bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-tuning Notch expression by lymphocytic Granzyme B production
Authors: Tibbs Ellis J , Cao Xuefang 
Published: January 2023

Abstract
Notch signaling has been studied for many years and has been found to play a role in many aspects of cellular development, tissue homeostasis, and progression of disease. Upon interaction with its ligand, Delta-like-4, the Notch1 molecule undergoes two proteolytic cleavage events. This eventually leads to the translocation of the intracellular domain (NICD) into the nucleus. Once there, NICD interacts with transcription factors such as CBF1/RBPJ. Recently, Notch has been found to play a role in the Th1/Th2 imbalance found in many diseases. Using a software to determine possible cleavage target sites for Granzyme B (GzmB), two were found following the start site of NICD. One group found that cleavage of Notch1 by GzmB disables its activity, however lymphocytes were not the target tissue of research. Thus, we hypothesize that Granzyme B production plays a functional role in the translocation of intracellular Notch1 in affecting CD4+ and CD8+ T lymphocyte activation.
We test our hypothesis by stimulating T lymphocytes collected from transgenic mice that are deficient in GzmB and measuring intracellular and extracellular Notch1 expression compared to wildtype following in vitro aCD3-CD28 stimulation. Flow Cytometry was used to measure Notch expression. Preliminary results show that 24hrs after stimulation, CD8+ and CD4+ T cells from GzmB-deficient mice show 12% and 6%, more NICD expression than WT counterparts and 19% and 14% more extracellular Notch1 expression, respectively. These results show that the presence of GzmB can cause an alteration in the fine-tuning expression of Notch1. This work helps us understand the role of Granzyme B in Notch activation and differentiation of lymphocytes.
ABCB7 is required to prevent ferroptosis in peripheral T cells
Authors: Lehrke Michael Jonathan , Belmonte Paul , McCue Shaylene , Rajcula Matthew , Shapiro Virginia 
Published: January 2023

Abstract
ABCB7 exports iron-sulfur (Fe-S) cluster intermediates from the mitochondria to the cytoplasm. Loss of ABCB7 results in mitochondrial iron accumulation in some cell types. We found that ABCB7 is required for peripheral T cell homeostasis, as CD4-cre ABCB7 cKO have normal thymic T cell development but a severe reduction in peripheral T cells, with a majority of peripheral T cells being recent thymic emigrants. The metal-specific dye Phen Green SK indicated iron accumulation was occurring in the absence of ABCB7. We hypothesized that ABCB7-deficient T cells are eliminated by ferroptosis, an iron-dependent form of regulated cell death that is marked by generation of lipid peroxides. Both Bodipy-C11 and Liperfluo, dyes specific for lipid peroxides, were elevated in ABCB7 cKO T cells. Interestingly, expression of GPX4, the master regulator of ferroptosis, was found to be normal in ABCB7-deficient T cells. A high vitamin E diet, which can reduce ferroptosis in GPX4-deficient T cells, did not restore peripheral T cell numbers in CD4-cre ABCB7 cKO mice. Additionally, treatment with the iron chelator deferoxamine did not restore peripheral T cell numbers. Thus, more than one mechanism may be involved in regulating T cell survival in the absence of ABCB7.
Novel roles for Cullin 3 in T cell-mediated immune responses
Authors: Yarosz Emily L , Chang Cheong-Hee 
Published: January 2023

Abstract
The E3 ubiquitin ligase Cullin 3 (Cul3) has been shown to play a key role in several processes in mammalian cells, including antioxidation, cell cycle regulation, and immunity. Published work has shown that T cell-specific deletion of Cul3 leads not only to a severe defect in natural killer T (NKT) cell development but also to enhanced T regulatory cell and T follicular helper cell differentiation. However, the role of Cul3 in controlling NKT and CD4 T cell proliferation, activation, and homeostasis remains unknown. To begin investigating this, we generated a tamoxifen-inducible CD4 ERT-Cre system to delete Cul3 in mature NKT cells. Surprisingly, Cul3 does not seem to play a role in NKT cell maintenance in either the spleen or the liver, yet activated NKT cells lacking Cul3 proliferate better than wild type cells. We also used a CD4-Cre driven Cul3 knockout mouse model to study CD4 T cell responses. In contrast to our NKT cell studies, the loss of Cul3 in this model severely impacted naïve and effector CD4 T cell frequencies the peripheral tissues. Interestingly, similar to NKT cells, deletion of Cul3 caused naïve CD4 T cells to proliferate better than wild type cells after activation. The proliferative advantage observed in Cul3-deficient naïve CD4 T cells appears to be IL-2 dependent, as these cells display increased IL-2 secretion and IL2Rα surface expression. Preliminary data suggests that major metabolic pathways within the cell may be differentially regulated in NKT and CD4 T cells, and we are currently investigating this possibility further. In all, Cul3 may have unique functions during NKT and CD4 T cell-mediated immune responses, and future work will focus on determining the mechanisms by which Cul3 exerts its effects on these T cell subsets.
Iron in infection and immunity in C. elegans
Authors: Rajan Malini , Anderson Cole P , Romney Steven Joshua , Dos Santos Maria Carolina Ferreira , Gertz Jason , Leibold Elizabeth A 
Published: January 2023

