bluuebunny/crossref_metadata_2025_split huggingface dataset:
Let’s talk about sex, baby: sex influences age-related changes in natural antibodies and natural antibody producing B-1a cells
Authors: Webster Sarah E , Ryali Brinda , Tsuji Naomi E , Clemente Michael J , Holodick Nichol E 
Published: January 2023

Abstract
Natural antibodies are primarily produced by B-1a cells and are essential for protection against Streptococcus pneumoniae. The incidence and mortality rate for pneumococcal infection increases dramatically after age 65, disproportionately affecting males in both human and murine systems. To date, there is a significant gap in our understanding of the relationship among sex, aging, natural IgM efficacy, and IgM repertoire. Our investigation demonstrates the protective capacity of serum IgM against pneumococcal infection is maintained in IgM obtained from aged female mice but absent in IgM from aged male mice. To understand this difference in protective capacity, we examined serum immunoglobulin, discovering that the protective change was not associated with shifts in levels of phosphorylcholine (PC) nor PPS3-specific IgM. Interestingly, we observed aged females have an increase in the total number of B-1a cells, higher serum IL-5 levels, and a larger percentage of aged female B-1a cells expressed CD86 as compared to aged males. Furthermore, single-cell IgM repertoire analysis from peritoneal and splenic PC+ B-1a cell subsets demonstrated greater diversity with age and a higher level of germline status in female mice than previously observed in studies of aged male mice. Aged female B-1a cells also expressed higher levels of transcripts associated with cell activity and self-renewal, such as Nanog and Hmga2. Together, these data indicate females maintain a more diverse and active B-1a cell pool and natural IgM repertoire, which has implications for sex-related susceptibility to infection and disease.
Supported by grants from NIH NIAID (R01AI154539)
Single-cell TCR and mRNA sequencing of antigen-specific T cells reveal spatial trajectories from single time points with HLA and VDJ bias
Authors: Andersen Anna Halling Folkmar , Schleimann Mariane Høgsbjerg , Rosas-Umbert Miriam , Olesen Rikke , Gunst Jesper Damsgaard , Krogsgaard Michelle , Tolstrup Martin 
Published: January 2023

Abstract
Yellow fever (YF) vaccination induces massive CD8 expansion, comprising up to 10% of all circulating CD8 T cells. We hypothesize that HLA type and VDJ gene usage implicate the highly biased response towards certain immunodominant epitopes. PBMCs were collected from healthy human donors 3 weeks after vaccination with the yellow fever vaccine, Stamaril, and enriched for YF-CD8 T cells using HLA class I tetramers. We focused on the immunodominant epitopes NS4B and NS2A, and the less dominant epitope NS3. Cells were analyzed by single-cell T cell receptor (TCR) and mRNA sequencing, yielding detailed gene phenotypes for around 2000–3000 quality cells from each donor. Data was analyzed using SeqGeq, VDJ explorer, Seurat and Monocle2. From three donors, we performed in depth analyses on both TCR gene use bias across epitope specificity, and established pseudotime cell trajectories from a single sampling time point. We found that within the CD8 population from the same donor, VDJ usage was highly biased for the target antigen. Based on mRNA expression of a panel of 259 T-cell relevant genes, we performed unsupervised clustering, that shows cells with different epitope targets cluster interchangeably, indicating similar functional patterns. However, cells specific for the immunodominant epitopes had lower TCR clonal divergence between naïve-like and activated clusters, indicating a higher degree of clonal expansion compared to less immunodominant clones. Taken together, we show antigen-driven T cell responses are biased based on donor HLA-types, which could implicate development and success of T-cell driven immunotherapies.
Supported by grants from Independent Research Fund Denmark (1029-00004B)
Enhanced T cell effector function upon differentiation of CD8+ and CD4+ T cells in the presence of BioE-1197 through potential off target ARK family inhibition
Authors: Helms Rachel Shannon , Patel Chirag H , Leone Robert D , Duvall Bridget , Gao Run-Duo , Tsukamoto Takashi , Slusher Barbara S , Pomerantz Joel L , Powell Jonathan D 
Published: January 2023

