bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of TCR signaling by CD2AP in CD4 T cells modulates antibody responses to chronic LCMV infection
Authors: Raju Saravanan , Shaw Andrey Shin-Yee , Egawa Takeshi 
Published: January 2023

Abstract
CD4 T cell-mediated help to CD8 T cells and B cells is a critical arm of the adaptive immune system required for control of pathogens. CD4 T cells express cytokines and co-stimulatory molecules that support a sustained CD8 T cell response and also enhance generation of protective antibody by germinal center B cells. However, the molecular components that regulate CD4 T cell functions in response to viral infection or vaccine is incompletely understood. Here we demonstrate that inactivation of the signaling adaptor CD2AP promotes CD4 T cell differentiation towards the follicular helper lineage, leading to enhanced control of viral infection by augmented germinal center response in chronic LCMV infection. The enhanced follicular helper differentiation is associated with extended duration of TCR signaling and enhanced cytokine production of CD2AP-deficient CD4 T cells specifically under TH1 conditions, while neither prolonged TCR signaling nor enhanced follicular helper differentiation was observed under conditions that induce other helper effector subsets. These results suggest that tuning of TCR signaling by targeting CD2AP improved protective antibody responses in viral infection.
Identification of a T cell immunomodulatory domain in histidyl-tRNA synthetase
Authors: Mertsching Elisabeth C. , Ampudia Jeanette , Adams Ryan , Rosengren Sanna , Nangle Leslie , Mendlein John , Cubitt Andrea , Ramsdell Fred , Ogilvie Kathy , King David 
Published: January 2023

Abstract
Histidyl-tRNA synthetase (HARS) is the autoantigen target of Jo-1 antibodies, which occur in the major form of anti-synthetase syndrome. These patients are characterized by an autoimmune myositis and interstitial lung disease. Circulating extracellular HARS is detected in healthy individuals, but is reduced or undetectable in Jo-1-positive individuals. Administration of ATYR1940, a recombinant form of HARS, ameliorates lung fibrosis and reduces T cell cytokine production in the bleomycin-induced lung injury model. Similar effects were observed with the N-terminal domain of HARS (the iMod domain) conjugated to IgG Fc, suggesting that this domain confers the immunomodulatory activity of HARS.
To confirm primary immune effects of ATYR1940 and ATYR1923 (iMod.Fc), human T cells were isolated from PBMC from healthy individuals and stimulated with anti-CD3/anti-CD28. Proteins containing the HARS iMod domain reduced in vitro activation of human CD4+ and CD8+ T cells, as evidenced by reduced secretion of IL-2, IFNγ, TNFα, IL-17, IL-13, and granzyme B, as well as decreased upregulation of activation markers such as CD69 and CD40L. ATYR1940 and ATYR1923 also inhibited cytokine release after ex vivo stimulation of human memory T cells in a NSG mouse xenogeneic GVHD model. T cell inhibition by ATYR1940 was dependent on its iMod domain, as demonstrated using an iMod-specific blocking monoclonal antibody. The ATYR1940-induced T cell gene signature reflected a general inhibitory effect on activation as well as on cell cycle protein expression. These results suggest that circulating levels of HARS may act to control the threshold stimulatory signal required to activate T cells. We propose circulating HARS as a soluble immune set-point modulator.
GRK2 transactivation of CXCR4 is required for TCR-mediated TCR-CXCR4 complex formation
Authors: Dinkel Brittney A. , Kremer Kimberly N. , Rollins Meagan R. , Medlyn Michael J. , Hedin Karen E. 
Published: January 2023

