bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold-induced stress impairs the production of Th1 protective cytokines during co-culturing of dendritic cells and naïve T helper cells of Chlamydia muridarum infected mice.
Authors: Belay Tesfaye 
Published: January 2023

Abstract
The purpose of this study was to determine how cold-induced stress affects the maturing of mouse bone marrow-derived dendritic cells (BMDCs) and to see the dynamics of cytokines production associated with T helper subtypes. Quantitative real time PCR and ELISA were used to measure gene expression and production of cytokines in co-culture of BMDC and Naïve CD4+ T cells. Culturing BMDC in vitro stimulated with LPS in the presence of norepinephrine (NE) or Feroterol, β-AR agonist resulted in a marked increase (75 pg/ml) of IL-10 compared to that of stressed mice. Treatment with β-AR antagonist, ICI 118,551 resulted in lowering production of IL-10 in BMDC of nonstressed (control) mice. In contrast, IL-12 production in stressed group was significantly low (132 vs 239 pg/ml) compared to that of control mice. Naïve T cells co-cultured with BMDC pretreated with NE or Feroterol showed decreased IL-12 production compared to controls. In contrast IL-4 production was increased with pretreatment of NE or Feroterol (64 vs 28 pg/ml) compared to control group. Increased IL-4 production in the genital tracks of mice compared to control (114 vs 0 pg/ml) was observed. The relative expression of GTAT 3 in T cells co-cultured with BMDC of stressed mice was high (2.8 vs 0.49) compared to control mice. The same gene expression trend of IL-4 in stressed mice group (1.8 versus 0.12) compared to control group was observed. In control mice, T-bet expression was (1.78 vs 1.0) and interferon gamma (2.12 versus 1.0) compared to that of stressed mice group. Our results demonstrate that stress influences the activation and differentiation of DCs stimulated by LPS shifting the Th1/Th2 ratio and impairing the production of Th1 protective cytokines during Chlamydia muridarum infection.
T-independent IFNγ and B cells synergize to prevent mortality associated with disseminated Chlamydia muridarum genital infection
Authors: Poston Taylor , O’Connell Catherine , Girardi Jenna , Sullivan Jeanne E. , Nagarajan Uma , Marinov Anthony , Scurlock Amy , Darville Toni 
Published: January 2023

Abstract
CD4 T cells and antibody are required for optimal acquired immunity to C. muridarum genital tract infection, and T cell-mediated IFNγ production is necessary to clear infection in the absence of humoral immunity. However, the role of protective T cell-independent immune responses against primary infection remain unclear. We addressed this problem by inoculating wild-type and immune-deficient mice with a plaque-purified strain (CM001) isolated from C. muridarum Nigg stock capable of enhanced extragenital replication. Genital CM001 inoculation resulted in transient dissemination to the lungs and spleen in wild-type mice prior to clearance. However, CM001 genital infection induced lethality in STAT1−/− and IFNG−/− mice, where IFNγ signaling is absent, and in Rag1−/− mice that lack T and B cells but are competent for innate IFNγ signaling. In contrast, muMT, nude, and Tcra−/− mice survived. These data collectively indicate that IFNγ prevents lethal CM001 infection in the absence of T cells and suggest a B cell co-requirement for protection. Adoptive transfer of convalescent immune sera, but not naïve IgM antibody, to Rag1−/− mice significantly increased survival time and transfer of naïve B cells completely rescued Rag1−/− mice against CM001 lethality. Protection was associated with a significant reduction in the lung chlamydial burden of genitally infected mice. These data reveal an important synergism between T-independent B cell responses and innate IFNγ in chlamydial host defense, and suggest cooperative interactions between T-independent IgG and IFNγ are essential for limiting extragenital dissemination.
Staphylococcus aureus colonization is influenced by cutaneous interferon production.
Authors: Sirobhushanam Sirisha , Parsa Navya , Sarkar Mrinal K. , Gudjonsson Johann E. , Kahlenberg Joann Michelle 
Published: January 2023

