bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toll-like receptor 9 signaling antagonizes B cell antigen capture, processing and presentation resulting in a failure to activate helper T cells
Authors: Akkaya Munir , Akkaya Billur , Kim Ann S. , Miozzo Pietro , Sohn Haewon , Pena Mirna , Roesler Alexander S. , Theall Brandon P. , Lu Jinghua , Pierce Susan K. 
Published: January 2023

Abstract
Key events in T cell-dependent antibody responses, including the formation of germinal centers and affinity selection, are dependent on the ability of B cells to capture antigen and present it to follicular helper T cells. Despite its importance, little is known about the regulation of this critical B cell function. Here we show that although TLR9 signaling induced B cell proliferation, secretion of cytokines and IgM, it blocked the ability of antigen-specific B cells to capture, process and present antigen. In the presence of the TLR9 agonist, CpG, B cells were less able to form synapses with antigen-containing membranes and to pull antigen from them. CpG also diminished the ability of the BCR to deliver internalized antigen to antigen processing compartments resulting in fewer MHC-peptide complexes on the B cell surface. Additionally CpG blocked the BCR-induced increases in the expression of both MHC class II and important co-receptors, including CD86, resulting in the inability of B cells to activate antigen-specific CD4+ T cells. A principle component analysis of RNA seq data showed little overlap between B cells stimulated through the BCR or TLR9 alone or together indicating that TLR9 antagonism of BCR-dependent antigen presentation is through the activation of a novel transcriptional program. In a chimeric mouse model and in a human clinical trial the TLR9 agonist, CpG, enhanced the magnitude of the antibody response to a protein vaccine but failed to promote affinity maturation. Thus, TLR9 signaling may enhance the magnitude of an antibody response at the expense of the ability of B cells to engage in germinal center events that are highly dependent on antigen capture and presentation.
Deconstructing T-B interactions by manipulation of IRF4 to understand regulation of T follicular helper cells.
Authors: Sievert Evelyn P. , Cook Sarah L. , Sciammas Roger 
Published: January 2023

Abstract
Germinal center (GC) derived high affinity antibody is important for protecting against infectious disease. Interactions between T follicular helper (Tfh) cells and GC B cells are requisite for affinity maturation. While it is clear that bi-directional signals are important for the generation of Tfh and GC B cells, a full understanding of the signaling dynamics that lead to efficient T and B cell differentiation is not known. Studying these B cell-derived signals and their role in Tfh cell commitment, maintenance, and function during GC reactions will lead to an improved understanding of this tightly regulated system. The transcription factor IRF4 is necessary and sufficient for generating GC B and plasma cell fates through graded expression. We have shown previously through gene ontology analysis that IRF4 targets include genes involved in T and B cell interaction. This raises the possibility that beyond cell-specific control of B cell fates, IRF4-regulated genes in B cells may facilitate interactions between B and T cells. We hypothesize that IRF4 controls a gene program in B cells necessary to generate efficient T cell activation and Tfh cell differentiation. Using in-vitro co-culture, we assessed changes in T and B cell activation and functionality by flow cytometry. We found that Irf4−/− B cells processed antigen poorly and led to quantitatively and qualitatively reduced T cell activation compared to Irf4+/+ B cells. This indicates a major role for IRF4 in controlling a B cell gene program necessary for efficient T cell activation. We are currently investigating the nature of these signals through in-vitro and in-vivo approaches in order to deconstruct the molecular nature of T-B interactions during the GC program.
Elucidating synergistic and antagonistic effects of B cell receptor and toll-like receptors 3, 4, and 9 in B cell activation
Authors: Theall Brandon P. , Henke Travis A. , Roesler Alexander S. , Akkaya Billur , Pena Mirna , Cimperman Clare K. , Tadesse Yeabsera , Pierce Susan K. , Akkaya Munir 
Published: January 2023

