bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early TNFα signaling results in pulmonary DC1 polarization and programing of murine myeloid precursor cells in the bone marrow towards DC1 polarization throughout Cryptococcus neoformans infection
Authors: Eastman Alison J , Potchen Nicole , Zhou Guolei , Xu Jintao , Neal Lori , Malachowski Antoni , Kunkel Steven L , Kryczek Ilona , Osterholzer John J , Olszewski Michal A 
Published: January 2023

Abstract
TNFα is required for protective Th1/Th17 immunity to Cryptococcus neoformans (CN), an opportunistic pulmonary fungal pathogen. The effects of TNFα are linked to the stable, early classical activation of dendritic cells (DC1), preventing alternative (DC2) activation. We hypothesized that TNFα signaling facilitates epigenetic modification of key DC genes during CN infection. We tested this hypothesis using CBA/J mice infected intratracheally with CN and injected once on day 0 intraperitoneally with control or a TNFα-depleting antibody (αTNFα). αTNFα mice had no difference in pulmonary CFU at 7 days post-infection (dpi), but had significantly higher fungal burden and extrapulmonary dissemination at 14 and 28 dpi. DCs from the lungs of control mice at 7 dpi had increased association of iNOS and IL-12b promoters with the activating modification histone 3 lysine 4 trimethylation (H3K4me3), while DCs from αTNFα mice did not. Because DCs have a relatively short half-life during infection, we assessed the bone marrow (BM) myeloid precursor cells (MPCs) from infected animals with and without TNFα. Intranuclear flow cytometry for H3K4me3 showed distinct patterns of global trimethylation between infected control and αTNFα mice as early as 7 dpi. We next tested whether BM-derived DCs (BMDCs) matured ex vivo from infected animals would yield DC1 or DC2 cells. BMDCs from control animals became DC1, and resisted changes to polarization when challenged with the DC2-skewing IL-4, while BMDCs matured from TNFα-depleted mice maintained DC2 polarization when challenged with IFNγ. We conclude that TNFα epigenetically modifies key DC1 genes in MPCs, thereby sustaining lasting DC1 programing of DCs required for clearance of CN from the infected lungs.
The mechanisms of Gamma delta T cells in the occurrence and development of hepatocellular carcinoma
Authors: Ye Yanshuo , Wang Zhanpeng , Li Zhuonan , Liu Hongyu , Li Wei 
Published: January 2023

Abstract
γδ T cells are unique population of T cells in which their function still remain unclear. We have demonstrated that γδ T cell mainly located in the liver in mice. Our previous data based on liver transplantation model suggests that γδT cells are involved in the processes of liver transplant tolerance and rejection, and may play a role in the induction of liver graft rejection. In contrast to Foxp3+ CD4+ CD25+ Treg, the majority of γδT cells were mainly located in the liver and did not express TCRαβ and NK receptors, but expressed moderate levels of PD-1 and PD-L1 molecules. It has recently been shown that γδT cells play an important role against tumors and infectious diseases.

Methods
In this study we employed mouse orthotopic hepatocellular carcinoma model, critically examine the role of γδ T cells in the liver and peripheral on liver cancer development.

Results
The ratio of CD3+ T cells were decreased, but γδ T cells were increased in the surrounding tissue of the tumor and the spleen. Anti-γδ T cells antibody plus IL-2 treatment to tumor barrier mice could further increase the γδ T cells in the liver and spleen and limited the growth of the tumor.

Conclusion
γδ T cell may plays an important role in immunologic defence against hepatocellular carcinoma. More studies underlying the mechanisms and interplay among liver immune cells are under investigation.
Dendritic cell subset positioning governs clonal diversity and magnitude of the CD8 T cell response
Authors: Gerner Michael , Kastenmuller Wolfgang , Germain Ronald N 
Published: January 2023