Abstract
Cutaneous inflammation is a recurrent manifestation of systemic lupus erythematosus (SLE), a severe autoimmune disease, and is triggered upon exposure to ultraviolet B (UVB) light. The exaggerated inflammatory response of SLE epidermis to UVB exposure is thought to be, in part, secondary to chronic exposure to type I interferons (IFN). S. aureus colonization has been found to stimulate cutaneous IFN. Indeed, our analysis of 54 SLE patients swabbed on their chest, nares and any active lesions demonstrated colonization of SLE patients at twice the rate (61%) of normal adult population (~30%). The rate increased further (67%) when active cutaneous lesions were sampled. We have also identified differences in expression of cutaneous IFN production in SLE patients, in particular IFNκ, and thus sought to investigate the role of IFNs in S. aureus adhesion to better define their impact on colonization. Immortalized keratinocytes (NTERTs), were grown to confluence, exposed to 20 mJ/cm2 UVB (310 nm) and 24hrs later exposed to ~107 cells of S. aureus. Following washing, the number of adherent cells were then determined by serial dilution and plating. Our results show that treatment with UVB increased S. aureus adhesion to WT-NTERTs. An increase in adhesion was observed in treatment of WT-NTERTs with 5ng/ml IFNα for 24 hours as well. NTERTs lacking IFNκ (IFNκ KO) unlike WT NTERTs exhibited lower S. aureus adhesion after UVB exposure which was reversed when functional IFNκ was added to growth media. These results suggest that increased IFN production in SLE skin may contribute to enhanced S. aureus colonization in these patients. The impact of S. aureus colonization on SLE skin remains to be determined.
Anatomically remote education of B cells is required for colonic health
Authors: Surana Neil , Kasper Dennis L. 
Published: January 2023

Abstract
Mucosa-associated lymphoid tissues contain roughly 80% of all immune cells and produce virtually all of the body’s IgA. Although the majority of IgA-secreting cells educated within a mucosal site home back to the same anatomic region, some cells are also found in distant mucosal tissues. These observations underlie the notion of a common mucosal immune system, which holds that anatomically unrelated mucosal sites are functionally connected by a shared immune system. However, the ontological basis of this separation between site of immune education and functionality has remained elusive. Here we show that mice lacking Peyer’s patches (PPs)—small-intestinal lymphoid tissue covered by antigen-sampling M cells—have no immunologic defect in the small-intestinal lamina propria. Surprisingly, the primary immunological abnormality in PP-deficient mice was a reduction in colonic B cells, including plasmablasts but not plasma cells. Adoptive transfer experiments conclusively demonstrated that PP-derived cells preferentially give rise to colonic—but not small-intestinal—B cells and plasmablasts. Finally, these PP-derived colonic B cells were critical for restraining colonic inflammation. Thus, PPs bridge the small-intestinal and colonic immune systems and provide a clear example of immune education being required in an anatomic compartment distinct from the effector site. Our findings, which highlight that the majority of fecal IgA is produced by colonic plasmablasts that originate from PPs, will help inform design of mucosal vaccines.
B cell-intrinsic epigenetic modulation of local and systemic antibody response by gut microbiota through catabolic short-chain fatty acids
Authors: Sanchez Helia N. , Gan Huoqun , Moroney Justin B. , Daw Cassidy C. , Taylor Julia , Zan Hong , Casali Paolo 
Published: January 2023

Abstract
Immunoglobulin class switch DNA recombination (CSR) and somatic hypermutation (SHM), as initiated by AID, and plasma cell differentiation, as mediated by Blimp-1, are critical for the maturation of the antibody response. This, as we have suggested, can be modulated by epigenetic modifications arising from environmental factors, such as the gut microbiota. Here we show that the gut microbiota regulates host immune responses through the production of metabolites such as short chain fatty acids (SCFAs). Butyrate and propionate are two of the major metabolic products generated by gut microbiota through processing of dietary fibers. They effectively dampened local and systemic IgG, IgA and IgE responses through B cell-intrinsic modulation of Aicda and Prdm1 gene expression, and, therefore, CSR/SHM and plasma cell differentiation. This SCFA-mediated reduction of class-switched B cells and plasma cells in PP, MLNs and the spleen curtailed the antibody response to T-dependent and T-independent antigens. It also virtually abrogated the allergic IgE responses to house dust mite and peanut as well as the lupus IgG autoantibody response. Mice fed fiber-free diets showed reduced levels of gut SCFAs and increased titers of serum IgG, IgA, and IgE, which were reversed by the administration of exogenous butyrate and propionate. SCFA-mediated modulation of B cell was not due to their G-protein coupled receptor signaling or their use as an energy source. Rather, it resulted from their HDAC inhibitory activity, which upregulated select miRNAs silencing Aicda and Prdm1 mRNAs. Thus, the gut microbiota modulates B cell differentiation and antibody responses through B cell-intrinsic epigenetic regulation, by fiber processing metabolic products.
Absence of B Cell Function Impairs Protective Mucosal Immunity to Brucellosis
Authors: Goodwin Zakia I. , Clapp Beata , Yang Xinghong , Hoffman Carol , Pascual David 
Published: January 2023

