bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing vaccine performance through improved cross-presentation with a nanoparticle adjuvant
Authors: Hernandez-Franco Juan F , Jan Imran M , Goldsmith Malaycia , HogenEsch Harm 
Published: January 2023

Abstract
Activation of CD8 T cells requires presentation of antigenic peptides by MHC I molecules and costimulatory signals provided by CD80 and CD86 on dendritic cells (DCs). Subunit and purified antigen vaccines often fail to induce CD8 T cell responses because the antigens have limited access to the endogenous MHC I pathway, a phenomenon known as antigen cross-presentation. Vaccine adjuvants are being investigated to promote cross-presentation, but adjuvants in currently licensed vaccines are not effective. The goal of this study was to determine if a combination adjuvant (NanoS100) comprised of cationic plant-derived adjuvant nanoparticles (Nano-11) and the synthetic STING agonist ADU-S100 stimulates cross-presentation in vitro and in vivo after intradermal and intranasal vaccination. Incubation of DCs with OVA adsorbed to NanoS100 significantly enhanced the presentation of antigen to the MHC I-restricted OVA-specific B3Z T cell hybridoma compared with OVA only. The cross-presentation was inhibited by preincubation of DCs with chlorpromazine and chloroquine, suggesting that NanoS100 supports endosomal processing of OVA. NanoS100 also significantly increased the expression of CD80 and CD86 on antigen-presenting cells in vitro. Vaccination of mice with OVA and NanoS100 increased humoral and cellular responses with a significant increase of IFNγ+ CD8 T cells in the spleen and the lungs. Intranasal immunization induced a greater percentage of IFNγ+ CD8 T cells in the lungs compared with intradermal immunization. These findings support the potential utility of NanoS100 as a vaccine adjuvant.
Intranasal administration of a novel synthetic TLR4 agonist suppresses allergen-specific Th2 responses in mice
Authors: Miller Shannon M , Buhl Cassandra , Whitacre Margaret , Ward Janine , Jackson Konner , Khalaf Juhienah K , Bazin Helene G , Evans Jay T 
Published: January 2023

Abstract
Allergen-agnostic immunotherapies to treat seasonal allergic rhinitis are not currently available. Antihistamines are the most common form of seasonal allergic rhinitis treatment – minimizing symptoms instead of addressing underlying immune dysfunction. Allergen specific immunotherapies (AIT) are also available for seasonal allergic rhinitis but require a known allergen and long-term treatment regiments that can be costly and take several years to complete. Here we report a novel synthetic TLR4 agonist that prevented Th2 allergic responses in an OVA-sensitized mouse model. This novel synthetic TLR4 agonist has improved stability compared to other TLR4 agonists used as vaccine adjuvants or immunotherapeutics. After sensitizing Balb/c mice to OVA using IP injections of OVA + alum, intranasal treatment with the novel TLR4 agonist at one, three, or seven days prior to intranasal OVA challenge reduced or ameliorated OVA-specific Th2 allergic responses. Specifically, intranasal TLR4 agonist treatment reduced OVA-induced airway hypersensitivity, eosinophil influx, and Th2 T cell cytokine secretion – hallmarks of Th2 allergic immune responses. Additionally, we have identified a particular formulation of our novel synthetic TLR4 agonist which has shown greater efficacy, stability, and reduced toxicity profile compared to initial formulations. These data suggest this novel synthetic TLR4 agonist can potentially treat the underlying immune dysfunction associated with allergic responses for a durable cure of seasonal allergic rhinitis.
Supported by NIH contract HHSN272201800036C
B cell ontology in a model marsupial
Authors: Sampson Jordan M , Morrissey Kimberly A , Miller Robert D 
Published: January 2023