Abstract
B cells are key components of the humoral immune response. Two forms of B cell activation come from engagement of the B cell receptor (BCR) with foreign antigens and from pathogen-associated molecular patters (PAMPs) binding to toll-like receptors (TLRs). For TLRs, MyD88 and TRIF are the major adaptors that lead to NFkB and IRF3 activation respectively. Among various TLRs that are present in B cells, TLR9 is only able to use MyD88 and TLR3 only signals through TRIF, while TLR4 uses both pathways. Therefore, these TLRs provide excellent tools to investigate the roles of TRIF and MyD88 pathways in B cell function and the interplay between them. Here, using stimulation through these three different TLRs either individually or in combination with each other and with/or without anti-IgM, we observed that there is synergy and antagonism between these pathways in terms of activation induced metabolic boost, cytokine production, IgM secretion, expression of various cell surface markers, and antigen presentation. We identified the TRIF pathway as an inducer of Type-I interferon secretion by B cells, which eventually favors the expression of costimulatory molecules such as CD86. On the other hand, MyD88 stimulation antagonized the expression of costimulatory molecules and dramatically induced rapid proliferation and production of IgM as well as proinflammatory cytokines such as IL-6 and TNF. Using B cells obtained from MyD88 or TRIF KO mice, we showed that the interplay between pathways is of limited scale; however, for TLR4 signaling MyD88 has a largely permissive effect while TRIF determines the magnitude of response. These results further our understanding of the complex TLR signaling machinery in B lymphocytes.
Hypoxia-induced reactive oxygen species contribute to immune checkpoint molecule expression in T cells undergoing rapid clonal proliferation
Authors: OConnor Roddy , Guo Lili , Ghassemi Saba , Snyder Nathaniel , Worth Andrew , Weng Liwei , OBrien Shaun , Kam Yoonseok , Philipson Benjamin , Nunez-Cruz Selene , Lee Joyce , Wellen Kathryn , Busch Theresa , Moon Edmund , Blair Ian , June Carl H. , Milone Michael 
Published: January 2023

Abstract
In response to antigen and costimulation, T cells undergo a series of metabolic transitions supporting clonal expansion and differentiation. We recently showed how CD28 and 4-1BB intracellular co-stimulatory domains induce glycolytic vs oxidative metabolic programs, respectively, in the context of a chimeric antigen receptor. Understanding how endogenous co-stimulatory pathways, in particular CD28, supports differentiation and memory cell development despite encountering hostile environments characterized by varying oxygen tension and metabolic checkpoints is of clear importance to cellular immunotherapy.
Immune checkpoint molecule (ICM) expression is associated with T cell exhaustion characterized by reduced proliferative capacity and diminished effector function. While studying the role of LCFAO in primary human T cell differentiation, we uncovered that the CPT1a inhibitor, etomoxir (ETO), induces expression of the PD-1, Tim-3, and Lag-3 ICMs. This is mediated by non-specific effects on oxidative metabolism, culminating in reactive oxygen species (ROS) production. The induction of ICM expression by ETO is calcineurin-dependent and reversed by the antioxidant N-acetylcysteine (NAC). We show that Tim-3 is upregulated by T cells in highly hypoxic xenograft tumors independent of TCR signaling. Transition of highly activated T cell cultures from normoxia (21% O2) to hypoxia (1% O2) induces Tim-3, which is reversed by NAC. These results suggest that ICMs, especially Tim-3, are part of a natural regulatory system that responds to oxidative stress and tempers T cell activation and associated metabolism to minimize oxidative damage to T cell clones expanding following antigen receptor activation.
Adipose T cell microRNAs influence the T cell expansion, microbiome and macrophage function during obesity
Authors: Singh Udai P. , Singh Narendra Prasad , Murphy E. Angela , Singh Santosh Kumar , Price Robert L. , Nagarkatti Mitzi , Nagarkatti Prakash S. 
Published: January 2023