Abstract
Mucosal vaccination with a live attenuated B. melitensis double-mutant (BMDM) confers sterilizing protection against pulmonary challenge with wild-type (wt) BM 16M. Although T cell-dependent immunity is essential for protection, we queried the role of B cells in this response. We hypothesized that B cells enable BMDM to persist in the lungs for stimulation of robust adaptive responses. Using BALB/c B cell-deficient (μMT) mice, early and long-term immunity subsequent mucosal vaccination was examined. Groups of BALB/c and μMT mice were orally primed, nasally boosted, and 4 wks later, splenic and lung lymphocytes were antigen-pulsed to determine cytokine responses. μMT mice showed significantly reduced pulmonary proinflammatory responses by three-fold relative to BALB/c mice. Nasal challenge with wt BM 16M of BMDM-vaccinated mice resulted in impaired protective immunity in μMT mice evidenced by the significantly increased brucellae colonization of lungs and spleens. To determine the types of myeloid cells involved in brucellae recognition, μMT mice nasally vaccinated with a mCherry variant of BMDM showed a 23-fold reduction in lung mCherry expression relative to similarly vaccinated BALB/c mice at 5 days post-immunization. mCherry expression associated with various myeloid and B cells. Interestingly, although antigen-presenting cells (APCs) increased similarly in both groups of mice, mCherry expression in lung neutrophils and monocyte-derived macrophages in BALB/c mice was 23- and 4-fold enhanced, respectively, to μMT mice. We believe B cell retention of BMDM mutant enhances APC activity within the lungs facilitating the development of potent local T cell responses. Work supported by NIH R01 AI123244 and AI124244-03S1.
Lactobacillus reuteri induces gut intraepithelial CD4+CD8αα+ T cells
Authors: barragan LUISA CERVANTES , Chai Jiani , Tianero Ma Diarey , Di Luccia Blanda , Ahern Philip , Merriman Joseph , Cortez Victor S. , Caparon Michael G. , Donia Mohamed S. , Gilfillan Susan , Cella Marina , Gordon Jeffrey , Hsieh Chyi Song , Colonna Marco 
Published: January 2023

Abstract
The small intestine contains CD4+CD8αα+ double-positive intraepithelial T lymphocytes (DP IELs), which originate from intestinal CD4+T cells through downregulation of the transcription factor ThpoK and have regulatory functions. DP IELs are absent in germ-free mice, suggesting that their differentiation depends on microbial factors. We found that DP IEL numbers in mice varied in different vivaria, correlating with the presence of Lactobacillus reuteri. This species induced DP IELs in germ-free mice and conventionally-raised mice lacking these cells. L. reuteri did not shape DP-IEL-TCR repertoire, but generated indol derivatives of tryptophan that activated the aryl-hydrocarbon receptor in CD4+ T cells, allowing ThPOK downregulation and differentiation into DP IELs. Thus, L. reuteri together with a tryptophan-rich diet can reprogram intraepithelial CD4+ T cells into immunoregulatory T cells.
Intracellular pairing of TCRα and TCRβ mRNA at the single-cell level using DNA Origami
Authors: Ulrich Peaches Rebecca , Schoettle Louie , Anderson Karen S. , Blattman Joseph 
Published: January 2023

