bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic regulation of histone H3 lysine 27 (H3K27) controls the division-specific timing of gene expression during B cell differentiation
Authors: Scharer Christopher , Barwick Benjamin , Bally Alexander , Boss Jeremy M 
Published: January 2023

Abstract
The differentiation of B cells to plasma cells is required for the generation of a protective antibody response. Following activation, B cells undergo multiple rounds of cell division that result in progressive differentiation and the acquisition of plasma cell phenotypic traits. However, how the epigenetic program is remodeled to facilitate differentiation, what the cis-regulatory elements that participate in this process are, and the molecular timing of these events during cellular division are poorly understood. To dissect B cell differentiation in vivo, five distinct divisions, representing unique stages of B cell differentiation were isolated by FACS. The changes in chromatin landscape were identified by the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and the effects on gene expression measured by RNA-seq. In parallel, histone modification profiles in naïve B cells and plasmablasts were defined. Interestingly, the loci with losses and gains in the histone modifications H3K27ac and H3K27me3 were highly correlated with enhancer activity and gene expression changes. To investigate the role of H3K27me3, B cells were differentiated in the presence of GSK343, a small molecule inhibitor of H3K27me3. Plasma cells differentiated at earlier divisions in the absence of H3K27me3 and a three-fold increase total plasma cells was observed. Together these data define the division coupled epigenetic events that regulate B cell differentiation, provide the first map of plasma cell cis-regulatory elements, and identify epigenetic processes that regulate the timing of differentiation during division.
Transcriptomic analyses reveal senescent and SnoRNA changes in B cells with age irrespective of vaccine-stimulation in mice.
Authors: Baudier Robin L , Czarny-Ratajczak Malwina , Eastwood James R , Zwezdaryk Kevin J , Norton Elizabeth B 
Published: January 2023

Abstract
Aging is associated with a decline in immune function that is not fully understood. Transcriptomic analysis is a powerful tool to evaluate age-related changes, but has not yet been reported for B-cells. To address this, we performed RNA-seq analyses on purified B-cells from naïve or vaccinated BALB/c mice of varying ages with the goal of expression profiling by age as opposed to any ongoing immunostimulation. Mouse age groups were Y (young, 15–20 wks), MA (middle-aged, 68–81 wks), and O (older, 103–111 wks) ± intramuscular Flulaval injection (n=5). Sequencing was performed using Ion Torrent/Ion Proton System. PCR and phenotype analyses were performed to validate selected results. In naïve groups, 230 genes were significantly differentially expressed by MA and O compared to Y. Nine of these were also significant comparing MA and O to Y in vaccinated groups. These included protein-coding genes: senescence-associated Cdkn2a; NFκB-mediator Edaradd; Klk4, a kallikrein implicated in cancer; and 4921504E06Rik, a gene region linked to inflammatory disease. Non-coding genes included: pseudogenes Gm2619 and RP24-374C7.3; antisense Gm16028; and box C/D small nuclear (sno) RNAs, Snord123 and Snord1a. The latter genes were particularly interesting as box C/D snoRNAs regulate rRNAs through methylation, and changes in their expression levels occur with neurodegenerative disorders, inflammatory diseases, and cancer. Altered DNA methylation or epigenetic drift is implicated in both healthy aging and age-related dysfunction but exact mechanisms are unclear. Our results suggest that Snord123 and Snord1a play a previously unappreciated role as regulators of altered methylation patterns contributing to age-related immune decline in B-cells.
Two different nonclassical MHC class I-restricted invariant T cell lineages with non-overlapping antiviral and anti-mycobacterial immune functions in the amphibian Xenopus
Authors: Edholm Eva-Stina , Park Jules , Robert Jacques 
Published: January 2023

Abstract
Unconventional T cells, including disparate populations of MHC class Ib-reactive innate T (iT) cells are emerging as key factors in the immune system partly due to their public antigen specificities and rapid effector responses. The biological relevance and evolutionary conservation of iT cells have, over the past few years, been strengthened by studies in the amphibian Xenopus, which have revealed an overrepresentation of several invariant TCRs in tadpoles and identified a prominent subset of iT cells (invariant Vα6 [iVα6]) restricted by the nonclassical MHC class Ib molecule XNC10. Recently, we showed that similar to CD1d restricted iNKT cells in humans and mice Xenopus iVα6 T cells are critical for early antiviral immunity. Here, using RNAi loss-of-function by transgenesis targeting another Xenopus nonclassical gene, XNC4, we have identified a different XNC4-dependent iT cell population expressing one of the 6 previously identified overrepresented TCRα rearrangements (TRAV45 joined to TRAJ1.14). We show that this invariant Vα45 [iVα45] T cell population is critical for antibacterial immunity against Mycobacterium marinum. These data suggest that functionally distinct populations of MHC class Ib-reactive iT cell populations play a prominent role in amphibian immune defense and as such may represent a more primordial immune cell type that previously thought.
Time-assessed modulation of SOCS1 expression through TLR4 and IFNγ signaling in RAW 264.7 macrophages.
Authors: Veal Antia E , Ganesh Bhagyalaxmi Sukka , Larkin Joseph 
Published: January 2023