Abstract
Marsupials, such as kangaroos and opossums, are members of a lineage of mammals that last shared a common ancestor with humans and mice ~160 million years ago. Although they share many of the same components of the adaptive immune system of humans and mice, they also have some significant differences. For example, in addition to conventional αβ and γδ T cells is the presence of a third T cell lineage, the γμ T cell. Like humans and mice, marsupials have homologues of the classical MHC class I and II molecules and many of the non-conventional MHCs such as CD1 and MR1, but in addition, opossums have another MHC class I family called the UT family. Like humans and mice, opossums also have FcRN. However, the development of B cells may also differ significantly. B cell development in the opossum is entirely postnatal. For example, opossums lack the VpreB1 and 2 and λ5 surrogate light chains; however, like birds, they have VpreB3. B cell development also occurs at a slower pace in the opossum and the sites of B cell development in marsupials remain largely unknown. To address these differences and unknowns, we will present our results regarding timing and location of B cell development, and the establishment of immuno-competence in a model marsupial, the laboratory opossum Monodelphis domestica.
Supported by NSF award IOS-2103367
scRNA-Seq profiling of stickleback fish splenocytes: Expansion of myeloid and B cells on immunization
Authors: Attaya Ahmed , Lohman Brian , Steinel Natalie 
Published: January 2023

Abstract
Threespine stickleback is characterized by wide phenotypic variations attributed to repeated evolutions that took place when colonizing new environments. This fish species is hence deemed a powerful model candidate for comparative immunology to gain new insights into the function and evolution of vertebrate immune system, given also fish small size, wide distribution, and easiness of husbandry. Harnessing single-cell RNA sequencing potential to dissect tissue cellular heterogeneity at high resolution, here we employed that technique to profile naïve, and immunized stickleback spleens identifying the different immune cell types present, and reveal the transcriptional changes driven by immunization. Analysis of the compiled splenic data revealed 18 cell clusters, including major leukocyte types (e.g., B cells, macrophages, and neutrophils), and erythrocytes. Surprisingly, none of the clusters could be recognized or presumed as a T cell population based on the genes expressed in each cluster. Fish immunization led to total cell expansion and interestingly to the emergence of distinct myeloid and B cell populations. The myeloid population lacks the expression of MHCII genes, but was found enriched in the expression of GRN2, S100A10, NCCRP, BPIFC, and PRDX1 genes, suggesting that additional cytotoxic roles are possibly played by that population. Despite the B cell population being enriched in the expression of proteolysis associated genes, i.e., TRY and PRSS59, it also, unlike other B cell populations, lacks the expression of MHCII genes. This study creates a comprehensive atlas of threespine stickleback spleen at single-cell resolution and raises new questions about the immune response evolving in such vertebrate species.
Supported by a grants from NIH (Grant number: NIH R01 AI146168)
Prediction of immunodominant CD4+ SARS-CoV-2 epitopes with TCR repertoire sequencing data
Authors: Pogorelyy Mikhail , Minervina Anastasia , Rosati Elisa , Mudd Philip , Ellebedy Ali , Thomas Paul G 
Published: January 2023

Abstract
The T cell receptor (TCR) is a hypervariable molecule defining the specificity of T cells for peptide-MHC complex. Defining exact epitopes is crucial to profile T cell responses in COVID-19 and yet very few MHC-II restricted SARS-CoV-2 epitopes are currently known. Here, we propose a reverse epitope discovery technique, which, instead of using large pools of peptides to identify reactive T cells, utilizes TCR repertoire sequencing data as the means to predict immunodominant epitopes. The core idea of the approach is to combine information from large, publicly available TCR repertoire datasets: TCRbeta repertoires from cohorts of COVID-19 patients and controls, and paired TCR repertoires of single T cells activated by SARS-CoV-2 peptides. Our pipeline allows us to predict the HLA-restriction of public SARS-CoV-2 specific TCR clonotypes, which in turn allows us to predict binding to a specific peptide. We applied this approach to single cell TCR repertoires of CD4+ T cells from COVID-19 patients, and predicted six MHC-II restricted immunodominant epitopes and alpha-beta TCR motifs recognising them and tested our predictions experimentally. We further applied this technique to bulk TCRalpha repertoires from T follicular helper cells from draining lymph nodes of healthy donors after BNT162b2 mRNA vaccination. We found that the DPB1*04 restricted S167–180 epitope is responsible for the largest public CD4+ response, and recognition of this epitope is driven by a semi-invariant TCR alpha chain. This finding led to generation of the DPB1*04 S167–180 tetramer, allowing to track SARS-CoV-2 specific CD4 cells in peripheral blood and lymph node samples with flow cytometry.
This work was partially supported by R01AI136514 grant.
This work was partially supported by R01AI136514 grant.
Spike BATTLE: Simultaneous evaluation of antigen-specific B and T lymphocytes following natural SARS-CoV-2 infection and subsequent mRNA vaccination
Authors: Newell Krista L , Waldran Mitchell J , Thomas Stephen J , Endy Timothy P , Waickman Adam T 
Published: January 2023