Abstract
Obesity is a global health problem that has reached epidemic proportions and the World Health Organization (WHO) estimates 500 million adults are obese. Obesity facilitates the development and progression of metabolic disorder diseases. Extensive evidence suggests that composition of the intestinal microbiota can influence susceptibility to obesity. T helper cells and macrophage in adipose tissue (AT) are strongly linked to the initiation of obesity-associated chronic inflammation. In this study, we investigated how high fat diet (HFD) impacts homeostatic expansion of T cells, adipose T cell microRNAs (miRs), macrophage and the intestinal microbiota during obesity. HFD consumption alters the body weight, fat mass and lean mass of mice as compared with a normal diet (ND). HFD also increases the homeostatic expansion of T cells in the epididymal AT as compared with a ND. Epididymal AT in mice fed a HFD exhibited significant downregulation of miR-10a, miR-125b, and miR-1247 when compared to mice fed a ND. These obesity-induced changes in miRs were validated by RT-PCR analysis. Pathways analysis also validated that downregulated miRs and gene target mRNAs are associated with T cells homeostatic expansion and macrophage function. We also noticed striking changes in microbial composition of firmicutes, bacteriodates, and ruminococeae during consumption of HFD as compared to ND. Taken together, these results indicate that HFD modulates AT miRs and intestinal microbiome to induce T cells homeostatic expansion and changes in macrophage function to sustain inflammation. This study supports a key role of AT miRs in mediating chronic inflammation during HFD induced obesity.
Self-reactivity controls the basal metabolism and in vivo function of CD4 T cells
Authors: Milam Ashley Viehmann , Bartleson Juliet , Donermeyer David , Horvath Stephen , Chang Chih-Hao , Buck Michael , Lam Wing , Durai Vivek , Raju Saravanan , Yu Haiyang , Zinselmeyer Bernd , Murphy Kenneth M. , Pearce Erika L. , Allen Paul M. 
Published: January 2023

Abstract
Relatively little is known with regard to CD4 T cell memory formation and metabolism, in part because CD4 T cell numbers remain low during a recall infection. Further, the contribution of self-peptide-MHC signaling (during both thymic T cell development and peripheral maintenance) to metabolic programming, if any, remains unknown. To address these questions, we have employed LLO-Hi5 and LLO-Lo5, two TCRtg CD4 T cells that recognize the same Listeria epitope with the same affinity. LLO-Hi5 CD4 T cells are highly self-reactive and respond poorly in a primary infection but robustly in a secondary infection. Less self-reactive LLO-Lo5 cells respond well during primary infection but poorly during secondary infection. We performed metabolic profiling to determine whether differences in response during infection were linked to metabolic differences between LLO-Lo5 and LLO-Hi5. We found that LLO-Lo5 had dramatically higher respiration and glycolytic rates relative to LLO-Hi5, and hypothesized that the decreased metabolism resulting from a strong interaction with self was mediated through TCR signaling. To test this hypothesis, we generated a knockin mouse expressing the Scn5a voltage gated sodium channel. This channel, when normally expressed in DP thymocytes, enhances TCR-mediated signaling. We found that overexpression of Scn5a in peripheral T cells increased TCR-proximal signaling. Further, Scn5a-expressing LLO-Lo5 cells displayed an impaired response during a primary infection. In this way, we demonstrate that tuning of TCR sensitivity to self can be used to alter in vivo immune responses. These studies highlight the critical relationship between TCR:self-pMHC interaction, metabolism, and the immune response to infection.
Triaging the innate immune system: Responding to lung infections suppresses the dermal wound healing response
Authors: Jamieson Amanda Mercedes , Crane Meredith , Xu Yun , Henry William , Albina Jorge 
Published: January 2023

Abstract
The development of pneumonia is a risk for hospitalized patients. Retrospective analysis of patient data revealed a strong correlation with the development of pneumonia and poor wound healing. Responding to lung infections and the healing wound response involve many of the same innate immune cell types, in particular macrophages, monocytes, and neutrophils. This study addresses the impact of lung infections on the ability to heal a dermal wound at a distal site. Using two in vivo models of injury combined with either bacterial (Klebsiella or Streptococcus) or viral (IAV) lung infections, this study unequivocally demonstrates that lung infections suppress the ability to heal wounds. Cutaneous wound healing is delayed in mice that have an ongoing lung infection. There is a decrease in trafficking of innate immune cells, in particular neutrophils and monocytes, into wounds of mice that have an ongoing lung infection. There are also decreased chemokines and cytokines in wounds from infected mice. Systemic changes of the innate immune system occur after wounding and infection that impact immune cell trafficking into wounds, but allow the immune response in the lung to remain intact. There are also alterations in the wound environment when there are simultaneous wounds and lung infections. By redirecting the innate immune response to the wounds we are able to increase wound healing. This information will allow for the better monitoring and supportive care for patients with this type of complex disease sequelae.
Gut dysbiosis and immunological profile in endometriosis
Authors: Alghetaa Hasan F. , Mohammed Amira , Nagarkatti Mitzi , Nagarkatti Prakash 
Published: January 2023