Abstract
T cell receptors (TCRαβ) are heterodimeric proteins that recognize MHC:peptide ligands. Coding sequences of TCRαβ is determined by semi-random and imprecise joining of variable, diversity, and joining gene segments. Complementarity determining region 3 (CDR3) spans the joint between these segments and typically makes the most contact with peptide during TCR recognition, largely determining specificity. A problem in identifying TCR from cells for clinical applications has been development of high-throughput methods for obtaining CDR3 sequence information from TCRαβ pairs from individual cells. We developed novel DNA origami nanostructures to simultaneously capture TCRαβ mRNA from single cells. T cells are transfected with the origami, and TCRαβ mRNA are co-captured onto bowtie-integral probes. Individual TCR sequences are then reverse transcribed and appended to origami-specific unique bowtie oligonucleotide barcodes that can be matched in downstream next-generation high-throughput sequencing. We have validated this approach using P14 TCR transgenic T cells, expressing known TCRαβ sequences. Following the synthesis of DNA origami with TCRα and TCRβ capture probes, transfection of P14 CD8+ T cells with the scaffold resulted in the specific capture and amplification of TCR sequences. Validation using Sanger sequencing confirmed capture of barcoded TCRα and TCRβ CDR3 sequences. We have developed an approach to single cell analysis of multiple mRNA species. Using a custom bowtie dual-barcoding system, we captured and re-isolated barcoded TCR sequences from individual cells. Although our focus is on the TCR repertoire, this technology is highly adaptable and can capture sequence information of any two genes of interest.
Autofluorescence Imaging of T cell Activation
Authors: Walsh Alex J. , Mueller Katie , Jones Isabel , Heaster Tiffany M. , Saha Krishanu , Skala Melissa C. 
Published: January 2023

Abstract
T cells can have different activities based on receptor expression and cytokine production. Current methods to classify and assess immune cell behavior include flow cytometry and immunohistochemistry, which require immune cell labeling and tissue fixation. A non-invasive method for determining T cell behavior is needed to study immune cell behaviors in tumors and evaluate novel immunotherapies. Activated T cells require high rates of glycolysis to maintain immune activities. Therefore, we are developing optical metabolic imaging (OMI) to assess the metabolic profile of T cell subtypes and activation states using cells isolated from human blood. OMI probes the fluorescence intensity and lifetime of the metabolic coenzymes NAD(P)H and FAD, to quantitate the redox state of the cell through the optical redox ratio (NAD(P)H fluorescence intensity divided by the sum of NAD(P)H and FAD fluorescence intensity) and co-enzyme binding. Our results show that the optical redox ratio is increased in activated populations of unsorted T cells, and of CD8+ T cells, consistently across four different donors. Single-cell analysis of the unsorted, unactivated T cell populations revealed a small portion of cells in an activated state. Inter-donor heterogeneity highlights the variability of immune responses between patients. These results indicate that OMI is a powerful tool for assessing T cell subtype and behavior. OMI utilizes the autofluorescent properties of NAD(P)H and FAD, and thus is contrast agent free, non-damaging, and requires no genetic manipulation. Therefore, OMI can be used to image T cell interactions with tumors in time-course studies of tumor development or assess the efficacy of immunotherapy.
Analysis of T cells made easy - Complete workflows improve the isolation and analysis of T cells
Authors: Evaristo Cesar , Pitzka Christina , Siemer Ramona , Foerster-Marniok Anna , Gotot Janine , Dose Christian , Richter Anne 
Published: January 2023

Abstract
T cells play a central role in immunity to pathogens and tumors, but also in autoimmunity. T cell research has generated knowledge that led to multiple clinical breakthroughs, such as the generation of T cell vaccines and tumor immunotherapy approaches. However, additional work is required to fully understand T cell biology, harness their therapeutic potential and control immunopathologies. Cutting edge experimental protocols that interrogate and manipulate T cell biology often require prior purification of T cell populations. Strategies to simplify and accelerate T cell purification are highly desirable to save time, reduce bias and allow complex experiments to be performed.
We established workflows combining automated tissue dissociation with T cell isolation. We developed new CD4, and CD8 T cell specific enrichment reagents that significantly accelerated the isolation protocol. T cells were isolated to purities above 90%, reducing time of downstream analysis. Importantly, culture of isolated T cells did not induce activation as measured by CD69 or CD25 upregulation, as compared to controls. Furthermore, magnetic isolation did not affect proliferation or cytokine expression following in vitro stimulation. Finally, T cell isolation could be fully automated and multiple samples could be processed in parallel.
Our new workflow greatly reduces time of downstream analysis while preserving cell phenotype and functional properties. We believe these innovative tools significantly shorten time-consuming experiments and can be used to increase reproducibility and the quality of data obtained in T cell research.
Effect of MHC clustering on antigen recognition and T cell responses
Authors: Anikeeva Nadia , Fisher Nicholas , Blanchette Craig , Sykulev Yuri 
Published: January 2023

