuvant combination. We also demonstrate the phenotypic reprogramming towards conventional type 1 dendritic cells by CpG + 2,3-cGAMP, and the ability of this adjuvant combination to induce similar immune responses in immune cells from newborns and older adults. Identification of the adjuvant combination CpG + 2,3-cGAMP may prove key to the future development of vaccines against intracellular pathogens such as respiratory viruses.
Cytosolic nucleic acid sensors stimulate protective bone cell responses to Staphylococcus aureus
Authors: Johnson Morgan , Sipprell Sophie , Suptela Samantha , Mills Erin , Marriott Ian 
Published: November 2024

Abstract
Staphylococcus aureus is the causative agent of osteomyelitis, an inflammatory infection of the bone. Despite available treatments, S. aureus invasion of resident bone cells limits antibiotic effectiveness and provides a protective niche for viable bacteria contributing to recurrent and persistent infections. Previously, we have demonstrated a significant increase in proinflammatory cytokines, chemokines, and osteoclastogenic factors in an in vivo model of localized Staphylococcal osteomyelitis. Interestingly, we also observed a significant production of type I IFNs in infected femurs compared to the contralateral control. It is now appreciated that resident bone cells express a variety of pattern recognition receptors for identification of pathogens and stimulation of immune responses. Here, we demonstrate that S. aureus infected osteoblasts produce significant increases in both mRNA encoding type I IFNs and protein. Our data demonstrates that cytosolic nucleic acids sensors, including the RNA sensor RIG-I and the DNA sensor cGAS, are upregulated by osteoblasts and initiate osteoblast responses to S. aureus challenge. Notably, S. aureus viability is necessary for stimulation of osteoblast production of type I IFNs. Furthermore, our data indicate that IFN-β serves to restrict intracellular S. aureus burden. Our ongoing studies seek to investigate the therapeutic potential of augmenting these protective bone cell responses in a murine model of Staphylococcal osteomyelitis.
Recall of cross-reactive memory B cells enhances antibody durability and breadth against SARS-CoV-2 variants
Authors: Chen Yuezhou , Wang Youyi , Hu Yuanhao , Gong Nuo , Li Yunfeng , Huang Jiayi , He Jiaxin , Huang Shun 
Published: November 2024

Abstract
Long-lasting antibody production with broad recognition breadth is crucial to combat with many pathogens. After infection or vaccination, B cell memory is preserved via two key elements: memory B cells, which can be efficiently recalled during subsequent encounters, and long-lived plasma cells, which continue to produce antibodies over the long term. It's critical to understand antibody durability and how memory can identify different viral variants following iterative exposures. We examined the recognition of SARS-CoV-2 variants, the dynamics of memory B cells, and the secretion of antibodies over time after recurrent infections and vaccinations. Within unvaccinated individuals who recovered from COVID, enhanced antibody stability over time was observed within a subgroup of individuals who recovered more quickly from COVID, had greater percentage of spike specific memory circulating T follicular helper (cTfh), and harbored significantly more memory B cells cross-reactive to endemic coronaviruses early after infection. These cross-reactive clones map to the conserved S2 region of SARS-CoV-2 spike with higher somatic hypermutation levels and affinity. Following SARS-CoV-2 inactivated vaccination, frequency of cross-reactive memory B cells after BF.7 infection links to antibody longevity and neutralization breadth to SARS-CoV-2 variants. We conclude that memory B cell recall shapes functional cross-variant antibody repertoire composition and longevity.
The inhibitory role of nitric oxide in encephalomyocarditis viral replication in pancreatic β-cells.
Authors: Gehant Alyssa , Stafford Joshua , Corbett John 
Published: November 2024