Abstract
T cell cytokine production was recently shown to depend not only on the T cell antigen receptor (TCR), but also on the chemokine receptor CXCR4. Our lab recently published that stimulation of the TCR results in the TCR associating with and transactivating CXCR4, which, in turn, activates a PREX-1/Rac-1 pathway that stabilizes cytokine mRNA. This pathway therefore normally significantly increases IL-2, IL-4, and IL-10 production by activated T cells. Here, we further characterize the molecular mechanisms responsible for the first step of this pathway: TCR-mediated TCR-CXCR4 complex formation. First, we used FRET and proximity ligation assay (PLA) to define the required structural motifs of CXCR4, showing that this pathway requires the CXCR4 cytoplasmic tail domain and phosphorylation of CXCR4-S339. Second, we showed that TCR-induced TCR-CXCR4 complex formation requires TCR-induced activity of Src family and ZAP-70 tyrosine kinases, as well as one or more Ser/Thre kinases. Third, we found that the G protein-coupled receptor kinase-2 (GRK2) is required both for TCR-induced phosphorylation of CXCR4-S339 and for the formation of TCR-CXCR4 complexes. Finally, we found that GRK2 is required for robust IL-2, IL-4, and IL-10 cytokine secretion by normal human T cells. Together these results identify a novel role for TCR-induced GRK-2 in inducing the TCR-CXCR4 complex formation that subsequently signals to increase TCR-mediated cytokine production. Targeting GRK2 or other mechanisms required for TCR-induced TCR-CXCR4 formation may therefore be therapeutically useful for limiting production of T cell cytokines in humans, for example, during graft versus host disease or immunotherapy.
Improve Your Publications Using Research Resource Identifiers
Authors: Vita Randi J. , Bandrowski A. E. , Grethe J. S. , Martone M. E. 
Published: January 2023

Abstract
Reproducibility was assessed in the scientific literature and the field of immunology did not fare well, as described in Vasilevsky et al 2013. Antibodies and constructs used in immunological publications could not be identified in more than 50% of the cases studied. Similarly, in publications describing the recognition of immune epitopes by the adaptive immune system, crucial details regarding the host, the source protein of the epitope, and the sequence of the epitope often could not be identified (Vita et al 2016). Newly trained scientists can remedy this situation through consistent use of Research Resource Identifiers (RRIDs) in their scientific publications. RRIDs are persistent and unique authentication tags for key biological resources such as antibodies, transgenic organisms, cell lines and software tools. The use of RRIDs promotes research resource identification, discovery, and reuse and is now required in NIH grants (NOT--OD--16--011). By including RRIDs, you can make your scientific publications more reproducible, findable and more widely read, as well as supporting NIH’s new guidelines for Rigor and Transparency in biomedical publications. Many well respected journals are starting to require RRIDs, such as Cell and Immunity, making this an increasingly common practice. SciCrunch (scicrunch.org ) is a data sharing and display platform that offers a central location for obtaining RRIDs. Here we describe Scicrunch as a free and easy to use resource that exists to make the inclusion of RRIDs in publications as simple as possible.
The use of concept maps in a non-majors virology class.
Authors: Minges Wols Heather A. 
Published: January 2023

Abstract
Columbia College Chicago is a leader in the arts and media. While the Science & Mathematics Department houses a major and 3 minors (including one in biology), the majority of the students matriculating through our courses are fulfilling general education requirements. One popular course is The Biology of AIDS: Life of a Virus. After teaching this course for nearly a decade, the HIV replication cycle continues to be a tough concept for students to grasp. This semester I utilized the free concept mapping software, Cmap, to help students tie together concepts, and prepare better for quizzes and exams, with the ultimate goal to reinforce the steps of the replication cycle. Because I found students were unfamiliar with, and thus initially uncomfortable with, the concept mapping approach, I introduced the methodology during week 2, starting with simplistic maps which required less input from the students, who worked in groups to complete. As the students became more comfortable with the practice, I provided fewer completed “concepts” and less verbal help. The students began to expect (and want) the concept maps, requesting them even when I didn’t have some prepared! When that happened, I “flipped” the concept and had the students create their own maps in groups to aid in their comprehension of the material. In the end, it was difficult to assess whether students performed “better” on quizzes and exams because of the concept mapping (no control group, varying levels of preparation, small “n,” etc.), but students did appreciate another approach to studying the material. In addition, the use of concept maps helped me better organize my lecture slides and connect them to student assessment.
Just-In-Time Active Learning Instructional Pedagogy for PharmD Integrated Immunology Course
Authors: Madiraju Charitha , Tellez-Corrales Eglis , Hua Henry , Brown Deborah M. 
Published: January 2023