Abstract
The development of effective vaccines and therapies against viral diseases requires reliable approaches for assessing durable immunological memory. Although a wealth of information is available from peripheral blood mononuclear cell samples, Conventional methods for quantifying and phenotyping antigen-specific lymphocytes can rapidly deplete irreplaceable specimens. This is due to the fact that antigen-specific T and B cells have historically been analyzed in independent assays each requiring millions of cells. A technique that facilitates the simultaneous detection of antigen-specific T and B cells would allow for more thorough immune profiling with significantly reduced sample requirements. To this end, we developed the B And T cell Tandem Lymphocyte Evaluation (BATTLE) assay, which allows for the simultaneous identification of SARS-CoV-2 Spike reactive T and B cells using an optimized Activation Induced Marker (AIM) T cell assay and a dual-color B cell antigen probes.
Using this assay, we demonstrate that antigen-specific B and T cell subsets can be identified simultaneously using conventional flow cytometry platforms and provide insight into the differential effects of mRNA vaccination on B and T cell populations following natural SARS-CoV-2 infection. While spike-specific B cell and CD8+ T cell responses were higher following mRNA vaccination than natural infection alone, the quantity of CD4+ T cells recognizing spike was enhanced only in subjects with low responses to natural infection. Our findings suggest divergent patterns of B and T cell subset mobilization with repeated antigen encounter and highlight the utility of examining these populations in concert.
Supported by the State of New York.
Vaccination modulates pulmonary eosinophil subsets upon breakthrough influenza infection.
Authors: Chang Lauren A , Rathnasinghe Raveen , Jangra Sonia , Choi Angela , García-Sastre Adolfo , Schotsaert Michael 
Published: January 2023

Abstract
Eosinophils play a critical role in mucosal tissue homeostasis, anti-helminth responses, and allergy. Lung eosinophilia is associated with aberrant T cell responses to respiratory viral infection and is also a consequence of vaccine-associated enhanced respiratory disease (VAERD). A growing body of literature has demonstrated there are different phenotypic subsets of eosinophils and, depending on subset, can play a protective role and aid in lung recovery following infection. Previous work by Choi et al. showed recruitment of eosinophils to the lung in BALB/c mice vaccinated with alum-adjuvanted trivalent inactivated influenza vaccine (TIV) following a sub-lethal H1N1 (A/New Caledonia/20/1999; NC99) influenza challenge. In this study, flow cytometric analysis of the lung showed an increase in total lung eosinophil numbers in all NC99-challenged mice compared to controls. Furthermore, in TIV-vaccinated then challenged mice, flux of inflammatory eosinophil (iEos) and resident eosinophil (rEos) numbers at 7 days post-infection (DPI) resulted in iEos/rEos ratios similar to that of OVA-sensitized allergic control mice; this effect was independent of alum adjuvant. Treatment groups with increased lung eosinophil numbers did not show signs of enhanced morbidity or inflammatory cytokine signatures compared to unvaccinated mice. Unsupervised clustering using CATALYST confirmed findings from manual gating analysis and revealed differences in eosinophil activation status based on surface expression levels of MHC Class II. Our findings provide a starting point for more sophisticated phenotypic characterization of eosinophil subsets and their distinct functional contributions to vaccine- and infection-induced immunity.
This research was partly funded by NIAID T32 Virus-Host Interactions Training Grant (5T32AI007647-22) and CRIP (Center for Research for Influenza Pathogenesis), a NIAID supported Center of Excellence for Influenza Research and Surveillance (CEIRS, contract # HHSN272201400008C).
Alveolar macrophages act as an early viral sponge inducing long-lived functional enhancement
Authors: Waldstein Kody , van de Wall Stephanie , Anthony Scott , Harty John T , Varga Steven M 
Published: January 2023