Abstract
We sought to evaluate PAS domain containing kinase (PASK) inhibition during T cell differentiation using the previously described PASK inhibitor BioE-1197. Notably, CD8+, Th1, and Th2 T cells activated and expanded in the presence of BioE-1197 display elevated lineage specific cytokine production upon restimulation compared to control differentiated T cells, suggesting BioE-1197 may prove to be a powerful means to enhance T cell function. Curiously however, BioE-1197 mediated these effects even in PASK KO T cells suggesting its mechanism of action was independent of PASK. BLAST alignment of the PASK kinase domain revealed members of the AMPK related kinases (ARK) family as potential targets of BioE-1197. ARKs phosphorylate class IIa histone deacetylases (HDACs) in response to activation. To assess whether BioE-1197 inhibits ARK family member activity, we activated and expanded CD8+ T cells with or without BioE-1197. Control differentiated CD8s show elevated phosphorylated and total HDAC7 over time after activation. However, BioE-1197 differentiated cells do not exhibit elevated phosphorylation or total expression of HDAC7 after activation. Concurrent reduction of phosphorylation and total HDAC7 is a phenotype previously reported in cells treated with ARK family kinase inhibitors, suggesting BioE-1197 may be functioning to inhibit an ARK family member(s). Ongoing work aims to definitively demonstrate that the ability of BioE-1197 to enhance effector function is via inhibition of ARK family members and the subsequent regulation of HDAC7. Overall these studies identify BioE-1197 as a novel agent to enhance effector T cell function and suggests potential utility in tumor immunotherapy and enhancing vaccine efficacy.
Supported by grants from NIH (P41EB028239-03, R01AI077610-10) and the Bloomberg-Kimmel Institute for Cancer Immunotherapy.
Immune requirements for protection during secondary Plasmodium infection
Authors: Fontana Mary F , Pepper Marion 
Published: January 2023

Abstract
Malaria, caused by Plasmodium parasites, is one of the top infectious killers of children worldwide. Decades-long efforts to develop a vaccine have so far resulted in a single licensed vaccine with modest efficacy; a better understanding of naturally acquired protective mechanisms could lead to improved vaccine design. Previous work in humans and animal models has identified roles for B cells, CD4+ T cells, and phagocytes in clearance of a primary or established infection, but we still lack a clear understanding of which immune factors are required to restrict Plasmodium from replicating in previously exposed, immune hosts. In this study, we tested whether various immune effectors were required to limit parasitemia in immune mice experiencing a second infection with the rodent-adapted strain P. chabaudi. We found that phagocytes and circulating antibody were critical for homologous secondary protection, whereas B cells were dispensable. CD4+ T cells were also required for full protection, indicating that they continue to play an important role even after antibody responses are established. We speculate that memory B cells may be important for protection from heterologous parasite strains, a hypothesis that remains to be tested. This study underlines the need for a vaccine to induce multiple immune axes in order to confer protective immunity from malaria.
Gut-derived vaginal microbiota protects female reproductive organ from viral infection through pseudonormoxia of immune cells
Authors: Park Jang Hyun , Lee Heung Kyu 
Published: January 2023

Abstract
The detrimental role of obesity in various diseases, including metabolic, cardiovascular, autoimmune, infectious, and cancerous diseases, has been known for many years. Conversely, a phenomenon wherein obesity exerts a positive effect in certain conditions has recently been discovered, and this is known as the obesity paradox. However, the obesity paradox remains controversial, and the underlying mechanisms are still not clear. In particular, a possible role for obesity in response to viral infection has not been fully elucidated. In this study, we investigated a case of the obesity paradox in vaginal herpes simplex virus 2 (HSV-2) infection and uncovered the mechanisms whereby obesity protects from vaginal HSV-2 infection by inducing vaginal dysbiosis. Critically, these obesity-related vaginal microbiota produce L-arginine, which promotes γδ T cell immunity that enhances early protection against HSV-2 infection. This study reveals that obesity-induced translocation of gut microbiota to vagina potentiates anti-HSV-2 immunity via reprogramming of γδ T cell metabolism which provides novel insight for development of anti-HSV-2 drugs and understanding the role of microbiota, antiviral γδ T cell immunity, and mechanisms of obesity paradox.
Supported by the National Research Foundation of Korea grant NRF-2019R1A2C208749013
The microbiome enhances transcriptional inflammatory signatures and delays clinical resolution in cutaneous leishmaniasis
Authors: Amorim Camila Farias , Lovins Victoria , Novais Fernanda O , Harris Jordan , Carvalho Lucas , Carvalho Edgar M , Beiting Daniel P , Grice Elizabeth , Scott Phillip A 
Published: January 2023