Abstract
Although the molecular requirements for CD8 T cell responses have been well characterized, subunit vaccine formulations struggle to generate robust CD8 T cell immunity. One possible basis for this may be the relationship of dendritic cell (DC) subset topography to micro-anatomically dictated antigen dispersal and subsequent down-stream innate and adaptive cellular engagement. To address this issue directly in situ we utilized advanced quantitative imaging approaches (histo-cytometry) and found that protein immunization led to non-linear concentration gradients across draining lymph nodes. This graded distribution in turn affected which DC subset had access to high vs. low concentrations of antigen. Because DC subsets are specialized in MHC-I vs. MHC-II antigen processing and presentation, the result of this intersection of antigen dispersal and cell positioning was the predominant residence of MHC-I presenting DC in regions with lower antigen bioavailability. Modulating the antigen dose directly influenced the fraction of MHC-I presenting DC with access to sufficient antigen to activate T cells, allowing for direct control over the clonal diversity and magnitude of the response. These findings indicate that tissue microanatomy related to DC subset distribution and antigen dissemination within the lymph node is a critical regulator of CD8 T cell immunity.
This research was supported by the Intramural Research Program of the NIH, NIAID.
Dysfunctional expansion of immature granulocytes in sepsis survivors.
Authors: Fei Yurong , Chiu Pui Yan , Diamond Betty , Sherry Barbara 
Published: January 2023

Abstract
Sepsis is one of the leading causes of death worldwide. Surprisingly, increased mortality persists for years in sepsis survivors. This project investigated the contribution of myeloid cells to immune impairment in sepsis surviving mice. Sepsis was induced by cecal ligation and puncture (CLP). Sepsis survivors (2 weeks post-surgery) had significant increases in the CD11b+ Ly6Chigh and CD11b+ Ly6Clow myeloid populations in spleen, bone marrow and blood compared to controls. The expanded CD11b+ Ly6C populations in survivors were F4/80 negative. More CD11b+ Ly6C cells expressed the chemokine receptors CX3CR1 and CCR2, and the adhesion molecule CD62L. CD11b+ Ly6C populations in survivors also had higher levels of the mannose receptor CD206, Mer tyrosine kinase and the inhibitory collagen receptor LAIR-1; they appeared to be M2 like macrophages with presumed immune suppressive activity. Approximately 12% of the CD11b+Ly6Chigh population were CD115+ monocytes/macrophages, while the CD11b+ Ly6Clow comprised mainly immature granulocytes. CD11b+ Ly6Clow granulocytes in sepsis survivors had significantly reduced phagocytic activity compared to controls. A significant reduction in CD11b+ Ly6Clow granulocytes after LPS treatment was observed in controls but not survivors. Importantly, survivors had diminished serum production of TNF in response to endotoxin challenge, even though CD11b+ Ly6C granulocytes from the same mice produced comparable intracellular levels of TNF. In summary, our data indicate impaired cell exit and cytokine secretion, which is in part due to altered cell surface properties. This dysfunctional expansion of immature granulocytes may contribute to the impaired immune response in sepsis survivors.
Kupffer cell subsets differ between young and aged murine livers.
Authors: Stahl Elizabeth C , Brown Bryan N 
Published: January 2023

Abstract
The immune system, and in particular macrophages, are heavily implicated in wound healing, response to infection, and cancer progression, all of which are linked to mortality in the elderly population. Recently, it has been shown that tissue-resident macrophages from spleen and peritoneum become dysfunctional with aging, likely due to the aged microenvironment. The liver contains approximately 80% of total mammalian tissue-resident macrophages, known as Kupffer cells. Kupffer cells can be divided into two F4/80+ macrophage subsets: CD68+ and CD11b+ cells, which have different origins and functions. Currently, it is unclear how these macrophage subsets are affected by aging.
We sought to characterize differences in the Kupffer cell compartment from young (8–10 week) and aged (18–20 month) C57/Bl6 mice using immunofluorescent staining on tissue sections and flow cytometry. Preliminary histological analyses showed that the area of F4/80+ staining did not differ between young and aged mice. Interestingly the area of CD68+ staining was significantly higher in the aged murine livers. In addition, the area of CD32+ staining, which marks both endothelial cells and macrophage precursors, was significantly greater in aged mice, consistent with previous reports of blood vessel thickening in aged livers. Flow cytometry analysis confirmed differences in the macrophage subsets between young and aged murine livers. In addition, functional changes in phagocytosis were noted with aging, suggesting dysfunction of innate abilities. Characterizing the differences in the subsets of tissue-resident macrophages during aging will increase our understanding of age-related pathologies that will aid in the design of therapies in the future.
MiR-150 negatively regulates CD8+ T cell memory formation
Authors: Chen Zeyu , Stelekati Erietta , Kurachi Makoto , Yu Sixiang , Manne Sasikanth , Wherry E. John 
Published: January 2023