Abstract
Alveolar macrophages (AM) are one of the first immune cells to encounter pathogens in the lung. However, the role of AMs early after infection remains to be completely defined. To track virally infected cells, mice were infected with a panel of fluorescent reporter-expressing respiratory viruses. By 6 hr post-infection (p.i.), AM numbers significantly declined. The remaining AMs accounted for the majority of infected cells at early time points, surpassing the epithelium, but did not support significant viral replication. Strikingly, AMs represented over 80% of all respiratory syncytial virus (RSV)-infected cells which was confirmed by intravital microscopy and ImageStream flow cytometry. To track cells that survive infection, we utilized a novel cre recombinase-expressing RSV in a floxed-reporter mouse in which infected cells are indelibly marked. Cre-mediated reporter activation required direct infection, and reporter-positive AM numbers remained constant up to 30 days p.i., long after viral clearance. Reporter-positive and -negative AMs were isolated at 30 days p.i., and their functional capacity was assessed ex vivo. Both reporter-positive and -negative AMs exhibited increased basal levels of pro-inflammatory cytokines as compared to naïve AMs which was further increased upon heterologous infection. Reporter-positive AMs displayed an enhanced inflammatory response as compared to reporter-negative AMs from the same lung, indicating innate immunity can be further increased post-direct infection. Our results confirm that AMs play an essential role in limiting early viral access to the respiratory epithelium by serving as a reservoir for non-productive infection resulting in long-lived functional enhancement.
Supported by grants from NIH (R01AI124093-01A1, T32AI007485) and fellowships from NASA (Iowa Space Grant Consortium) and the University of Iowa Graduate College.
Innate lymphoid cells; essential responders to pulmonary cytomegalovirus infection
Authors: Mundy Miles Alexander , Brossay Laurent 
Published: January 2023

Abstract
Cytomegalovirus (CMV) is a β-herpesvirus that is ubiquitously spread throughout the human population. In healthy individuals, there is minimal impact to the host and the virus remains in a latent state. However, in elderly individuals, neonates and immunocompromised hosts, CMV can subvert immune responses and reactivate leading to significant pathology, including interstitial pneumonia. CMV induced pneumonitis is among the most common manifestations of perinatal human cytomegalovirus (HCMV) infection. Although an abundance of research has been conducted on the immune response to CMV, the true route of initial infection is still in contention. Through research with murine cytomegalovirus (MCMV), it is thought that infection first occur in the upper respiratory tract, specifically the olfactory epithelium, with a subsequent primary seeding of susceptible cells in the lung. While the role of innate lymphoid cells (ILCs) in combatting CMV infection in the periphery has been well established, the importance of these cells in the context of pulmonary CMV remains largely unknown. Utilizing an intranasal infection method in murine models, we have begun to uncover the role of ILCs such as natural killers (NK), ILC1 and ILC2s in pulmonary CMV infection. Our preliminary results have suggested an outsized role of NK cells in response to pulmonary CMV as compared to other ILC compartments as shown by early interferon gamma response by NK cells, as well as their increased abundance as compared to ILC1. Additionally, though ILC2 are the most predominant tissue resident ILC compartment in the lung, our data suggests that their contribution may not be critical to the antiviral response, though they may potentially aid in the resolution of tissue damage.
Supported by NIH Research Grants AI046709 and AI12221 and T32 HL134625 Training Grant from NHLBI
Distinct antibody profiles against Ebola virus track with the development of Post-Ebola Syndrome.
Authors: Velazquez Jalene V , Bond Nell G , Schieffelin John S , Gunn Bronwyn M 
Published: January 2023

