bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal Candida cell-surface-specific monoclonal antibodies protect mice against multidrug-resistant Candida auris bloodstream infections
Authors: Rosario-Colon Jonothan A , Eberle Karen , Xin Hong 
Published: August 2023

Abstract
Candida species are the leading cause of life-threatening fungal infections in humans, especially among immunocompromised and hospitalized individuals. Of utmost concern is the emerging “superbug” Candida auris which has the potential to disseminate into bloodstream infections with up to 60% mortality in susceptible populations. Importantly, C. auris is the first inherently multidrug-resistant fungal pathogen, which contributes to a delay in effective treatment and increased mortality rates. Consequently, C. auris is the first fungal pathogen to cause a serious global public health threat.
Our lab has identified and isolated a panel of universal monoclonal antibodies (mAbs) specific to Candida cell wall epitopes that share high homology among various human pathogenic Candida species. Using an established murine model of disseminated infection, we showed that passive transfer of mAb C3.1 (anti-β-1,2-mannotriose) significantly extended survival and reduced fungal burdens and inflammation during early infection. We also showed that mAbs C3.1 and 9F2 (anti-phosphoglycerate kinase 1) significantly enhanced phagocytosis of C. auris yeast by macrophages and inhibited the proliferation of multiple C. auris clinical isolates in vitro.
Since there are currently no approved antifungal vaccines or antibodies and current treatments are inadequate, critically needed antifungal antibodies can provide long-awaited effective therapies against this deadly pathogen. Our future directions include developing humanized mAbs to evaluate their protective efficacy in genetic mouse models of human immunodeficiency. We will then utilize Fc engineering to derive human IgG1 variants for enhanced complement-based effector efficacy.
Supported by grants from NIH /NIAID (R21AI168929) and the Department of Defense (PR171482)
Development of a next generation pertussis vaccine: An unbiased biochemical approach to identify novel CD4+ T cell recognized antigens from Bordetella pertussis
Authors: Shamseldin Mohamed Medhat , Hernandez Gabrielle , Verzani Eva , Hall Jesse M , Caution Kyle J , Carr Steven A , Deora Rajendar , Abbelin Jenn , Dubey Purnima 
Published: August 2023

Abstract
Waning acellular pertussis vaccine (aPV) efficacy has brought about the reemergence of pertussis despite global vaccine coverage. Decreasing vaccine efficacy is correlated with the emergence of vaccine escape mutants lacking bacterial antigens expressed in current laboratory strains. Recent work shows that systemic and mucosal CD4+ T cells are necessary for improved vaccine efficacy and increased duration of immunity. However, the antigens recognized by these T cells are undefined. We hypothesize that the efficacy and duration of aPV-induced immunity will be improved by the addition of new bacterial antigens that induce a strong CD4+ T cell response. Here we used the natural antigen processing machinery of mouse bone marrow derived dendritic cells to identify peptides derived from the laboratory Bp strain Bp536 and a clinical isolate, H762, that are presented on MHC Class II. Bioinformatics analysis selected the highest affinity peptides for both mice and human MHC Class II. The immunogenicity of each peptide was tested ex vivo using ELISA and an Activation Induced Marker (AIM) assay. We stimulated splenic T cells from convalescent or whole cell vaccine (wPV) immunized mice and human PBMCs. This unbiased biochemical approach generated a list of Bp-specific MHC Class II epitopes that are recognized by CD4+ T cells. These data suggest that Bp expresses multiple novel CD4+ T cell recognized antigens that may improve vaccine efficacy and the duration of protection when incorporated in a next generation aPV.
Potent suppression of viral rebound after analytical treatment interruption in ART-suppressed SHIV-infected animals by a CD4 binding site bNAb
Authors: Fox Madison L , Shrader Hannah , Hait Sabrina Helmold , Talana Chloe Adrienna , Lovelace Sarah , Choe Misook , Del Prete Gregory , McCarthy Elizabeth , Paul-Todd John , Woodward Ruth , Koup Richard , Pegu Amarendra 
Published: August 2023