Abstract
MHC proteins that present peptide ligands to T cells form nano-scale clusters on the cell membrane of antigen-presenting cells. While MHC clustering is thought to influence antigen presentation to T cells and may depend on cell type and pathophysiological conditions, how the extent of MHC clustering controls productive TCR engagement and T cell responses has not been systematically studied. To evaluate the effect of MHC clustering on T cell responses, we utilized nano-scale discoidal membrane mimetics to capture and present pMHC ligands at various densities. We examined the binding parameters of these model membrane clusters interacting with live CD8+ T cells and their impact on the triggering of TCR signaling. Our data show that not just the level of expression of pMHC ligands but the extent of their clustering controls antigen recognition and responses by T cells. Variations in the density of pMHC with MHC clusters regulate CD8-MHC and TCR-pMHC interactions, each contributing in a unique way to antigen recognition and the quality of TCR-mediated signaling. Along with well-documented co-clustering of TCR and CD8 on activated, but not naïve T cells, these findings provide new understanding of how the immune receptor clustering controls the specificity and effectiveness of antigen-specific responses by naïve and activated T cells during acute and chronic viral infection.
Utilizing the Multi-parameter Capability of the ZE5 to Monitor T-Cell Exhaustion Following Immunotherapy.
Authors: Green Angela M. , Brampton Chris , Alexander Matt , Talaga Yasha , Jordon Eliabeth 
Published: January 2023

Abstract
The immune systems as evolved sophisticated mechanisms to distinguish between self and non-self, and dangerous and non-dangerous signals leading to appropriate and controlled immune responses against infection and cancer or tolerance to avoid attacking the host body. One pathway of immune suppression is T-cell exhaustion which shuts down effector T-cells. T-cells or T-lymphocytes, are an immune cell that help protect the body from infection and fight cancer. T-cell exhaustion is exploited by chronic viral infections and cancers to escape being targeted by the immune system. It results in a sustained expression of suppressive cell surface markers and effector function in these cells, meaning they are no longer able to function to remove the cancerous and infected cells.
Recently, researchers have focused on using monoclonal antibody drugs to block these suppressive cell surface markers and re-invigorate the T-cells, restoring their effector capability to clear viral infection and cancer cells from the body.
In this study, we use a 15-parameter panel to examine in-depth changes to the T-cell phenotype, exhaustion and cellular subset identity markers before and after chronic stimulation and in combination with a monoclonal antibody drug treatment targeting the receptor Programmed Cell Death 1 (PD-1).
Comprehensive assessment of immune cells in mouse and human atherosclerosis by single cell RNA sequencing and mass cytometry
Authors: Winkels Holger , Ehinger Erik , Vassallo Melanie , Buscher Konrad , Dinh Huy , Kobiyama Kouji , Hamers Anouk , Cochain Clement , Vafadarnejad Ehsan , Saliba Antoine Emmanuel , Zernecke Alma , Bala Pramod Akula , Ghosh Amlan , Michel Nathaly Anto , Hoppe Natalie , Hilgendorf Ingo , Zirlik Andreas , Hedrick Catherine , Ley Klaus , Wolf Dennis 
Published: January 2023

Abstract
Atherosclerosis, an inflammatory disease of large arteries, is – through its clinical manifestations stroke and myocardial infarction – globally the leading cause of morbidity and mortality. Although cells of the innate and adaptive immune system are found in atherosclerotic plaques, their phenotypic and functional diversity is poorly understood. Here, we applied single cell RNA-sequencing (scRNAseq) and mass cytometry (CyTOF) to assess leukocyte diversity in depth, thus defining an immune cell atlas in atherosclerosis.
Single cell transcriptional profiling of aortic leukocytes from 20-week old chow (CD) and western diet (WD) fed Apoe−/− and Ldlr−/− mice revealed 11 phenotypically different leukocyte clusters, whilst WD changed their abundance. Gene set enrichment analysis of single cells established that multiple pathways, e.g. for lipid metabolism or cytokine secretion, pertained to particular leukocyte clusters. Applying a novel 35-marker CyTOF panel confirmed the phenotypic diversity of aortic leukocytes. Among lymphocytes, we detected three principal B-cell subsets defined by scRNAseq, CyTOF, and flow cytometry. These B cell subsets harbor distinct surface marker expression, functional gene pathways, and ex vivo cytokine production. Finally, we used leukocyte cluster gene signatures to assess leukocyte frequencies in 121 human plaques by a transcriptomic deconvolution strategy revealing similar immune cell complexity.
The definition of leukocyte diversity by high-dimensional analyses enables a fine-grained analysis of aortic leukocyte subsets, reveals new immunological mechanisms and cell-type specific pathways, and may result in novel diagnostic risk stratification tools.