Abstract
During type 1 diabetes (T1D) onset, insulin-secreting β-cells are selectively destroyed by T-cells. In addition to known genetic factors, viral infection (specifically by members of the picornavirus family) is an environmental factor that has been implicated in T1D onset. Viral infection stimulates macrophage release of IL-1, and in islets, stimulates the production of micromolar levels of nitric oxide (NO) by β-cells. NO impairs β-cell function via inhibition of mitochondrial oxidative metabolism, resulting in depletion of ATP. Since β-cells have a limited capacity for self-renewal, and are essential for organismal survival, we hypothesize that the cytokine-mediated production of NO by β-cells functions in a protective manner during a viral infection. In support of this hypothesis, we’ve shown that NO inhibits encephalomyocarditis viral (EMCV) replication and mediated lysis in a β-cell selective manner. EMCV is an inflammatory, mouse-tropic virus that induces diabetes in several mouse models. In this study, we have identified inositol hexakisphosphate kinase-1 (IP6K1, KmATP=1 mM) as an indirect target of NO (via the loss of ATP) that is responsible for the inhibition of EMCV replication in β-cells. We show that inhibition of IP6K1 attenuates EMCV replication and mediated β-cell lysis in a manner comparable to the actions of NO. Current studies are focused on the mechanism by which inhibition of IP6K activity attenuates EMCV replication and EMCV-mediated lysis in β-cells.
The CD40/CD40L dyad, an immune checkpoint regulator, plays a protective role against Mouse hepatitis virus-induced neuroinflammatory demyelination
Authors: Das Sarma Jayasri , Hazra Bishal 
Published: November 2024

Abstract
Murine ꞵ-coronavirus, RSA59, infection results in meningoencephalitis, demyelination, and axonal loss. CD40-CD40L dyad serves as an important immune checkpoint regulator during this disease pathobiology. C57BL/6 WT, CD4-/-, CD40L-/- and CD40-/- mice were intracranially inoculated with RSA59 to study the acute phase neuroinflammation and chronic phase demyelination. Studies suggested that CD4+ T cells play a protective role against RSA59-induced demyelination because, in the absence of CD4 gene, mice were more susceptible to acute poliomyelitis and chronic demyelination with axonal bulbar vacuolation. CD40L expressed by CD4+ T cells is crucial for host immunity against RSA59. Without CD40L in activated CD4+ T cells, RSA59-infected mice experience increased disease severity, dampened microglia/macrophage activation, reduced T cell infiltration in the CNS, and impaired T cell priming in the cervical lymph node. In the chronic phase, extensive CNS virus replication leads to severe demyelination and axonopathy due to altered microglia/macrophage populations caused by the absence of the CD40L gene. CD40-deficiency revealed increased acute phase encephalitis in the RSA59-infected groups due to increased infiltrating neutrophils, leading to heightened bystander neuroinflammation. Hence, it is evident that the RSA59-induced demyelination model elucidates an extensively robust innate immune system upon which adaptive immunity is built during the chronic stage of infection.
NLRP3 Cys126 palmitoylation by ZDHHC7 Promotes Inflammasome Activation
Authors: Yu Tao 
Published: November 2024

Abstract
Macrophages could response to pathogen and damage-associated molecular patterns through NLRP3-mediated inflammasome. Hyperactivation of NLRP3 is associated with human chronic inflammatory diseases. Therefore, accurate regulation of NLRP3 activation is important. Recent works show that NLRP3 is localized on trans-Golgi network (TGN), which is crucial for NLRP3 activation and consequently ASC recruitment. However, what regulates NLRP3 TGN localization is unknown. Here, we demonstrated that NLRP3 is palmitoylated on Cys126 by palmitoyl-acyltransferase ZDHHC7 in macrophages, which promotes resting NLRP3 localization to TGN and activated NLRP3 localization on dispersed TGN. As a result, ZDHHC7-mediated NLRP3 Cys126 palmitoylation is critical for recruitment and oligomerization of ASC after NLRP3 activation. Perturbating NLRP3 palmitoylation by ZDHHC7 knockout, pharmaceutically inhibition, or modification site mutation, will diminish NLRP3 activation and consequential Caspase-1/GSDMD cleavage, and cytokines secretion in macrophages. Furthermore, NLRP3 palmitoylation on Cys126 is vital for inflammasome activation in vivo, including endotoxic shock and peritonitis mouse models. Notably, this palmitoylation-regulated NLRP3 activation also contributes to multiple sclerosis development in mice. Therefore, our study provides new insight into NLRP3 regulation and suggests targeting ZDHHC7 or NLRP3 Cys126 could be a potential therapeutic strategy to treat human NLRP3-related disorders.
The transcription factor Runx3 promotes diversity in effector cell precursors that pattern the memory CD8 T cell compartment
Authors: Albao Dominic , Diao Huitian , Pipkin Matthew 
Published: November 2024