Abstract
Broadly neutralizing antibodies (bNAbs) are promising immunotherapeutic biological agents against HIV-1 that can be used to complement small-molecule combination antiretroviral therapy (cART) drugs for the treatment of HIV-1 infection. There have been several analytical treatment interruption (ATI) studies utilizing bNAbs in ART-suppressed HIV-1-infected patients in which bNAbs are infused during an ART cessation period. To model these clinical studies, bNAbs can be administered to ART-suppressed SHIV-infected rhesus macaques (RM). However, delivery of human bNAbs to RMs induces formation of anti-drug antibodies (ADA) which shorten the half-life of the bNAb and limit the time during which effectiveness can be assessed. In this study, we infused six ART-suppressed SHIV-infected RMs with four 6–10 mg/kg doses of VRC01v23, a next generation CD4-binding site bNAb, every 2–4 weeks for a total duration of 10 weeks. Prior to bNAb treatment, three 50 mg/kg doses of an anti-CD20 antibody were given two weeks apart in order to deplete peripheral B cells and eliminate ADA. Five of six animals had persistent B cell depletion and showed no evidence of ADA after infusions of VRC01v23 and cessation of ART. No viral rebound was observed in these five animals. The sixth animal developed ADA against VRC01v23 resulting in rapid clearance of VRC01v23 from circulation and viral rebound. These data demonstrate that B cell depletion can limit the development of ADA against human bNAbs allowing for the assessment of long-term therapeutic potential of human bNAbs in RMs.
Supported by intramural NIAID funding
Combination adjuvants and antigens provide heterosubtypic protection against lethal influenza infection
Authors: Brown Deborah M , Briere Jenna , Cheang Hoi Lam , Custer Dylan , Reiley William C , Laferriere Ethan 
Published: August 2023

Abstract
Influenza A virus (IAV) is a negative strand RNA virus that undergoes antigenic drift and shift, leading to serologically distinct strains that can cause tens of thousands of deaths annually in the US. The wide variety of hemagglutinin (HA) and neuraminidase (NA) proteins necessitates yearly reformulation of the vaccine to protect against novel seasonal and pandemic strains. Current IAV vaccines do not contain adjuvants, however, immune modulators such as pattern recognition receptor (PRR) agonists may enhance antigen presentation to T cells and provide broader protection against IAV strains that differ in HA and NA outer coat proteins. We set out to investigate whether TLR4 (lipopolysaccharide) and TLR3 (poly IC) agonists in combination with HA (H3N2) and nucleoprotein (NP) or NP and matrix (M1) proteins could provide protection against lethal challenge with mismatched IAV strain H1N1. Mice given H3 and NP with LPS + pIC in a prime/boost strategy demonstrated 80% survival after heterosubtypic H1N1 challenge while H3 + NP in PBS showed 20% survival. Similar results were seen using LPS + pIC in combination with NP and M1 protein with 90% survival. High endpoint titers of anti-NP antibodies (that also bound H1N1 virus) correlated with heterosubtypic protection suggesting a role for non-neutralizing antibodies in promoting survival. In addition, LPS and pIC enhanced dendritic cell (DC) function in vitro and increased migratory monocyte DC in the lymph node in vivo, coupled with early upregulation of T cell marker CD69. This strategy may provide increased efficacy over current IAV vaccines by inducing non-neutralizing antibodies and enhanced T cell responses to internal proteins.
Supported by Trudeau Institute and Clarkson University.
Evolution of the Structure and Organization of the Mammalian Immunoglobulin Loci
Authors: Sampson Jordan M , Miller Robert D 
Published: August 2023

Abstract
There are three extant lineages of mammals: placentals (e.g. humans and mice), marsupials (e.g. kangaroos and opossums), and monotremes (e.g. platypus). Of the three lineages, the marsupials are unusually and uniformly limited in their immunoglobulin heavy chain (IgH) isotype content. All marsupials studied have only one IgM, IgG, IgE, and IgA and lack IgD. Comparatively, there is a greater complexity of IgH isotypes and subclasses in both placentals and monotremes. Marsupials also have a greater complexity in their light (L) chain V genes than IgH chains. Transposable elements (TEs), like retroelements, have been hypothesized to contribute to gene copy variation and genome evolution. Recently, these TEs have been found in the IgH loci. Here we investigate the impact these TEs have on the evolution of marsupial IgH and IgL loci. We have found that some of the TEs in the opossum IgH locus are short and non-functional, potentially contributing to the restriction seen in the locus. Conversely, the TEs in the L chain loci are longer and may explain the differences in complexity in both the V and C regions between the H and L chain loci.
Supported by National Science Foundation Award IOS-2103367.
Does the upper respiratory tract microbiome change in dairy calves fed milk replacer containing probiotics?
Authors: Chitko-McKown Carol G , McDaneld Tara G , Kritchevsky Janice E , Bryan Keith A , Eicher Susan 
Published: August 2023