Abstract
Cutaneous leishmaniasis (CL) is a protozoal infection in which the immune response plays a major role in lesion development. The activation of local responses such as cytolysis by CD8+ T cells and release of IL-1β by myeloid cells is associated with poor clinical outcome in patients. We found that lesions from cutaneous leishmaniasis patients also exhibit a bacterial dysbiosis, but whether this dysbiosis affects immune responses and consequently impacts chemotherapy to heal the patients is unknown. We carried out an integrative multi-omics analysis of 64 patients, including RNA-seq and 16S-seq from lesion biopsies and clinical metadata. Staphylococcus was the dominant overrepresented genus in lesions from most patients, so we generated an in-house S. aureus pangenome to quantify transcript abundances through dual RNA-seq mapping analysis. Increased overall bacterial burden assessed by qPCR and the presence of S. aureus assessed by dual RNA-seq indicated enrichment for cytokines (e.g., IL1B), inflammatory responses (e.g., PTGS2), and chemotaxis (e.g., CXCL8) by Gene Ontology analysis. Of particular importance, we found that lesions with increased S. aureus transcript abundances exhibited high expression of inflammatory-related genes that have been associated with treatment failure, such as PRF1, GNLY, and GZMB. Correspondingly, we found that patients with a Staphylococcus spp. dysbiosis exhibited a delay in resolving their lesions following treatment. These results indicate that the microbiome influences the local immune responses in CL, affecting how patients respond to therapy by delaying the healing time. These results suggest that the use of antibiotics combined with chemotherapy may improve treatment outcome for CL.
Supported by grant from NIH (R01 AI149456)
Contribution of PU.1 and STAT6 to fibrosis-mediated growth suppression of the Diphyllobothriidae family cestode, Schistocephalus solidus.
Authors: Steinel Natalie C , Weber Jesse , Peng Foen , Shim Kum Chuan , Lohman Brian , Fuess Lauren , De Lise Stephen , Bolnick Daniel I 
Published: January 2023

Abstract
Threespine stickleback (Gasterosteus aculeatus) fish are naturally infected with the Diphyllobothriidae family tapeworm, Schistocephalus solidus. The anti-parasite response to this body cavity infection varies greatly among wild stickleback populations. Some populations generate extensive peritoneal fibrosis which suppresses cestode grown, thereby preventing the parasite from reaching sexual maturity and blocking its ability to infect its terminal host. In extreme cases this response can encapsulate the cestode. On the other hand, other fish populations tolerate S. solidus, carry heavy parasite burdens, grow parasites 34-fold larger than resistant fish, and do not produce fibrosis. Combined genetic mapping and population genomics identified regions of the genome associated with this resistance-tolerance axis. Quantitative trait loci (QTL) mapping of the fibrosis phenotype led us to a 78bp deletion in SPI1b which encodes the transcription factor PU.1 which is associated with the initiation of tissue fibrosis. This deletion was fixed in tolerant fish, but not resistant fish. SPI1b expression increases with infection and is higher in fibrotic fish compared to non-fibrotic controls. QTL mapping of cestode mass detected STAT6 on Ch 12, which is associated with alternatively activated macrophages and fibrosis. In tolerant fish, but not resistant, a deletion in stat6 exon 5 is nearly fixed. Several additional QTL were also found containing genes associated with fibrosis initiation or regulation, evidence for strong selection on this anti-parasite mechanism and identifying pathways involved in the regulation of a pathologic fibrotic response against a Diphyllobothriidae cestode.
Malaria antigens are presented to CD8 T cells via the non-classical HLA-E
Authors: Wilder Brandon Keith , de Lacerda Luna , Barbosa Camila R R , Aleshnick Maya , Martinson Thomas , Morrow David , Zhao Zeshou , Gaiha Gaurav , Junqueira Caroline 
Published: January 2023