Abstract
Just-In-Time Teaching (JiTT) is an active learning pedagogy that has been successfully adopted by various disciplines. Our previous studies showed that JiTT presents value to a pharmacy curriculum. The current study implemented JiTT as an active-learning tool for an Integrated Immunology course offered during the first year of a PharmD program. At the end of the course, 38 students provided feedback on a survey that asked for their degree of agreement to various statements about JiTT usage in the course: 18 items were phrased positively (e.g., “Overall, JiTT questions are beneficial to me”), and 4 items were phrased negatively (e.g., “JiTT made the course more difficult”). These statements were rated on a scale ranging from 1 (strongly disagree) to 5 (strongly agree). The aggregate raw score for the 4 negatively-phrased items (M = 2.20, SD = 0.80) suggests that, overall, students typically disagreed with negatively-phrased statements about JiTT. After the negatively-phrased items were reverse-coded, all items were aggregated into a single measure (Cronbach’s alpha = .95) such that higher scores indicate positive overall perceptions of JiTT. This overall mean score for the survey indicates that students strongly perceive JiTT as beneficial (M = 4.00, SD = 0.84). Our results suggest that students in a pharmacy program perceive JiTT to be beneficial and valuable.
The Mammalian Target of Rapamycin (mTOR) / Peroxisome Proliferator-Activated Receptor γ (PPARγ) axis drives immune dysfunction and outcome after burn injury.
Authors: Maile Robert , Stepp Wesley H. , Eitas Timothy , Cairns Bruce A. 
Published: January 2023

Abstract
Burn patients suffer from mixed antagonist response syndrome (MARS) with dysregulation of immune responses. Acutely, a hyper-inflammatory period can result in multiple organ dysfunction (MOD). Patients surviving MOD often exhibit a subsequent immune suppression resulting in bacterial susceptibility, with Pseudomonas pneumonia a common cause of mortality. Induction of the Mechanistic/Mammalian Target of Rapamycin (mTOR) pathway positively regulates inflammatory responses and induces Peroxisome Proliferator-Activated Receptor γ (PPARγ) which in turn represses immune responses. We hypothesized that the mTOR/PPARγ axis regulates immune function after burn injury. Using a mouse model, we inhibited mTOR activity with systemic administration of rapamycin daily, starting 7d before a 20% Total Body Surface Area (TBSA) contact burn or sham. P. aeruginosa was inoculated 3 or 14 days after burn. mTOR pathway inhibition reduced hyper-activation of innate immune cells and inhibited bacterial susceptibility after burn. In peripheral blood mononuclear cells (PBMC) collected from burn patients early following burn injury, heightened mTOR signaling (higher levels of phospho-S6) was observed in moderate/severe burn patients relative to controls. Quantitative global gene expression analysis revealed that expression of mTOR-induced immune-inhibitory molecules PPARγ and SOCS3 were also significantly elevated in severely burned patients. Regression analysis revealed PPARγ expression significantly correlated with patient %TBSA and poor outcome. These data suggest a role for the mTOR/PPARγ axis in the immune pathology following burn injury and highlights therapeutic targets not previously considered for burn patients.
Pore-forming toxins impair pro-inflammatory macrophage responses
Authors: Thapa Roshan , Bhattacharjee Pushpak , Keyel Peter A. 
Published: January 2023

Abstract
Necrotizing soft tissue infections (NSTIs) are lethal microbial infections. One virulence factor common to most bacteria responsible for NSTIs such as Streptococcus pyogenes is a pore-forming toxin (PFT). PFTs promote immune evasion through unknown mechanisms and lyse cells by forming pores. One mechanism by which cells resist these PFTs is intrinsic membrane repair which is sequestering and shedding toxin pores on microvesicles. It is possible that intrinsic membrane repair is hijacked by bacteria to promote immune evasion. We hypothesized that PFTs promote immune evasion by inducing immune receptor shedding during intrinsic membrane repair. We tested this hypothesis by challenging murine bone marrow derived macrophages with sublytic toxin doses prior to LPS or IFNγ challenge. We measured surface receptor expression and intracellular TNFα by flow cytometry in live cells. We found that toxins from one family of PFTs, cholesterol-dependent cytolysins (CDCs), suppressed LPS or IFNγ-stimulated TNFα production and CD69 and CD86 upregulation in a cell-intrinsic manner independently of cell death. CDCs further induced partial shedding of TLR4 and IFNγR, which might contribute to macrophage dysfunction. In contrast, we found that a toxin from a second PFT family, aerolysin, prevented TNFα production by inducing cell death in macrophages at equivalent hemolytic doses. Overall, these results suggest that different PFT families use different strategies to impair macrophages. CDCs may hijack intrinsic membrane repair to impair TNFα production, while aerolysin kills macrophages at similar doses. These findings might explain the immune suppression and lethality observed during NSTIs.
Clostridium difficile TcdB toxin differentially regulates pyrin via differences in activity of RhoA between proliferating and non-proliferating mammalian cells
Authors: Habyarimana Fabien , Napolitano Nina , McAndrew Christian C. , Mitra Srabani , Sarkar Anasuya , Gavrilin Mikhail A. , Wewers Mark 
Published: January 2023