Abstract
Central memory (TCM) CD8 T cells maintain the regenerative capacity of long-term adaptive immunity to intracellular pathogens, but recent studies indicate that TCM cells are heterogeneous. Previous analyses of the transcription factor Runx3 has shown it has pleiotropic effects on memory CD8 T cell development, including potential diversity among TCM cells: Runx3-deficient cells preferentially form Tcf7hi CD62Lhi TCM-like cells but accumulate inefficiently, whereas enforced Runx3 expression promotes increased numbers of CD62Lhi TCM – like cells and more efficiently form memory precursors upon secondary infection. Using single cell RNA sequencing during acute LCMV infection we identified two distinct effector cell states enriched with TCM gene expression that differentially correlated with Runx3-dependent transcription (Runx3 signature). One state exhibited a stem-like signature and a low Runx3 signature score, whereas the other was less stem-like and exhibited a higher Runx3 signature. Retroviral expression indicated that wildtype Runx3 promoted formation of CX3CR1int peripheral memory-like and TCM-like cells, and repressed effector memory (TEM) cell formation, whereas expression of Runx3 lacking the C-terminal VWRPY motif caused divergence into a TEM-like state. These results suggest that the dynamic activity of Runx3 and the potential interactors with its specific domains mediate complex regulation that patterns antiviral memory CD8 T cell development.
SATB1 is essential in regulating the stemness of antigen-specific CD8+ T cells
Authors: Lin Siying , Cui Weiguo 
Published: November 2024

Abstract
In chronic infection and cancer, a subset of self-renewing, antigen-specific CD8+ T cells, termed progenitors, is crucial for long-term immunity and immunotherapy effectiveness. The mechanisms governing their stemness, however, are not fully understood. Our single-cell RNA + ATAC sequencing analysis revealed that SATB1 (special AT-rich sequence-binding protein) is exclusively expressed in the progenitor CD8+ T cells during chronic infection. Known for its key role in chromatin organization during T-cell development, SATB1’s unique expression in the progenitor CD8+ T cell led us to hypothesize that it plays a pivotal role in regulating the stemness of the antigen-specific CD8+ T cells. Using the lymphocytic choriomeningitis virus (LCMV) Clone 13 mouse model of chronic infection, the SATB1 gene was deleted in CD8+ T cells via CRISPR/ RNP technology. At day 21 post-infection, the SATB1 deletion resulted in a reduction of virus-specific progenitor CD8+ T cells and a decrease of TCF1 expression. The transcriptomic and epigenomic studies further revealed that SATB1 plays a key role in regulating the chromatin accessibility and transcriptional activities of stemness-associated genes, such as Tcf7, Bach2, and Myb. Overall, our results underscore the critical role of SATB1 in maintaining the transcriptional integrity of progenitor CD8+ T cells in response to antigen activation, which sheds light on the genetic pathways that regulate the stemness of antigen-specific CD8+ T cells.
Age-related dynamics of CD8+ regulatory T cells: Implications of NKG2D in Immune Aging
Authors: Srinivasan Saranya , Ma Chaoyu , Wang Liwen , Mishra Shruti , Fan Kenneth , Im John , Segura Courtney , Zhang Nu 
Published: November 2024