Abstract
Iron is essential for survival of most organisms, but is toxic in excess. All organisms have thus developed mechanisms to sense, acquire and sequester iron. In C. elegans, iron uptake and sequestration are regulated by HIF-1. We previously showed that hif-1 loss of function mutants are developmentally delayed when grown under iron limitation. Here we identify nhr-14, encoding a nuclear receptor homologous to vertebrate HNF4, in a genetic screen conducted for mutations that rescue the developmental delay of hif-1 mutants under iron limitation. NHR-14 is highly expressed in intestinal cell nuclei and in cells in the head, and its subcellular localization and expression are not regulated by iron. Loss of nhr-14 leads to the upregulation of the intestinal metal transporter SMF-3 that increases iron uptake in hif-1 mutants, rescuing the low iron-dependent developmental delay. Loss of nhr-14 also promotes the nuclear localization of the zinc-finger transcription factor PQM-1, which activates smf-3 through the interaction with GATA-like DAF-16-associated elements (DAEs) in the smf-3 promoter. In addition to smf-3, RNA-seq analysis revealed upregulation of innate immune response genes as well as DAF-16/FoxO-suppressed Class 2 genes. Consistent with the RNA-seq results, nhr-14 mutants showed enhanced resistance to the human pathogen Pseudomonas aeruginosa that depends in part on iron uptake as well as the upregulation of innate immune response genes. Our data provide insight into how C. elegans utilizes nuclear receptors to regulate innate immunity and iron availability, and show iron sequestration as an important component of the innate immune response.
Specific Cell-Surface Glycans on Phagocytes Mediate Binding of Pseudomonas aeruginosa
Authors: Sanchez Hector Felipe , Hopkins Daniel , Demirdjian Sally , Gutierrez Cecilia , O’Toole George , Berwin Brent 
Published: January 2023

Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that, as an opportunistic pathogen, substantially contributes to high morbidity and mortality rates in susceptible individuals such as those with cystic fibrosis or neutropenia. Previous studies identified that the downregulation or loss of bacterial flagellar motility, typically observed within chronic infections, enables bacteria to evade interactions with phagocytic cells that would result in phagocytic uptake. Our recent work demonstrated that exogenous addition of a negatively charged lipid, PIP3, induces binding and phagocytosis of non-motile strains of P. aeruginosa. Based on this work, we hypothesized that the engagement of P. aeruginosa by host innate cells, and subsequent phagocytosis, is mediated by motility-dependent interactions with cell-surface polyanions. We now report that endogenous polyanionic N-linked glycans and heparan sulfate mediate bacterial binding of P. aeruginosa by human monocytic cells. These specific cell-surface interactions result in P. aeruginosa phagocytosis, bacterial type 3 secretion system (T3SS)-mediated cellular intoxication and the IL-1β inflammatory response of the host innate immune cells. Concomitantly, inhibition of host cell N-glycan synthesis reduces T3SS-mediated cytotoxicity and the IL-1β response induced by the bacteria. Importantly, the bacterial interactions with the glycans were motility-dependent and could be recapitulated with purified, immobilized glycans. Therefore, this work describes novel interactions of P. aeruginosa with specific phagocyte cell-surface glycans that modulate relevant host innate immune responses to the bacteria, including phagocytosis, inflammation and cytotoxicity.
IL-15 complex modulates the Plasmodium-specific CD4 T cell response in mice
Authors: Burrack Kristina Stoermer , Dileepan Thamotharampillai , Jenkins Marc K , Frosch Anne E.P. 
Published: January 2023