Abstract

Background
Pyrin is a member of the TRIM family of proteins. Pyrin senses RhoA posttranslational modifications that inactivate RhoA, resulting in the formation of a pyrin inflammasome. Clostridium difficile TcdB toxin inactivates RhoA by glycation of threonine 37. Previous studies have shown that active RhoA predominates in proliferating cells. Thus, TcdB may differentially regulate the pyrin inflammasome in proliferating versus non-proliferating mammalian cells.

Methods
We used a RhoA activation assay (Rhotekin) to test this hypothesis in proliferating monocytic cells (THP1), PMA-differentiated THP1 cells and non-proliferating human monocytes. Pyrin function was determined by its interaction with 14-3-3ɛ and IL-1β release.

Results
We noted that TcdB did not inactivate RhoA in proliferating THP1 cells. However, the toxin drastically reduced the level of active RhoA in non-proliferating human monocytes and PMA-differentiated THP1 cells. TcdB synergized with LPS to induce IL1β release from TcdB- and LPS-stimulated THP1 and PMA-differentiated cells. In contrast, TcdB alone was sufficient to generate a robust IL1β release from TcdB-stimulated human monocytes. TcdB disrupted pyrin’s interaction with 14-3-3ɛ in human monocytes and differentiated THP1 cells, suggesting a decrease in the level of phosphorylated pyrin.

Conclusion
Our data indicate that TcdB is capable of turning off active RhoA in non-proliferating cells but not in proliferating cells. Hence, cellular proliferation may impair pyrin inflammasome assembly and activation.
Themis integrates signalling from self pMHC and cytokines in mature CD8+ T cells
Authors: Gascoigne Nicholas R. J. , Zhao Xiang , Mehta Monika , Gautam Namrata , Brzostek Joanna 
Published: January 2023

Abstract
Optimal T cell responses require integration of T cell receptor (TCR) and cytokine signals. We have identified a new role of Themis, a recently discovered LAT signalosome component, in regulation of CD8 T cell responses to self peptide-MHC (pMHC) and cytokines. Themis plays a critical role in modulation of TCR signal strength during thymic development through interaction with the phosphatase Shp1, and we have now demonstrated that Themis affects the phosphatase activity of Shp1 in thymocytes. Germline deletion of Themis leads to severe perturbation in numbers and phenotype of peripheral T cells, but this is a result of the abnormal thymic development. We have now developed a conditional knockout mouse model to investigate the role of Themis in peripheral T cells. Post-selection deletion of Themis reduces the number of CD8+ T cells in the periphery. Unlike thymocytes, Themis-deficient lymphocytes show largely unimpaired functional responses to TCR stimulation in vitro and in vivo. However, Themis deficiency results in reduced Akt phosphorylation after TCR stimulation. Unexpectedly, Themis-deficient CD8+ T cells have reduced homeostatic proliferation in vivo and reduced proliferative responses to self pMHC and pro-inflammatory cytokines in vitro. This reduced responsiveness to self pMHC and cytokines is accompanied by decreased expression of molecules critical for metabolism, such as c-Myc, and nutrient transporters. Our work suggests a novel role for Themis in regulation of signaling from self pMHC and cytokines in mature CD8+ T cells.
Neutrophils and M1 macrophages contribute to vascular injury and lung Pathogenesis during Orientia tsutsugamushi infection
Authors: Trent Brandon J. , Xing Yan , Wei Yang , Liang Yuejin , Shelite Thomas , Bouyer Donald H. , Soong Lynn 
Published: January 2023