Abstract
Aging is a complex biological process that impacts various physiological functions, including the immune system. Our study investigated the impact of aging on CD8+ regulatory T cells(CD8+Treg), which showed a pattern of initial increase up to 12 months, then a decline by 24 months in a C57BL/6 mouse model, unlike memory T cells, which consistently increase with age. Functionally, CD8+Treg, irrespective of age, did not produce cytokines in response to TCR stimulation, highlighting a stark functional contrast with memory cells. However, upon IL-15 stimulation, CD8+Tregs, unlike their memory cell counterparts, demonstrated enhanced cytokine production. Transcriptomic analysis revealed an abundance of Klrk1 (killer cell lectin-like receptor subfamily K member 1)gene transcripts in aging CD8+Tregs. Klrk1 gene encodes Natural Killer Group2 Member D (NKG2D), an activating receptor NK cells express. This upregulation was specific to CD8+CD122hiLy49+ and absent in CD8+CD122hiLy49-. To explore this correlation further, we utilized a Klrk1-/- mouse and observed an increased CD8+Treg population, suggesting a potential negative regulatory role of NKG2D in CD8+Treg homeostasis. Transcriptome analysis of Klrk1-/- CD8+Tregs showed enrichment of aging-related gene signatures, further corroborating the link between NKG2D and the aging process. Our findings suggest NKG2D's involvement in aging and immune dysfunction, providing avenues for intervention in the elderly.
Development of single-cell ROS regulome profiles of CD8+ T cells
Authors: WANG YI-CHUAN 
Published: November 2024

Abstract
Cells under oxidative stress regulate their functions, but current methods for detecting this stress mostly use mass spectrometry or fluorescent probes sensitive to reactive oxygen species (ROS). While valuable, these methods can't simultaneously characterize specific ROS-mediated pathways at the single-cell level. Thus, we developed an approach to characterize the ROS regulome of single-cells together with their phenotypic identity, termed single-cell ROS regulome profiling (scROP). To accomplish this, we first assessed over 100 commercially available antibodies by fluorescent cell barcoding screening and then selected a subset of ROS antibodies (n = 25). We combine our method with in vitro-activated OTI-CD8+ T cells to quantify the proteins that regulate the activity of the ROS pathway, it provides a more detailed sequential progression of how ROS regulome response through oxidative and redox pathways in different CD8+ T cell states that lead to exhaustion. Moreover, our results show that T cell exhaustion rates differ under hypoxic conditions or in the presence of antioxidants. We confirmed our findings using clinical samples, such as blood from hemodialysis patients, CD8+ T cells from CAR-T patients, and various tumor sections from hepatic carcinoma patients. Overall, our novel single-cell ROS regulome profiling approach revealed a comprehensive molecular roadmap of CD8+ T cells in response to sustained stimulations.
Human Immune repertoire and gene expression in pediatric and adult SARS-CoV-2 infected patients using single cell multi-omics approaches
Authors: ji xuhuai , Yonker Lael , Miranda Molly , Kinane Thomas Bernard , Chang Matthew , Suresh Sundari , Kiany Samaneh , Weinacht Katja , Maecker Holden 
Published: November 2024