Abstract
Survivors of Ebola virus disease (EVD) have reported a wide range of symptoms following recovery from infection. These long-term sequelae, collectively termed post-Ebola syndrome (PES), can significantly impact the daily lives of EVD survivors, yet little is known about the underlying mechanism of PES pathogenesis. Antibodies against Ebola virus provide protection against infection through both neutralization and recruitment of innate immune effector functions via the antibody Fc region, yet persistent antibody-mediated inflammation may contribute to PES manifestations. To investigate the potential role that virus-specific antibodies have in PES, we analyzed the antibody immune profiles in a cohort of EVD survivors and household contacts that had been previously characterized for clinical sequelae. Antibodies isolated from survivors an average of 2.5 years after recovery were measured for induction of Fc-mediated innate effector function against the immunodominant antigen Ebola glycoprotein-coated targets. We found that antibodies in asymptomatic EVD survivors were qualitatively different from survivors experiencing musculoskeletal and gastrointestinal manifestations of PES. Specifically, antibodies from asymptomatic individuals induced higher levels of antibody-dependent complement deposition and monocyte-mediated phagocytosis, but not neutrophil-mediated phagocytosis, and differed in NK cell activation profiles compared with individuals with PES. Together, these data suggest that the development of qualitatively different antibodies may shape susceptibility to/protection from the development of PES and may help identify potential therapeutic targets for EVD survivors suffering from PES.
Supported by Washington State University, College of Veterinary Medicine
Iron chelators and HDAC inhibitors are potent inducers of Epstein-Barr Virus Lytic cycle in Stomach Adenocarcinoma
Authors: Chakravorty Srishti , Wang Luopin , Kazemian Majid 
Published: January 2023

Abstract
Epstein-Barr Virus (EBV) is a complex oncogenic γ-herpesvirus that infects around 90% of the global adult human population. Upon primary infection, EBV typically persists asymptomatically in form of a latent infection. However, under certain circumstances the virus can malignantly transform lymphocytes and epithelial cells leading to cancers such as Diffuse Large B Cell Lymphoma (DLBCL) and Stomach Adenocarcinoma (STAD) respectively. Unfortunately, it is difficult to target latent EBV using the current immuno-therapeutic strategies, specifically due to reduced antigen expression. Cytolytic Virus Activation (CLVA) therapy is an approach that can specifically target and kill tumor cells that harbor EBV in a lytic state. The switch from latent to lytic phase can be mediated by a plethora of chemical compounds or lytic inducers. Recently, in our lab, we have developed an intuitive in-silico drug prediction approach to rapidly screen and identify FDA-approved or clinically available compounds that can be repurposed to induce lytic cycle in different EBV+ tumors. Using this strategy, we identified a range of HDACi and Iron chelators as inducers of lytic cycle in EBV+ epithelial cancers. Interestingly, these drugs also significantly induced the expression of Programmed Death Ligand-1 (PD-L1) protein, a major target of Immune checkpoint blockade (ICB) therapy. This led us to hypothesize that by utilizing such an in-silico drug prediction approach, we can identify cancer specific drugs that are potent inducers of EBV lytic cycle. To better understand the underlying mechanisms, we are now investigating the effect of these cytolytic compounds in vivo using xenograft mouse models.
Supported by SIRG Graduate Research Assistantship Award PCCR-SIRG-FY2022-01 (P30CA023168) from Purdue University
Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors, including endolysosomal TLRs and a STING dependent sensing pathway.
Authors: Nemazee David , Peng Linghang , Blane Tanya , Huang Deli , Gavin Amanda 
Published: January 2023

Abstract
We have studied the biochemistry and genetics of Phospholipase D3 (PLD3) and PLD4 because polymorphisms of these proteins have been associated with several important inflammatory and autoimmune diseases, including rheumatoid arthritis, systemic sclerosis, systemic lupus erythematosus and Alzheimer’s disease. We found that both PLD3 and PLD4 are 5’ exonucleases able to degrade both ssDNA and ssRNA. Deficiency in PLD3, PLD4 or both results in a variety of inflammatory defects, with the most serious being lethal hemophagocytic lymphohistiocytosis (HLH) in double knockout mice. Pld3−/− Pld4−/− mice represent a unique spontaneous model of HLH apparently independent of microbes, whereas Pld4−/− mice develop a range of phenotypes depending upon genetic background ranging from macrophage activation syndrome to lupus like disease. Evidence will be presented showing that the diseases in these mice result from autorecognition of nucleic acids and can be reversed by mutation of nucleic acid sensing pathways. PLD3 and PLD4 tend to limit TLR9 recognition but have a more complex effect on recognition by TLR7 and TLR8. Unc93b13d/3d Pld3−/− Pld4−/− mice spontaneously signal through STING suggesting that PLD3 and PLD4 also may regulate cytoplasmic nucleic acid sensing.
Supported by NIH grants R01 AI142945 and R56AG070775