Abstract
Innate immune cells, such as macrophages (MΦ), play a critical role in the initiation and duration of inflammatory responses directed against foreign pathogens. The elaboration of immune effector by MΦ are coordinated by interactions of microbial stimuli, such as LPS, and critical immuno-modulatory cytokines with receptors present on the MΦ. The interactions mediate a cascade of signal transduction events that ultimately culminate with the activation and nuclear translocation of transcription factors which facilitate appropriate immune responses. Notably, TLR4 stimulation by LPS mediates the activation of NF-κβ , while the immuno-modulatory cytokine IFNγ mediates nuclear translocation of phosphorylated STAT1 dimers. In addition to mediating pro-inflammatory signals, NF-κβ and IFNγ also modulate a critical limiter of pro-inflammatory signals, suppressor of cytokine signaling-1 (SOCS1). Notably the regulation of SOCS1 molecules in response to multiple external stimuli, such as LPS and IFNγ are not well understood. In this study we investigate the mechanisms through time kinetics of SOCS1 upregulation through TLR4 and IFNγ signaling in RAW 264.7 MΦ as it relates to its transcription regulators, NF-κβ and pSTAT1. We found LPS treatment mediated the phosphorylation and subsequent degradation of Iκβ, which is indicative of NF-κβ nuclear translocation, at 0.5–3 hrs, with reaccumulation at 6–12 hrs. LPS-mediated pSTAT1 was detected at 3–6 hrs. In contrast, basal levels of SOCS1 were reduced subsequently to at 0.5–3 hrs, with reaccumulation at 12–48 hrs. While IFNγ stimulated pSTAT1 at 0.5–12 hrs and basal protein levels of SOCS1 were initially reduced further showed enhanced at 6–24 hours.
Studying human hepatic immunology through the isolation and culture of liver slices and purified cellular subpopulations
Authors: Roberto Jessica Brownell , Knupp Allison , Kenerson Heidi , Yuen Sebastian , Brempelis Katherine , Crispe Ian Nicholas 
Published: January 2023

Abstract
Although advances in culture techniques have allowed us to better understand hepatocyte inflammatory signaling under both normal and diseased conditions, still little is known about how non-parenchymal cells (NPCs) such as liver sinusoidal endothelial cells (LSECs), hepatic stellate cells (HSCs), and hepatic macrophages (i.e. Kupffer cells) impact these events in the intact human liver. In order to investigate this network of cellular cross-talk, we have developed two novel ex vivo culture systems. In Method A, 250 μm slices of human liver tissue were cultured in a transwell system. These slices induced inflammatory and tissue repair signals following both physical injury and challenge with pro-inflammatory ligands (polyI:C, LPS, and LTA). Responses following physical injury were consistent with an acute phase response, while pro-inflammatory ligands induced responses consistent with TLR activation and production of type I interferon. In Method B, we perfused wedges of liver tissue and isolated purified hepatocyte and NPC populations. Hepatocytes isolated by this procedure were successfully maintained in culture for up to 14 days on collagen-coated plates. Isolated NPCs were further purified by FACS analysis into individual populations of LSECs, HSCs, and Kupffer cells. Purified Kupffer cells recovered from sorting were also successfully maintained in culture. Together, these systems will ultimately allow us to examine how the presence of intact liver structure and/or various NPC populations impacts liver cellular signaling in response to different immune stimuli.
TCF-1 regulates effector T cell responses upon FTY720 treatment in multiple sclerosis
Authors: Gandhi Roopali , Mazzola Maria , Raheja Radhika , Gopal Murugaiyan , Rajabi Hasan , Kumar Deepak , Pertel Thomas , Regev Keren , Griffin Russell , Aly Lilian , Kivisakk Pia , Nejad Parham , Patel Bonny , Gwanyalla NGuen , Hey Hillary , Glanz Bonnie , Chitnis Tanuja , Weiner Howard L , Gandhi Roopali 
Published: January 2023

Abstract

Background
Cytokine producing effector T helper cells are the prime mediators of inflammation during multiple sclerosis (MS) and other autoimmune diseases. The basic immune mechanisms associated with increased pro-inflammatory effector T cell function in MS are not understood. TCF-1 (T cell factor 1, also known, as TCF-7) is a transcription factor that plays an important role in T cell biology in mice.