Abstract
SARS-CoV-2 represents a global health crisis, yet major knowledge gaps remain about the human immune response against the virus infection and related treatment in both pediatric and adult patients. Immune repertoires (TCR and BCR) and related gene expression at massive single cell level play a crucial role in early-stage infection and late virus clearance. By using single cell multi-omics approaches, we analyzed immune repertoire and gene expression in 9 COVID-19 patients and 3 controls. We used single-cell mRNAseq and observed increased expression of inflammatory cytokines and transcription factors such as CXCL1, RNASE2, EGR1, CXCL2, and CXCL8 in either adult or pediatric COVID-19 infected patients compared to controls. Ten surface proteins such as CD62L, CD16, CD20, CD56, CD14, and CD45RA were quantitated by AbSeq. CD14+ cells were more prevalent in adult COVID-19 patients and CD3+ T cells were less prevalent. We conducted comparative analyses of TCR and BCR repertoire using single-cell V (D)J sequencing approach. The clonotypes were defined by using either combined alpha and beta chains or beta chains only. Distinct clonotypes were identified in both pediatric and adult COVID-19 patients. We did not see any significant clonotype expansion in this sample set yet but further analysis is warranted. The combination with the highest frequency in COVID-19 was TRAV29-TRBV27. Our study provides novel insights and bioinformatic analysis tools on immune repertoire in COVID-19.
Efficient, cost-effective isolation of functional antigen specific antibodies using Nanovial technology
Authors: Kershaw Kathleen , Bosler Lucienne , Kuo Wei-Ying , Wu Alex , Di Carlo Dino , Liang Jesse , de Rutte Joseph 
Published: November 2024

Abstract
The therapeutic application of monoclonal antibodies has been invaluable in improving the quality of life for countless patients across numerous indications. Despite advances in streamlining the process, enhanced screening methods still necessitate substantial investments in equipment, reagents, and training. To address this gap, we have developed a workflow utilizing Nanovials, hydrogel nanoliter containers, to enable the discovery of functional antibodies from single cells with a simple workflow without any new equipment or protracted hands-on assay steps.
We demonstrate this workflow using a hybridoma producing anti-Hen egg lysozyme (HEL) antibodies. As a proxy for rare “on target” cells, HEL hybridoma was spiked into a non-antigen specific hybridoma at known percentages and functional, HEL specific clones were enriched and isolated with a Nanovial assay. Nanovials specifically enrich the target antigen specific secreting cells at concentrations as low as 1% and isolate desired clones by sorting. Further improving the functional screening capabilities without lengthening the assay, multi-cell Nanovial assays were performed combining a target antibody secreting cell and reporter cell to specifically sort cells based on antibody binding or pathway modulation. By providing increased functional assay capabilities while reducing the time and material needed to isolate functional, antigen specific antibodies, Nanovials enable the rapid discovery of potent antibody therapeutics.
New automation-friendly 96-well plate ready-to-use 8-color dry antibody panel for basic phenotyping of human whole blood and peripheral blood mononuclear cells using flow cytometry
Authors: Bowers Rita , Dupas Nathalie , Kapinsky Michael , Lacaille Vashti , Mazumder Saumyabrata , Edicheri Alinkeezhil Gopikrishnan , Saif Samee 
Published: November 2024

Abstract
Automation-friendly 96-well plate flow cytometry solutions are ideal for pharmaceutical, academic, and CRO laboratories that perform testing on large numbers of samples and/or large number of test conditions. Our ready-to-use pre-formulated dry antibody panel in 96-well plate format provide researchers all the reagents within the wells of the plate where the test is conducted in a stable dry format, resulting in dependable reagent performance and reduction of manual pipetting steps with the added benefit of time and material (reagent and sample) savings. In addition, the 96-well plate format is compatible with automated liquid handlers for walk-away flexibility and higher-throughput sample processing. Here we show flow cytometry data for both whole blood and PBMC samples stained with the first ready-to-use DURAClone IM Phenotyping BASIC plate (RUO) in a shallow 96-well plate containing a dry reagent antibody panel to identify major lymphocyte and monocyte subpopulations for the following markers: CD45, CD16, CD56, CD19, CD14, CD3, CD4 and CD8. Processing of whole blood samples using the shallow 96-well plate format was achieved using FLEXLyse, a lysing solution with low volume ratio of lysis/whole blood, applicable for no-wash and wash protocols. Our experiments were performed using automation on the Biomek i7 liquid handling automated workstation integrated with a CytoFLEX LX flow cytometer and microplate centrifuge demonstrating a fully automated flow cytometry workflow.