Abstract
CD8 T cells have long been known to target infected hepatocytes during the intracellular liver stages of Plasmodium—the causative agent of malaria. Current T cell vaccine strategies are limited by the inability to obtain sufficient amounts of Plasmodium-infected hepatocytes to identify peptides presented on MHC-I (“immunopeptidomics”). Recently, we demonstrated that the blood stages of Plasmodium vivax are also susceptible to CD8 T cell killing and performed immunopeptidomics on Pv-infected reticulocytes. Peptides mapped to proteins conserved across Plasmodium spp. and were common across volunteers. Furthermore, ~50% of the peptides detected are not predicted to bind classical HLA-I molecules and thus could be presented by non-classical HLA. In support of this, blocking HLA-E during in vitro stimulation of PBMCs with a pool of newly-identified peptides substantially reduced the CD8 T cell response. Mechanistic studies conducted in the rhesus macaque/P. cynomolgi malaria model demonstrated that CD8 T cell killing of infected reticulocytes is conserved in this model as are CD8 responses to the newly identified peptides. In vitrostimulation assays showed that CD8 T cell responses to at least 3 of 9 peptides tested are completely restricted to MHC-E. This is supported by in vitro binding assays showing peptide binding to HLA-E. In summary, we demonstrate for the first time that malaria infection induces HLA/MHC-E-restricted CD8 T cell responses to newly identified peptides that are conserved across host and parasite species. Given the extreme conservation of MHC-E, these results pave the way to explore a universal, species-transcending vaccine for malaria based on MHC-E presentation of novel antigens.
Hypoxia promotes cytolytic activity of CD8 T cells and pathogenesis in cutaneous leishmaniasis
Authors: Fowler Erin , Novais Fernanda O 
Published: January 2023

Abstract
Leishmaniasis is a disease caused by protozoan parasites of the genus Leishmania and the most common form of the disease is cutaneous leishmaniasis (CL). A fundamental question in CL is what regulates the development of severe disease, information that is critical to develop therapies to ameliorate disease. In a series of studies, we demonstrated CD8 T cell-dependent cytotoxicity as the main inducer of immunopathology in CL. This result was unexpected since IFN-γ production by CD8 T cells plays a protective role by promoting pathogen elimination. To resolve this paradox, we studied the CD8 T cells in different anatomic sites and found that the effector function of CD8 T cells in CL depends on their location: while CD8 T cells are cytotoxic (GzmB+) and produce little IFN-γ in leishmania lesions, CD8 T cells in the draining lymph nodes (dLN) have the opposite profile. Importantly, GzmB− CD8 T cells from dLN quickly upregulate GzmB after injection into CL lesions. By transcriptional profiling, we found that CD8 T cells in lesions and not dLN have a hypoxic signature. In vivo, we observed that leishmania lesions are hypoxic using the Oxyphor G4 oxygen probe and pimonidazole staining. In vitro, we found that induction of hypoxia was sufficient to convert GzmB− into GzmB+ CD8 T cells. In vivo, blocking the dimerization of HIF-α, a master regulator of hypoxia, with acriflavine decreased lesion development in mice. Transcriptional profiling in patients showed that hypoxia is a signature of human CL and correlates with GZMB expression. Together, our results suggest that the hypoxic microenvironment of leishmania lesions alter the function of CD8 T cells and convert protective CD8 T cells into pathogenic cytotoxic T cells.
Supported by Host Defense and Microbial Biology (OSU)
Small Intestine Epithelial CD4 Cytotoxic T Lymphocytes Provide Innate-Like Protection against Enteric Pathogens without Risk of Immunopathology
Authors: Chen Angeline , Thiault Nicolas , Iwaya Hitoshi , Cheroutre Hilde 
Published: January 2023

Abstract
CD4 T helper (Th) cells reprogram to cytotoxic T lymphocytes (CTLs) in the small intestinal epithelium. In the present study, CD4 CTLs were evaluated for their potential to promote tolerance during steady state as well as their ability to fend off enteric pathogens during infection.
The CD4 T cell adoptive transfer model of colitis was used to determine if CTLs can promote tolerance. Naïve CD4 T cells were differentiated towards a CTL, Treg, or inflammatory Th (Th1 or Th17) fate and transferred into RagKO recipients. Strikingly, the recipients that received CTLs, like the Treg condition, had minimal disease; in contrast, the Th conditions all exhibited pathology. To determine if the forced presence of Th cells exacerbates colitis disease, CD4 T cell adoptive transfers were performed using cells that were forced to stay Th or predisposed to becoming CTLs. Altogether, the conversion of Th to CTL mitigated disease pathology and promoted tolerogenic conditions.
The protective role of CD4 CTLs to rapidly respond to enteric pathogens and contain infections was also examined. Using Salmonella as a bacterial model, the data show that pre-existing CD4 CTLs have the capacity to kill infected cells, thereby preserving the integrity of the barrier and preventing bacterial dissemination. Functionally, CD4 CTLs represent a strategy of protective tolerance by the immune system to fortify the epithelium with quiescent but primed CTLs that can provide rapid immunity during enteric infection.
Supported by grants from the NIH (U01 AI125957, F31 DK124078)
Gene signatures for intestinal and peripheral innate lymphoid cells in pigs reveal tissue-specific imprinting and similarities to human cells via single-cell RNA sequencing
Authors: Wiarda Jayne E , Trachsel Julian M , Sivasankaran Sathesh K , Tuggle Christopher K , Loving Crystal L 
Published: January 2023