Abstract
Ectopic growth of normal cells or debris originating from endometrium, the inner layer of female reproductive tube leads to endometriosis. The main symptoms are dyspareunia, dysmenorrhea, and sometimes chronic pelvic pain. Unfortunately, it has no cure or treatment, only symptoms relief medication or surgical removal. Endometriosis causes estrogen imbalance leading to intestinal bacterial estrobolome dysregulation and subsequent change in immune response. Our study aims to investigate the linkage between gut dysbiosis and immunological response in endometriotic mice. Balb/c mice were ovariectomized (OVX) 7 days before intraperitoneal transplantation of 2mm2 endometrial tissue from OVX donors to OVX- or intact ovary recipients. Colonic content was collected 2 weeks post transplantation for 16s rRNA pyrosequencing. Peritoneal exudate was collected and stained to determine the phenotype of infiltrating cells by flow cytometry. Results revealed a significant increase in the number of exudate cells, natural killer (NK) cells and myeloid derived suppressor cells (MDSCs) in endometriotic mice. Phylogenetic taxonomy showed an increase in the biomass of the bacteria in endometriotic OVX mice in comparison with endometriotic nonovariectomized mice. However, the abundance of Phylum Tenericutes, Order Clostridiales, Dehalobacterium sp. and Anaeroplasma sp. were decreased. Collectively, endometriosis changed estrogen metabolism and gut microbiota which resulted in the immune modulation. (Supported by NIH P01AT003961, R01AT006888, R01MH094755, P20GM103641, R01AI129788 and R01AI123947 to PN and MN, and MoHESR to AKM).
Regulation and In Vivo Function of Dendritic Cell CTLA-4
Authors: Halpert Matthew , Vasquez-Perez Jonathan , Konduri Vanaja , Chen Yunyu , Liang Dan , Levitt Jonathan M. , Decker William K. 
Published: January 2023

Abstract
CTLA-4, the target of the blockbuster cancer immunotherapeutic ipilimumab, is the best characterized of the T-cell immune checkpoints. In contrast to T-cell expressed CTLA-4, almost nothing is known about CTLA-4 expression or function in non-lymphoid cell types. Recently we reported expression and secretion of microvesicle-bound CTLA-4 from myeloid lineage dendritic cells. Previous data indicated that microvesicular CTLA-4 bound B7, leading to vesicle internalization and downregulation of B7 expression in vitro. Further, siRNA knockdown of DC-expressed CTLA-4 resulted in upregulation of CD8+ cell proliferation and enhanced antitumor and antiviral immunity in vitro and in vivo. Here we report that DC CTLA-4 can be regulated by interferons a, g, and especially b, whereas TLR ligands appeared to have little effect on regulation. Additional experiments suggested negative regulation of DC CTLA-4 by miR-223 and the transcription factor C/EBP-b. To better understand the role of CTLA-4 in dendritic cell function in vivo, Balb/c conditional knockout animals were generated and characterized under conditions of homeostasis and following nonlethal challenge with H3N2 A/HongKong/8/68 influenzavirus. T-cells derived from conditional knockout animals lacked expression of CD62L and exhibited downregulated CCR7 expression with upregulation of exhaustion markers PD-1 and GITR. Knockout animals challenged with influenza exhibited higher levels of NP tetramer-specific CD8+CD25+ cells and a lengthily extended period of morbidity. The sum total of the data reflect the broad hypothesis that dendritic cell CTLA-4 serves as a regulatory checkpoint to prevent non-specific, inappropriate, or excessively pathologic T-cell priming.
The NLRC4 inflammasome regulates extra- and intra-macrophage expression of its own pathogen-derived ligand flagellin to impact Salmonella survival.
Authors: Akhade Ajay Suresh , Atif Shaikh M. , Lakshmi Bhavna S. , Qadri Ayub , Subramanian Naeha 
Published: January 2023