Abstract
Malaria, which results from infection with Plasmodium parasites, remains a major public health problem with over 200 million cases and nearly 500,000 deaths annually. CD4 T helper cells, especially T follicular helper (Tfh) cells, provide help to B cells to induce effective antibody responses. Although long-lived, sterilizing immunity does not develop in humans following repeated exposure to Plasmodium parasites, protection against symptomatic disease correlates with the acquisition of humoral immunity. The study of parasite-specific CD4 T cell responses has been hampered by the lack of defined parasite-derived T cell epitopes. Utilizing newly identified CD4 T cell epitopes, we generated novel peptide:MHC class II tetramers to track Plasmodium-specific CD4 T cells in mice following infection with multiple rodent Plasmodium strains, including Plasmodium berghei ANKA (PbA), P. berghei NK65 and P. yoelii. Infection of susceptible mice with PbA results in a fatal severe malaria disease. We previously showed that treatment of mice with IL-15 complex (IL-15C; IL-15 bound to an IL-15Rα-Fc fusion protein) induces IL-10 expression in NK cells and protects mice from PbA-induced death. IL-15C treatment results in reduced Ag-specific CD4 T cells on day 6 post-infection but an increased ratio of regulatory T cells to Tfh cells. These data suggest that IL-15C treatment, via its induction of IL-10 from NK cells, modulates the Ag-specific CD4 T cell response, with potential downstream effects on the germinal center reaction and antibody responses. We propose that analysis of the Plasmodium-specific CD4 T cell response will inform the design of therapeutics and vaccine strategies for Plasmodium infection.
Distinct host immune programs in lung macrophages elicit cell-type specific Mycobacterium tuberculosis transcriptional responses
Authors: Delahaye Jared L , Cohen Sara B , Peterson Eliza , Adams Kristin , Plumlee Courtney R , Plaisier Christopher , Baliga Nitin , Urdahl Kevin B 
Published: January 2023

Abstract
During Mycobacterium tuberculosis (Mtb) infection, bacteria are inhaled into the lung where they first infect resident, alveolar macrophages (AM). The majority of the infection remains in AM until D14, when other cells, including recruited monocyte-derived macrophages (MDM) begin to become infected. By the peak of infection (D28) MDM represent the major infected cell type. However, even at this time point, a small population of infected AM remain. This led us to ask how these cell types control Mtb. Using microscopy, we observed that AM harbor more bacteria than MDM on a per cell basis at multiple time points, including after the initiation of the T cell response. Using RNA-seq, we identified multiple differentially expressed pathways between the two cell types. While infected MDM upregulate proinflammatory signaling pathways associated with Mtb control, infected AM are enriched for proliferation and fatty acid metabolism pathways. We performed validation studies using dyes to track cell division and mitochondrial metabolism and observed that AM were more proliferative and had sustained engagement of mitochondrial metabolism relative to MDM. In parallel, we analyzed the bacterial transcriptome and found that Mtb in MDM have a signature associated with late hypoxia. These bacterial responses also suggested that Mtb may differ in its drug tolerance in a cell type specific manner, which we are currently investigating. Together, this work is in agreement with other studies demonstrating differences in the response to Mtb by tissue resident and recruited macrophages and suggests that these differences may lead to distinct transcriptional changes in the bacteria, which could have important implications for therapeutic interventions.
Differential immune cell response to Mycobacterium intracellulare colony morphotypes
Authors: Claeys Tiffany , Clary Gillian , Robinson Richard 
Published: January 2023

Abstract
Mycobacterium intracellulare is an opportunistic pathogen which causes disease in immunocompromised individuals. Like several other nontuberculous mycobacteria (NTM) species, a single strain of M. intracellulare forms bacterial colonies with varying morphologies; however, the relative virulence and immunogenicity of differing M. intracellulare morphotypes are unknown. We have obtained a strain of M. intracellulare isolated from an infected patient and further subcultured it to distinguish the component colony morphotypes present within the parent isolate. To determine whether these distinct colony morphotypes have the ability to stimulate differential immune responses in an infected host, C57BL/6J mice were aerosol infected with either the parent clinical strain or each of the isolated component colony morphotypes. Differential immune response and virulence characteristics of the morphotypes were evaluated by tracking host bacterial load, cytokine expression profiles, and histology. In addition, bone marrow-derived macrophages were isolated and infected in vitro with the different morphotypes and parent isolate. From this study, we have found that the component colony morphotypes are able to differentially activate macrophages and affect the host immune response to infection. These results may establish an important immunological basis for patient clinical outcomes.
Increased cervical neutrophil survival during bacterial vaginosis in Canadian women from the THRIVE study
Authors: Farr Christina , Noel-Romas Laura , Birse Kenzie , De Leon Marlon , Kratzer Kateryna , Perner Michelle , Ayele Hossaena , Wiwchar Cobi , Pymar Helen , Berard Alicia R , Poliquin Vanessa , Burgener Adam 
Published: January 2023

Abstract

Introduction
Bacterial vaginosis (BV), characterized by Lactobacillus depletion and replacement by facultative or anaerobic bacteria, impacts up to 30% of women and associates with negative reproductive health outcomes. We used a systems immunology approach to investigate cellular and molecular inflammation associated with BV.