Methods
T cells from MS patients and healthy controls were isolated to measure gene expression profiles using nanostring and qPCR. Cytokine protein expression was measured using luminex assay and flow cytometry analysis. Lentivirus vector carrying shRNA was used to knock down the expression of specific genes in CD4+ T cells. Chromatin immunoprecipitation was performed to assess TCF-1 binding to promoter regions. Luciferase assays were performed to test the regulation of IFN-γ and granzyme B by TCF-1. Western blot analysis was used to assess the phosphorylation status of Akt and GSK3β.

Results
We found that TCF-1 expression is decreased in MS T cells, and FTY720 increased the expression of TCF-1 in treated T cells. We found that FTY720 treated T cell have decreased effector phenotype as measured by decreased T cell proliferation, decreased cytokine and granzyme B production. The decreased effector phenotype of the T cells is dependent upon regulatory transcription factor, TCF-1. TCF-1 blocked T cell effector function by directly binding and negatively regulating the expression of cytokines and granzyme B. Thus, our study for the first time showed that TCF-1 regulates human effector T cell function and its decreased expression could be related to altered T cell function in MS.
Dysregulation of T helper-type cytokines appears prior to and concurrent with appearance of autoantibody specificities during early SLE pathogenesis and contributes to prognosis of transition to classified disease
Authors: Munroe Melissa , Lu Rufei , Guthridge Joel M , Bean Krista M , Fife Dustin A , Chen Hua , Slight-Webb Samantha R , Keith Michael P , Harley John B , James Judith A 
Published: January 2023

Abstract
Autoantibodies and immune dysregulation are associated with systemic lupus erythematosus (SLE), but how these factors influence disease development is unknown. This study evaluates timing and changes in SLE-linked autoantibodies and soluble mediator pathways in the years preceding SLE classification. Serial sera from 84 SLE cases spanning pre- and post-SLE classification (average time = 5.98 years) and matched healthy controls (HC) were obtained from the Department of Defense Serum Repository. Adjusting for multiple comparison, a number of soluble mediators, including IL-5 (q=4.35×10−6), IL-6 (q=8.26×10−6), and IFN-γ (q=0.037), were significantly elevated in cases vs. HC &gt;3.5 years pre-classification, prior to (IL-5 and IL-6) and concurrent with (IFN-γ) the earliest SLE-specific autoantibody specificity, anti-Ro/SSA. Th1-type, Th17-type, and TNF superfamily soluble mediators increased longitudinally in cases approaching SLE classification, but not in HC (q&lt;0.05). In particular, serum levels of BLyS and APRIL were comparable in cases and HC until &lt;10 months pre-classification (q=0.003 and q=0.019, respectively). Random forest models incorporating IL-5, IL-6, and IFN-γ levels (79–82% accuracy) distinguished future SLE patients better than models with ANA alone (58% accuracy) &gt;3.5 years before classification. These data indicate that pre-clinical immune system perturbations allow for the accumulation of autoantibodies preceding clinical symptoms and SLE classification.
A novel paradigm in the clinical context of rheumatoid arthritis: role of Tfh and Th17 Cells in autoimmunity
Authors: Zhang Xin , Budziakowska Magdalena , Shahzad Arif , Zakem Jerald , You Zongbing , Davis William , Quinet Robert 
Published: January 2023

Abstract

Introduction
Rheumatoid Arthritis (RA) is an autoimmune disease characterized by chronic inflammation of synovium causing progressive joint destruction. Recently, T follicular helper (Tfh) cells and Th17 cells have emerged as novel T cell subsets controlling autoimmunity. Identifying their roles may break the traditional Th1/Th2 axis dichotomy and bridge knowledge gap of T cell lineages on RA immunopathogenesis. We examined the frequency of circulating Tfh (cTfh) and cTh17 cells in RA patients, and investigated their correlation with disease activity, autoantibody level, and inflammation.