Abstract
Inflammasomes have been implicated in the detection and clearance of a variety of bacterial pathogens, but whether the process of inflammasome activation per se regulates expression of microbial effectors is unknown. Here we show that inflammasome activation regulates expression of the NLRC4 ligand, flagellin, on Salmonella. Lysophospholipids released upon macrophage pyroptosis increase expression of flagellin on Salmonella and its ability to induce further NLRC4 inflammasome-dependent pyroptosis, establishing a positive feedback loop that potentiates Salmonella detection and clearance. As infection progresses, this positive feedback is checked by inhibition of NLRC4 expression and lysophospholipid biosynthesis, thus switching Salmonella to a flagellin-negative phenotype inside macrophages. While inhibition of inflammasome activation could be a host strategy aimed at preventing overt cell death and enabling generation of a productive adaptive immune response post infection, our study demonstrates that Salmonella hijacks this host response to facilitate its intracellular survival. Our data reveal a host-dependent mechanism by which Salmonella downregulates flagellin within macrophages and identify the modulation of expression of a pathogen-derived inflammasome ligand by the very process of inflammasome activation as a novel mode of host-pathogen cross talk during infection with a bacterial pathogen.
STAT5b Isoform Controls IgE-mediated Mast Cell Function
Authors: Kiwanuka Kasalina N. , Ryan John J. 
Published: January 2023

Abstract
Signal Transducers and Activators of Transcription (STATs) are latent transcription factors that control survival, proliferation and many other cellular functions. This protein family consists of seven members, including the closely related STAT5A and STAT5B, which show 96% amino acid sequence homology. We previously found that Stat5B is required for IgE-mediated cytokine production by mast cells in vitro, but have not tested in vivo correlates to this finding. In the current study, we show that Stat5B deficiency (KO) reduces IgE-induced passive systemic anaphylaxis (PSA) and IL-13 secretion in vivo, without altering mast cell tissue distribution. These results were corroborated by reduced PSA in response to anti-FceRI antibody injection. However, we were surprised to find that reduced PSA was not matched by lower plasma histamine levels. Further investigation revealed that Stat5B KO mice have a &gt;5-fold increase in basal IgE levels and are hyperresponsive to histamine-induced anaphylaxis. These data support the conclusion that Stat5B is critical for IgE-induced mast cell activation in vivo, but also indicate that it contributes to basal IgE production and suppresses vascular responses to histamine. Thus Stat5B is involved in several overlapping aspects of the systemic mast cell response that warrant further study.
Chromatin accessibility modulates the induction of innate immunity in cells of myeloid lineage.
Authors: Song Ran , Dozmorov Igor , Wakeland Benjamin , Arana Carlos , Liang Chaoying , Zhang Bo , Zhou Jinchun , Pasare Chandrashekhar , Wakeland Edward K. 
Published: January 2023

Abstract
The Toll-like receptors (TLRs) of the innate immune system play a key role in the recognition of pathogens. TLRs signal through the recruitment of specific adaptor molecules, leading to activation of the transcription factors, such as AP-1, NF-κB and interferon regulatory factors (IRFs). Although TLRs are mainly expressed in immune cells, a systematic comparison of immune cells activation programs induced by specific individual TLRs is not yet available. Here, we used whole transcriptome sequencing to evaluate global changes in gene expression on monocytes, monocyte-derived macrophages (MDM) and monocyte-derived dendritic cells (MDDC) of five human donors before and after 18 hours stimulation through the TLR2, TLR4, TLR7 and TLR7/8 agonists (Pam3CSK4, LPS, R837 and R848). Cluster analysis demonstrated eight distinct clusters of unresponsive or responsive genes by the four TLR agonists in monocytes, MDM and MDDC. TLR7/8 stimulation by R848 led to the most robust cytokine and chemokine transcription in all cell types, especially in monocytes. Interestingly, we found that interferon-stimulated genes were strongly induced only by TLR4 activation in MDM and only by TLR7 and TLR8 activation in monocytes. Unexpectedly, there was no difference of activation of MAPK, NF-κB and IRF by LPS or R848 in these cell types. Surprisingly, we revealed that chromatin accessibility is significantly correlated with genes that are induced by specific TLR agonists on specific cell type(s), using ATAC-seq. Therefore, our results suggest in spite of robust early signal transduction events, factor that regulate chromatin accessibility play a critical role in regulation of inflammatory gene expression by TLR agonists in cells of the innate immune system.