Methods
Matched cervical cytobrush and cervicovaginal lavage were collected from BV− (n=16) and BV+ (n=11) women. Cytobrushes were immunophenotyped by flow cytometry and lavages were analyzed by tandem mass spectrometry. Differences in immune cell levels were evaluated with Mann-Whitney U tests, and assessed against host and bacterial proteins using Spearman’s Rank correlations.

Results
There were no clinical or demographic differences between BV+ and BV− women, including age (range 22–49), birth control use and STI history. Proteomic analysis identified 1085 human proteins and 516 bacterial proteins from 14 genera, including Lactobacillus, Gardnerella, and Mobiluncus. Long living neutrophils (CD49d+) were significantly increased in BV+ women (p=0.0005), and associated with cell adhesion (p=4.04E-5), T cell mediated immunity (p=0.004), and regulation of myeloid differentiation (p=8.63E-16) pathways. CD49+ neutrophils correlated positively with Mobiluncus (p=0.040, R2=0.49) and negatively with Lactobacillus (p=0.035, R2=−0.498).

Discussion
This data indicates that cervical neutrophil survival is increased in women with BV. These cells associated with anaerobic bacteria and molecular pathways of immune activation. Studies are ongoing to delineate the relationship between BV-associated bacteria and neutrophil functionality, which may have implications for BV treatment.
Crosstalk between skin homing innate T cells and epithelial cells via cholesterol byproduct messengers is required for tissue immunity
Authors: Frascoli Michela , Miu Bing , Ferraj Enxhi , Lee Jisu , Esposito Kelsey , Spidale Nicholas , Cowan Jennifer , Bhandoola Avinash , Kang Joonsoo , Reboldi Andrea 
Published: January 2023

Abstract
Innate T cells and innate lymphoid cells (ILCs) in the mucosal tissues are essential for both barrier tissue fitness and immunity against pathogens. γδTCR+ lymphocytes that secrete IL-17 (Tγδ17) localize to dermis and are critical regulators of skin immune responses. Despite their functional importance, how Tγδ17 cells mediate their unique function in the skin is largely unknown. Tγδ17 cells express the two prototypic G-protein coupled receptors (GPCRs) CCR6 and GPR183 (EBI2) that marks most type 3 cytokine (IL-17 and IL-22) producing lymphocytes. Mice lacking both receptors had significantly diminished dermal Tγδ17 cells and were resistant to psoriasis induction. The deficit in dermal Tγδ17 cells in Ccr6−/−Gpr183−/− double knock-out (DKO) mice was attributed to a block in their maturation in the thymus. EBI2 recognizes oxysterols generated by the cholesterol hydroxylase CH25H and functional oxysterols were detected in both the thymus and skin. Analysis of Ch25h-reporter mice showed that a subset of immature medullary thymic epithelial cells (mTEC) is the depot for oxysterols. We confirmed this finding by single cell transcriptome analyses of TECs. These results demonstrate that developing Tγδ17 cells must be conditioned by sensing cholesterol byproducts synthesized by a discrete subset of mTECs. This conditioning is likely to be required to position Tγδ17 cells in specific niches in the skin where oxysterols are generated. Given that CH25H expression can be regulated by infection and inflammation, this sensory circuit directed by cholesterol is predicted to program skin innate T cells’ ability to rapidly survey for perturbations in the skin.
Skin-resident natural killer T cells induce cutaneous allergic inflammation in atopic dermatitis
Authors: Park Chang Ook , Sun ZhengWang , Kim Ji Hye , Lee Kwang Hoon , Kupper Thomas S 
Published: January 2023