Methods
Peripheral blood was collected from 51 RA patients and healthy donors. RA patients were divided into remission (&lt;2.6) and active groups (&gt;2.6) based on disease activity score (DAS-28). Clinic parameters including Rheumatoid Factor (RF), Anti-CCP, ESR and CRP were obtained. The frequency of cTfh, cTh17 cells, and plasmablasts were measured by flow cytometry. Correlation of the frequency of cTfh and cTh17 cells with DAS-28, plasmablasts, and clinic parameters were statistically determined.

Results
Both cTfh and cTh17 cells were significantly increased in RA patients, expecially in active patients comparing to healthy donors (p&lt;0.05). The frequency of cTfh cells correlated with the percentage of plasmablasts and the level of pathogenic anti-CCP antibody, whereas the frequency of cTh17 cells correlated with serum level of RF and CRP as well as DAS-28.

Conclusions
Tfh cells may contribute to B cell differentiation and autoantibody production, while Th17 cells may involve in the inflamation and pathogenesis of RA. Thus, disrupting the signals provided by Tfh and Th17 cells may offer new therapeutic stategies for active RA patients.
Functional Characterization of the role of Eos (lkzf4) in CD4+ and CD8+ T cells
Authors: Gokhale Ameya Sanjeev , Gangaplara Arunakumar , Rieder Sadiye , Shevach Ethan M 
Published: January 2023

Abstract
Eos is a member of the Ikaros family of transcription factors and is preferentially expressed in T regulatory cells (Treg), and activated T conventional (Tconv) cells. The role of Eos in Treg function is controversial. One study using siRNA knock down of Eos demonstrated that Eos was critical for Treg suppressor function. In contrast, Treg from mice with a global deficiency of Eos had normal Treg phenotype and function in vitro and in vivo, but had a deficiency in IL-2 production with an enhanced Th17 response. To further dissect the function of Eos in CD4+ and CD8+Tconv cells, we evaluated the immune responses of Eosfl/flX CD4-Cre mice. IL-2 production in vitro by both CD4+ and CD8+ T cells was diminished upon polyclonal stimulation of cells from Eosfl/flX CD4-Cre mice. EAE was much more severe in the Eosfl/fl X CD4-Cre mice as compared to WT mice. The percentages of CD4+, Foxp3−, IL17+, IFNg+ T cells were significantly higher in spleen, draining lymph nodes, and spinal cord from Eosfl/fl X CD4-cre mice when compared to WT mice. However, the percentages of Treg cells were significantly higher in the WT mice. We also determined if Eos plays any role in the activation of CD8+ cells during LCMV Armstrong infection. On day 9 following infection, no differences between Eos−/− and WT mice were observed in the expansion, expression of activation markers, and cytokine production by tetramer+ LCMV-peptide-specific T cells. Virus was completely cleared on day 7 and anti-viral CTL activity both in vitro and in vivo was similar in the Eos−/− mice and WT mice. Eos appears to play a major role in regulating IL-2 production in vitro in both CD4+ and CD8+ Tconv, but only modulates CD4+, but not CD8+, T effector function in vivo.
This Research was supported by the DIR, NIAID, NIH.
CD8 T cells mediate polyomavirus-associated CNS demyelination
Authors: Mockus Taryn E , Frost Elizabeth L , Shwetank Fnu , Meadowcroft Mark , Lukacher Aron 
Published: January 2023

Abstract
JC polyomavirus (JCV), a common member of the virome in healthy humans, can cause the frequently fatal brain demyelinating disease Progressive Multifocal Leukoencephalopathy (PML) in immunocompromised individuals. PML, a pre-HAART AIDS-defining disease, has reemerged and is increasing in incidence in patients receiving immunodulatory therapies for autoimmune and inflammatory disorders. Lack of an animal model has hampered understanding of PML pathogenesis. We have developed a novel mouse model using intracerebral (i.c.) inoculation of mouse polyomavirus (MPyV), which mimics JCV-associated demyelination and shows similar histological features to PML. By one month after MPyV inoculation, C57BL/6 mice develop diffuse subcortical white matter demyelination, predominantly in the corpus callosum. Diffusion tensor magnetic resonance imaging in infected mice reveals severe peri-ventricular edema and a loss of structural integrity predominately in the corpus callosum and caudate. Virus-specific CD8 T cells robustly infiltrate the CNS and are stably maintained after CNS entry. Antibody-mediated depletion of CD4 and CD8 T cells prior to infection abrogates demyelination in the corpus callosum, despite resulting in a 50–100 fold increase in virus levels. Additionally, CD8 T cell-depletion alone was sufficient to cause higher virus levels in the brain. MPyV was controlled in the absence of CD4 T cells; however, MPyV-specific CD8 T cells in CD4 T cell-deficient mice expressed lower levels of CD103 (aE integrin), which binds epithelial E-cadherin. These data demonstrate that CD8 T cells infiltrating the CNS of MPyV-infected mice play a major role in this demyelinating leukoencephalitis.
Role of GITR and its ligand in sustaining T cell responses against influenza infection
Authors: Chu Kuan Lun , Clouthier Derek L , Watts Tania H 
Published: January 2023