Abstract
Our overall hypothesis is that feeding probiotics to dairy calves will alter overall immunity and may additionally change the microbiome in the respiratory tract as well as the gut. A group of 20 dairy calves were split into two treatment groups: Control (N=10, milk replacer), and Probiotic (N=10, milk replacer + 0.5 g/day Bovamine Dairy). On day 0 birth weight was obtained and the calves were provided colostrum as per the dairy SOP. On day 2, probiotics were added to the milk replacer of the treated group. Blood was collected along with nasal and tonsil swabs on days 0, 7, 14, 21, 28, 42, and 48. Calves were monitored daily for fecal, nasal, and ocular discharge scores. Our preliminary data showed no significant differences (P&lt;0.5) between the Control and Probiotic groups in immune cell populations in peripheral blood. DNA was extracted from nasal and tonsil swabs to evaluate the bacterial populations in the upper respiratory microbiome. Hypervariable regions 1 through 3 along the 16S ribosomal RNA gene were amplified by PCR and sequenced by Illumina MiSeq to determine the bacterial taxa present. Evaluation of these samples revealed a greater percentage of operational taxonomy units (OTU) were classified at the genus level in the tonsil compared to the nasal samples. The microbiome of the tonsils was more stable over time points compared to the nasal samples. Evaluation of each timepoint for nasal and tonsil samples identified bacterial taxa that changed in relative abundance with the addition of the probiotic compared to the control diet. Addition of probiotic changed the relative abundance of OTU (P&lt;0.01) in the nasal and tonsil sampling sites and at multiple timepoints. Analyses are ongoing.
Project supported by fund from the USDA Agricultural Research Service.
LAIR-1 expression on SIV-specific CD8 T cells is associated with T cell impairment and disease progression
Authors: Govindaraj Sakthivel , Sharma Asish Arunkumar , Ali Syed , Babu Hemalatha , Busman-Sahay Katheleen , Bosinger Steven , Estes Jacob , Sekaly Rafick-Pierre , Villenger Francois , Amara Rama Rao , Velu Vijayakumar 
Published: August 2023

Abstract
Functional impairment of CD8 T cells is characteristic of chronic HIV infection. HIV-specific CD8 T cells undergo exhaustion, lose effector function and fail to control the virus. Leukocyte-associated Ig-like receptor-1 (LAIR-1), a transmembrane glycoprotein, expressed on human blood mononuclear leukocytes and act as an inhibitory receptor of cytotoxic cells. However, the role of LAIR-1 expression on virus-specific CD8 T cells during SIV/HIV infection remains unknown.
We examined a total of 14 macaques infected with the Simian Immunodeficiency Virus (SIVmac251) and studied the dynamics of LAIR-1+ SIV-specific CD8 T cells for their phenotype and function using flow cytometry. We performed immunohistochemistry to stain for LAIR-1 in lymph nodes and used RNA seq to study the transcriptomic profile of LAIR-1+ CD8 T cells.
Here we report that LAIR-1 is significantly up regulated on SIV-specific CD8+T cells during chronic SIV infection. and the expression of LAIR-1 on total and SIV-specific effector memory CD8 T cells correlated directly with the SIV viral RNA levels. In addition, the level of LAIR-1 in the lymph node was higher compared to naïve animals. Transcriptionally, the LAIR-1+ CD8 T cells exhibited an heightened type I IFN-signaling coupled with reduced TCR signaling, cell cycling and cell metabolism pathways. Indeed, In vitro blockade of LAIR-1 using LAIR-1-Fc/anti-LAIR-1 antibody resulted in enhanced proliferation of SIV-specific CD8 T cells with cytotoxic function.
These data indicate that the immunoregulatory LAIR-1/Collagen pathway is operative during SIV infection and serve as a foundation in vivo trials of LAIR-1 blockade to potentially enhance/restore antiviral SIV-specific CD8 T cells for the HIV cure strategy.
This work was supported in part by NIH grants CFAR ERASE AIDS-R03, R01AI148377 (to VV), U19 AI109633 (to RRA, macaque core to VV),
PD-1 mediated regulation of CD8+ T cells in the murine submandibular gland
Authors: Borys Samantha , Zemmour David , ImmGen T , Brossay Laurent 
Published: August 2023