Abstract
Natural killer T (NKT) cells are unconventional T cells that bridge innate and adaptive immunity. NKT cells have been implicated in the development of atopic dermatitis (AD). Here, we demonstrate that CXCR4 and its cognate ligand CXCL12 are significantly up-regulated in human AD skin in global transcriptomic analysis; proteomic analysis revealed that CXCR4+ NKT cells are enriched in AD skin and are consistently elevated in our AD mouse model. Adoptive transfer of allergen-specific NKT cells confer antigen-specific cutaneous inflammation, and predominant skin NKT cells are CXCR4+ and CD69+, similar to tissue-resident memory T (TRM) cells. Skin-resident NKT cells uniquely expressed CXCR4, which was confirmed using a parabiosis system. Intravital imaging showed that CXCR4+ NKT cells preferentially trafficked to a CXCL12-rich area, forming an enriched CXCR4+ NKTRM/CXCL12+ cell cluster, which developed acute and chronic allergic inflammation. CXCR4+ NKTRM cells may form a niche to develop AD, where CXCL12 is highly expressed.
Transcriptomic, phenotypical, and functional characterization of human liver sinusoidal CD69+CD4+ T cells
Authors: Koh June-Young , Han Ji Won , Rha Min-Seok , Park Jun Yong , Joo Dong Jin , Park Su-Hyung , Shin Eui-Cheol 
Published: January 2023

Abstract
Tissue-resident memory T (TRM) cells are non-circulating T cells that rapidly respond to the local antigen stimulation. Human liver CD8+ T cells have been reported to have phenotypes of TRM and respond to hepatotropic viruses. However, characteristics of human liver CD4+ T cells are still unclear. Here, we examined transcriptomic, phenotypical, and functional characteristics of human liver CD4+ T cells by analyzing liver sinusoidal mononuclear cells (LSMCs) from liver perfusates of healthy donors obtained during liver transplantation. The liver sinusoidal (LS) CD4+ T cell population had a significantly higher frequency of CD69+ cells than the peripheral blood (PB) counterpart. However, CD103 was barely expressed in the both populations. In transcriptomic analysis, LS CD69+CD4+ T cells were distinctly clustered and showed tissue-resident features. In flow cytometry analysis, we found that the LS CD69+CD4+ T cell population had significantly higher frequencies of CXCR6+, LFA-1+, or CD49a+ cells than the PB CD4+ T cell population and the LS CD69−CD4+ T cell population, confirming that LS CD69+CD4+ T cells have tissue-resident phenotypes. Moreover, LS CD69+CD4+ T cells were mostly PD-1+ effector memory cells, which is consistent with the characteristics of TRM cells. In functional analysis following anti-CD3 stimulation, we found that LS CD69+CD4+ T cells had a higher capacity for IFN-γ production than LS CD69− CD4+ T cells. In addition, TH1-associated gene sets were enriched in the LS CD69+CD4+ T cells. In summary, these findings indicate that LS CD69+CD4+ T cells are TRM-like cells with TH1 effector functions. Roles of LS CD69+CD4+ T cells in various liver diseases need to be further elucidated.
Immunosuppressive therapy of immune-mediated GI damage may impair epithelial regeneration
Authors: Arnhold Viktor , Takashima Shuichiro , Vinci Paola , Kuttiyara Jason , Egorova Anastasiya , Calafiore Marco , Hanash Alan 
Published: January 2023

Abstract
Glucocorticoids (GC) are a standard therapy of immune-mediated gastrointestinal (GI) damage. However, there is little understanding of the effects that GC use may have on intestinal epithelium and its regenerative function. Using ex vivo organoid models of immune-mediated intestinal injury, we sought to investigate direct effects of GC on intestinal epithelium and test the impact of GC on cytokine- and T-cell-mediated effects. GC suppressed proliferation of small intestine (SI) organoids, reducing organoid size and decreasing cell cycle progression of Lgr5+ intestinal stem cells. Consistently, GC treatment of C57BL/6J mice suppressed epithelial proliferation, decreasing crypt height and reducing the percentage of Ki67+ crypt cells in vivo. We next investigated the role of GC-mediated epithelial suppression in the setting of tissue damage, modeling immune-mediated GI pathology by culturing organoids in the presence of IFNγ and by co-culturing organoids with allogeneic T-cells. Culture with GC in addition to IFNγ significantly increased the toxicity of IFNγ leading to reduced efficiency of organoid formation. Consistently, GC pretreated organoids were more susceptible to allogeneic T-cells with reduced formation efficiency. Finally, we studied cytokine-mediated epithelial regeneration in the context of GC treatment. Culturing organoids with both GC and IL-22 indicated that IL-22 could promote regeneration of intestinal epithelium in the presence of GC. Taken together, our findings indicate that GC, which are necessary clinically for suppressing pathologic inflammatory immune responses, may have direct effects on the epithelium potentially impairing protective regeneration responses and augmenting toxicity.