Abstract
Members of the TNFR family play a critical role in determining the magnitude of T cell responses against viral infections. Previous studies using TCR transgenic models showed that GITR, an NF-κB activating TNFR family member, is required intrinsically on CD8 T cells for maximal response against influenza virus. However, it remains unknown how GITR affects the overall endogenous T cell responses during influenza infection. Here, we examined the effect of GITR on endogenous T cell responses against influenza virus in competitive mixed bone marrow chimeras. We found that GITR is intrinsically required for the accumulation of antigen-specific CD4 and CD8 T cells in the lung and secondary lymphoid organs during influenza infection. GITR affected influenza PA224-233-specific CD8 T cells more dramatically than NP366-374-specific CD8 T cells. GITR also had a small positive effect on the number of Tregs. Among different APC subsets in the lung and its dLN, we observed highest GITRL expression on inflammatory DCs and inflammatory macrophages in both organs. Interestingly, we observed peak GITRL expression on these inflammatory subsets on day 3 and day 5 post-influenza infection in the lung but earlier in the dLN. The finding that GITRL is expressed on inflammatory APCs in the lung at the time when T cells enter the lung raises the possibility that GITRL plays a role in the lung tissue and not just in lymphoid organs. We are currently investigating when and where T cells receive signals through GITR, whether early in the dLN or later in the lung during influenza infection. A more thorough understanding of GITR/GITRL axis will provide valuable insights for influenza vaccine development.
T cell help amplifies innate signals in CD8+ DC for optimal CD8+ T cell priming
Authors: Bedoui Sammy 
Published: January 2023

Abstract
DC often require stimulation from CD4+ T cells to propagate CD8+ T cell responses, but precisely how T cell help optimizes the priming capacity of DC and why this appears to differ between varying types of CD8+ T cell immunity remains unclear. We show that CD8+ T cell priming upon HSV-1 skin infection depended on DC receiving stimulation from both IFN-α/β and CD4+ T cells to provide IL-15. This was not an additive effect, but resulted from CD4+ T cells amplifying DC production of IL-15 in response to IFN-α/β. We also observed that increased innate stimulation reversed the helper-dependence of CD8+ T cell priming and that the innate stimulus, rather than the CD4+ T cells themselves, determined how ‘help’ was integrated into the priming response by DC. These findings identify T cell help as a flexible means to amplify varying suboptimal innate signals in DC.
ThCTL expressing NKG2A/C/E represent a unique CD4 cytotoxic effector subset.
Authors: Vong Allen M , Marshall Nikki B , Kuang Yi , Swain Susan L 
Published: January 2023

Abstract
Activated CD4 T cells differentiate into effector subsets tailored to fight widely diverse pathogens. CD4 T cell effectors can help antibody responses, secrete effector cytokines, and lyse infected cells. Cytotoxic CD4 T cells, termed ThCTL, synergize with antibody to provide strong protection against a lethal infection with influenza A virus (IAV) in mice and correlate with better disease outcome in humans. However, their regulation in vivo is not well studied. We find that IAV-generated ThCTL is localized to the lung, the site of viral replication, and express NKG2A/C/E, which is expressed only on a fraction of CD4 effectors. The expression of this marker does not impact cytotoxicity but may play a role in the infiltration or survival of the ThCTL. We used NKG2A/C/E to further characterize the ThCTL subset. We found that ThCTL can secrete effector cytokines, IFNg and TNFa and that they express markers consistent with high levels of activation and cytotoxicity. Microarray analysis indicates these ThCTL down-regulate markers for circulation: Ccr7, S1p1r, and Klf2, while up-regulating cytotoxic molecules: Prf1, Gzmc, and Gzmf. We find the generation of ThCTL in vivo is regulated by the context of late antigen and co-stimulation, such that ThCTL can be induced from effectors at day 6 post infection. Taken together, ThCTL consist of an activated subset of CD4 T cells with unique properties to combat IAV infection.