Abstract
Immune checkpoints, including programmed cell death protein 1 (PD-1), restrain the immune response, maintain self-tolerance, and prevent excessive collateral damage. Immune checkpoint blockade has revolutionized cancer immunotherapy by unleashing exhausted immune cells to kill tumor cells, but can lead to immune related adverse events (IrAEs). Patients receiving PD-1 blockade can develop IrAEs including vitiligo, colitis, endocrinopathies, and sicca syndrome, an autoimmune disease characterized by the accumulation of immune cells in the salivary and lacrimal glands, leading to deterioration and dysfunction. Because PD-1 is highly expressed on CD8+ T cells in the naive submandibular gland (SMG), we hypothesized that loss of PD-1 is likely to disrupt the previously reported hyporesponsive microenvironment of the SMG, leaving patients particularly susceptible to IrAEs affecting this gland. Our data indicates that genetic loss of PD-1 results in increased CD8+ T cell number and frequency in the SMG of naïve C57BL/6 animals. To characterize this expanding population, we recently collaborated with the ImmGen T consortium to perform single-cell RNA-seq on SMG T cells of wildtype and PD-1 knockout mice. Preliminary analysis indicates that the expanding CD8+ T cells in the salivary gland of PD-1 deficient animals have a unique phenotype. These cells exhibit exhaustion characteristics including expression of transcription factors Nr4a2 and Tox, and inhibitory receptors LAG-3 and TIGIT. Altogether, our data provide insights for IrAE prevention and treatments in patients receiving PD-1 blockade.
This work was supported by NIH research Grants AI46709 (L.B.), AI-072073 (ImmGen T), and a Brown University Presidential Award (S.B.).
PI3Kδ: a key driver of effector differentiation under conditions of T cell exhaustion
Authors: Pichler Andrea C , Cannons Jennifer L , Golec Dominic P , Reilley Julie , McGavern Dorian B , Schwartzberg Pamela L 
Published: August 2023

Abstract
In chronic infection and cancer, prolonged antigen exposure drives a state of T cell hyporesponsiveness, called exhaustion. A small subset of TCF1+ progenitor exhausted stem-like T cells (pTex) cells, is required to maintain exhausted T (Tex) cells and respond to checkpoint blockade. Understanding mechanisms regulating these populations may help identify approaches to counter exhaustion. Phosphatidylinositol 3-kinase-d (PI3Kd) is an important component of T cell signaling. We have found that TCF-1 is repressed in CD8+ T cells from patients with Activated PI3K Delta Syndrome and in a mouse model (Pik3cd E1020K/+ mice) in acute viral infections. How activated-PI3Kδaffects T cell exhaustion is unknown. Using chronic LCMV clone 13 infection, we found that Pik3cdE1020K/+ mice rapidly die, yet surviving mice recover faster than WT. RNA sequencing revealed decreased expression of Tcf7, encoding TCF-1, in antigen-specific CD8+ T cells, along with loss of TCF-1+Tim3− CD8+pTex cells in Pik3cdE1020K/+ mice upon cl13 infection. Tex cells that were maintained during chronic infection in Pik3cdE1020K/+ mice displayed an effector-like phenotype, with expression of CX3CR1+ and KLRG1+, and increased effector functions, suggesting that these cells might induce early immunopathology yet increase viral clearance. P14 cell transfers, in conjunction with CRISPR-mediated gene disruption, revealed that loss of FoxO1 leads to loss of TCF-1+ cells, whereas the increase of effector cells is at least partially cell-extrinsic. Our findings suggest that PI3Kδ is a critical rheostat that balances effector vs exhaustion differentiation, providing insight for therapeutic strategies for exhaustion.
Pinpointing molecular regulators of CD8 T cell differentiation through multimodal single-cell profiling
Authors: Green William D , Gomez Amber , Mullins Genevieve Nicole , Green Jarred , Baldwin Albert , Milner Justin 
Published: August 2023