Abstract
Acute lung injury (ALI) leading to acute respiratory distress syndrome is a prevailing pathologic manifestation during O. tsutsugamushi-induced severe scrub typhus in humans. In this study, we tested a hypothesis that lung pathology in scrub typhus is due in part to dysregulated activation of inflammatory responses, leading to vascular malfunction and ALI. Following infection with a lethal dose of O. tsutsugamushi in mice, lung tissues had a significant increase in ICAM1, VEGFR2, and angiopoietin-2 (Ang2), as measured by flow cytometry and immunofluorescence. Several unique features were also observed. First, a progressive decrease or loss of endothelial functional markers (Ang1 and Tie2) and CD41+ platelets, even after the peak of bacterial replication (around day 6), implying continued endothelial cell stress and tissue damage. Second, a sustained neutrophil influx and activation as disease progressed, and lung-recruited neutrophils became highly activated in releasing azurophilic granules or myeloperoxidase around day 10 (prior to host death). Finally, lung-derived macrophages were highly polarized to an M1 phenotype (CD80+CD64+CD11b+Ly6G−) at day 6-day 10, with no signs of M2 activation (CD206+CD64+CD11b+Ly6G−). This study reveals specific biomarkers for vascular stress/dysfunction and uncovers a type 1-skewed, but type 2-suppressed, immune responses in the lungs of lethally-infected mice. More importantly, it furthers findings from human patients and cells, implying an immunopathogenic role in ALI development during severe scrub typhus. Understanding of leukocyte effector molecules and endothelial stress pathways triggered by bacterial vs. host factors will help control this neglected tropical disease.
Differential expression of PD-L1 and Th1 response of lymphocytes co-cultured with human gastric organoids infected with Helicobacter pylori strains isolates from different gastric pathologies
Authors: Peniche Alex , Estes Mary K. , Yamaoka Yoshio , Reyes Victor E. 
Published: January 2023

Abstract
Helicobacter pylori (Hp) bacteria successfully establishes chronic infection leading to chronic gastritis, peptic ulcer disease (PUD), and gastric cancer (GC). Since we have previously shown that Hp hijacks expression of checkpoint immunoregulators (i.e., PD-L1), we hypothesized that strains from different gastric pathologies differ in their ability to evade the host response. We used human gastric organoids (hGOs), which recapitulate polarized epithelium, gastric gland and pit cell markers observed in the stomach. We cultured hGOs in transwell inserts which were exposed to Hp on the apical surface and cultured with naïve T cells on the basolateral side of polarized epithelial cells, thereby reproducing the interactions observed in vivo. After 7 days of culture, we recovered all cells and evaluated levels of PD-L1, B7-H3, B7-H4, and CTLA4; and in CD4+ T cells markers of Th1, Th2, Th17 and Treg. Infection of hGOs with Hp strains isolated from cases of gastritis, PUD or GC, all led to increased expression of negative immune checkpoint regulators, predominantly PD-L1, which binds PD-1 on T cells and promotes loss of effector functions, apoptosis, and reduced T cell-target cell contact. Interestingly, PUD strains are the stronger inducers of PD-L1 and GC strains were the lowest inducers of Th1 cells (Tbet+, IFNγ+), which suggest that different strains differ in their orchestration of the host response, which may contribute to the type of pathology elicited. Our data suggest that this co-culture system to evaluate expression of immune checkpoint regulators and CD4+ T cell differentiation in the context of strains comparison may provide insights in differential expression of candidate biomarkers of disease and future therapies.
Intracellular Salmonella enterica infection is controlled in mononuclear phagocytes that attract CXCR3+ Th1 cells in vivo and persists in those that do not
Authors: Goldberg Michael F. , Roeske Elizabeth , Ward Lauren N. , Kotov Dmitri Ivanovich , Dileepan Thamotharampillai , Jenkins Marc K. 
Published: January 2023

Abstract
Salmonella enterica (Se) is a prototypical bacterial pathogen that persists in myeloid cells in secondary lymphoid organs and is controlled by interferon-g-producing CD4+ Th1 cells. How Th1 cells limit the infection without eliminating it is not understood. Using a PhoNdTomato S. enterica strain, we found Se bacteria inside tissue macrophages and recruited monocytes, some of which expressed inducible nitric oxide synthase (iNOS) or CXCL9 and CXCL10 ligands for CXCR3 expressed by Se-specific Th1 cells. The iNOS+ cells were clustered in red pulp regions devoid of T cells and surrounded by CXCL9/CXCL10+ cells and interspersed Th1 cells. Ablation of CD4+ T cells or blockade of CXCR3 lead to preferential loss of bacterial control in the CXCL9/CXCL10+ areas. These results suggest that Se bacteria are controlled inside myeloid cells in regions that attract CXCR3+ Th1 cells and harbored inside myeloid cells in areas that do not.