Abstract
Intestinal innate lymphoid cells (iILCs) impact intestinal health outcomes, but study of iILCs in humans is limited. Human peripheral ILCs (pILCs) are easily obtained but may vary substantially from iILCs, thus requiring comparison of iILCs and pILCs to determine applicability of pILCs as surrogates to study iILC function. Pigs have anatomic, physiological, nutritional, and immune similarities to humans that are lacking in rodent models, making pigs a relevant biomedical model; however, ILCs are poorly defined in pigs. Single-cell RNA sequencing was performed to compare porcine iILCs to pILCs and determine potential similarities of porcine to human ILCs. Porcine pILCs matched porcine natural killer (NK) cell descriptions, while iILCs were annotated as group 1 and group 3 ILCs. Gene modules obtained independent of cell annotations were distilled to core signatures of genes most highly specific to pILCs, pan-iILCs, group 1 iILCs, and group 3 iILCs. The pILC signature included conventional NK cell genes, while the group 3 iILC signature included genes associated with type 3 immunity. Pan-iILC and group 1 iILC signatures included genes associated with tissue residency, cell activation, and metabolism, indicating tissue-specific, activation-associated imprinting. Gene profiles were used to develop in situ iILC detection methods, establishing group 1 iILCs were intraepithelial, while group 3 iILCs resided in lamina propria/gut-associated lymphoid tissue. Findings indicated iILCs were ILC subsets distinct from pILCs, thus opposing pILCs as surrogates to study iILC dynamics. Moreover, gene profiles and in situ locations of iILCs drew close parallels to human iILCs functions, supporting pigs as a biomedical model for iILC research.
Research was supported by appropriated funds from USDA-ARS CRIS 5030-31320-004-00D, an appointment to the Agricultural Research Service (ARS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA). ORISE is managed by ORAU under DOE contract number DE-SC0014664. All opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of USDA, ARS, DOE, or ORAU/ORISE. This research used resources provided by the SCINet project of the USDA ARS project number 0500-00093-001-00-D.
Microbially-induced exosomes in dendritic cells promote paracrine immunosenescence: Novel mechanism of inflammatory alveolar bone loss in mice
Authors: Elsayed Ranya M , Elashiry Mahmoud , Cutler Christopher W 
Published: January 2023

Abstract
Periodontitis (PD) is a chronic inflammatory disease of aging or inflammaging that affects 70.1% of Americans 65 years and older. Age related immunosenescence is implicated in chronic inflammation and impaired immune surveillance, but role in PD is unclear. The aim of this study was to determine cellular mechanisms of immunosenescence in PD in-vivo. Variables including age, bacterial infection with key stone oral pathogen, Porphyromonas gingivalis (Pg), and senolytic agent rapamycin (Rap) were assessed for influence on ligature accelerated PD in young (2–3 mo) and old (24 mo) B6 mice (n=30). Senescence profiling of gingiva and lymph node (LN) was performed by confocal microscopy, flow cytometry and qPCR. Increased SA-BGal, p16INK4A, p21Waf1/Clip1, CD57+ CD28− T cell, Th17/Treg ratio and IL6/TNFa/IL1b were observed in DCs and T cells in gingiva and/or LN as a function of advanced age, or exposure of young mice to Pg gavage. This was associated with a significant increase in bone loss shown by micro CT 3D analysis which was abrogated by Rap. In-vitro analysis revealed a~2-fold increase in secreted exosomes from DCs infected with Pg (PgDCexo). These exosomes were enriched in age-related, anti-apoptosis/anti-autophagy miRNAs, Pg fimbrial adhesin protein mfa1, and IL6/TNFa/IL1b. PgDCexo were injected intragingivally in young mice promoting a premature senescence profile in the gingiva and LN and inflammatory bone loss compared to exosomes from uninfected DCs. We conclude that advanced age and microbially-induced immunosenescence contribute to the pathogenesis of inflammatory bone loss in mice which can be inhibited by rapamycin. P. gingivalis-induced exosomes in dendritic cells promote paracrine senescence of normal bystander cells.