Abstract
CD8 T lymphocytes control infection and malignancy through differentiation into specialized cell states with discrete functional attributes. While CD8 T cell fate commitment is a transcriptionally and epigenetically controlled process, the transcription factors and chromatin modifiers governing CD8 T cell differentiation remain ill-defined. Here, we leveraged mouse models of viral infection and cancer to simultaneous profile the chromatin and transcriptomic landscapes of virus-specific and tumor-specific CD8 T cells at single-cell resolution. Through in-depth comparison of antigen-specific CD8 T cells across distinct disease settings, we define uncharacterized CD8 T cell states and clarify roles for molecular regulators of T cell heterogeneity. Comparison of uniquely accessible regions of chromatin along with predicted transcription factor activity uncover regulatory networks that both guide and enforce CD8 T cell fate commitment into novel and established states spanning T cell memory, residency, and exhaustion. Further, we have functionally defined novel roles for several transcriptional regulators in controlling CD8 T differentiation during infection and cancer, including undescribed roles for the transcription factor Runx3. Together, our findings clarify CD8 T cell heterogeneity and differentiation trajectories across acute infection, chronic infection, and cancer. We show our findings can be leveraged to enhance promising immunotherapy approaches.
AAI Intersect Fellowship Program for Computational Scientists and Immunologists (2022-2023)
Investigating memory CD8 T cell-mediated immunopathology
Authors: Wall Sarah M , Jarjour Nicholas N , Jameson Stephen C 
Published: August 2023

Abstract
Bystander memory CD8 T cells can respond to other pathogens independently of their T cell receptors (TCRs). Current dogma is that these memory CD8 T cells can improve control of unrelated acute infections via TCR independent, innate-like functions. Contrary to this, we observed that mice with memory CD8 T cells with the transgenic P14 TCR that is specific for lymphocytic choriomeningitis virus (LCMV), or P14 memory chimera mice, succumb to a typically sublethal bacterial infection with Listeria monocytogenes (Lm). However, mice with a reduced number of transferred P14 T cells are less susceptible to Lm, suggesting that a high frequency of P14 CD8 T cells leads to increased lethality of Lm infection. At day 3 post Lm infection, LCMV-experienced mice have significantly higher bacterial burdens in the spleen and liver compared to controls. Preliminary data also suggests that certain cytokines may be involved in this process. We are investigating possible mechanisms of bystander memory CD8 T cell-mediated immunopathology. This work highlights that bystander CD8 memory T cells are not unequivocally protective but can also enhance susceptibility to non-cognate infections.
Supported by NIH grant, R01 AI38903.
Viral infection in the brain induces priming and maintenance of a novel antigen specific CD8 T cell population within the bone marrow that dysregulates the stem cell niche
Authors: Wolf Delaney , Tritz Zachariah P , Reesman Rachael A , Rangel Frances A , Bamkole Michael A , Pfaller Christian K , Maynes Mark A , Hansen Michael J , Jin Fang , Fain Cori E , Johnson Aaron J , Ayasoufi Katayoun 
Published: August 2023

Abstract
Bone marrow is a primary immune organ responsible for stem cell maintenance and hematopoiesis. While the bone marrow niche is mainly studied in the context of hematopoiesis, aging, and mechanisms underlying stem cell and plasma cell survival, changes of the niche during brain viral infections and primary T cell responses is unknown. Intracranial infection with the neurotropic Theiler’s Murine Encephalomyelitis Virus (TMEV) results in an acute infection in the C57BL/6 mouse which is cleared 30 days post infection due to generation of an antigen specific CD8 T cell response raised against the immunodominant epitope VP2121–130. We determined that 7–10% of CD8 T cells present in the sternal and femoral bone marrows and 15–20% in the cranial bone marrow were antigen specific 7 days post intracranial TMEV infection. Over 70% of these CD8 T cells were located outside of the vasculature as determined by IV labeling. Importantly, continuous treatment with FTY720, which sequesters T cells outside of the blood, did not eliminate antigen specific CD8 T cells in any bone marrow compartment. CD8 T cells in the bone marrow established durable memory following viral clearance and were reactivated upon cognate antigen reencounter. Both acute TMEV infection and antigen specific reactivation caused an increase in lineage−, Sca-1+, ckit+ (LSK) cells in the bone marrow. This LSK dysregulation was abrogated upon CD8 T cell depletion. We conclude that brain viral infections induce in situ effector and memory T cell responses within the bone marrow compartment. Both acute and memory recall CD8 T cell responses cause stem cell dysregulation. Our data hence paves the way for crucial studies of bone marrow resident antigen specific CD8 T cells in health and disease.
Supported by grants from NIH (K99NS117799-01A1 (KA), R01NS103212 (AJJ), and RF1NS122174(AJJ)