Abstract
MicroRNAs play an important role in CD8+ T cell differentiation and anti-viral immune responses. However, how microRNAs regulate CD8+ T cell memory formation remains poorly defined. Here, by microRNA profiling of CD8+ T cell during acute or chronic LCMV infection, we identified microRNAs that are specifically enriched in memory CD8+ T cells comparing to naïve, effector or exhausted CD8+ T cells. MiR-150, a microRNA that has been shown to be important in multiple biological processes, was identified as a potential memory CD8+ T cell biased microRNA. Functional interrogation of the role of miR-150 demonstrated that absence of miR-150 in CD8+ T cells enhanced memory CD8+ T cell differentiation, by both increasing KLRG-CD127+ memory precursors population during effector phase and enhancing CD127+CXCR3+ central memory phenotype long-term. Overexpression of miR-150 in CD8+ T cells, in contrast, negatively regulated CD8+ T cell memory formation. Furthermore, we found that miR-150 KO CD8+ T cells had higher expression of c-Myb comparing to miR-150 WT CD8+ T cells, a result observed using both in vitro CD8+ T cell differentiation and following infection with LCMV-Armstrong in vivo. Gene expression analysis implicated a relationship between the level of c-Myb expression and CD8+ T cell memory formation through potential anti-apoptotic molecules such as bcl-2. Thus, our studies identify a key role for miR-150 in CD8+ T cell memory and implicate a mechanism of CD8+ T cell memory effect by this microRNA through regulation of c-Myb.
TCR signal strength regulates Akt substrate specificity to induce alternate Th and Treg differentiation programs
Authors: Morel Penelope A , Hawse William F , Sheehan Robert P , Boggess William C , Faeder James R 
Published: January 2023

Abstract
T regulatory (Treg) cells are induced following stimulation of naïve CD4 T cells with low dose antigen to an extent that is negatively correlated with signaling via the Akt/mTOR pathway. Strong TCR signals induce high levels of Akt activity that inhibit development of Treg by poorly understood mechanisms. Here, we show that high dose stimulation of T cells results in the phosphorylation of Akt on two regulatory sites, Serine (S) 473 and Threonine (T) 308, whereas low dose stimulation results in only T308 phosphorylation. Mathematical modeling shows that the phosphorylation of Akt on both S473 and T308 is controlled by a feedback loop involving PTEN, mTORC2 and the transcription factor FoxO1 that creates a sharp activation threshold with respect to antigen dose and stimulus duration. Using mass spectrometry to analyze phosphorylated Akt substrates at different levels of stimulation, we find profound differences in the substrates phosphorylated, suggesting that a switch in substrate specificity coupled to the phosphorylation status of Akt may lead to alternative cell fates. Proteins differentially phosphorylated by these two states of Akt include RNA splicing factors, and we find changes in the splice variant expression levels of key TCR signaling proteins, such as CD3ζ and CD45 that correlate with the observed differences in cell fate. Knockdown of specific splicing factors impacted the ratios of Th versus Treg cells induced. Together, this work demonstrates that alternative splicing can affect the outcome of T cell fate decisions and identifies alternate Akt-mediated signaling networks that drive CD4+ T cell differentiation.
Early signalling changes in T cells with aging
Authors: Fulop Tamas , Le Page Aurélie , Dupuis Gilles , Larbi Anis 
Published: January 2023

Abstract
Aging is accompanied by many physiological changes and the immune system is not escaping this. This effect of time is affecting most cells of the immune system. Numerous changes have been described but most of them are phenomenological, a typical example is the change of phenotypes in T cells. We are interested since years to uncover the intracellular signaling associated with phenotypic and functional changes of various immune cells. We identified several signaling alterations starting from the early to the most downstream events in several cells like neutrophils, monocytes and T lymphocytes. We not only were interested in the forward signaling driven by kinases but also by the feedback or regulatory signaling mediated by phosphatases. We found profound alterations of regulatory phosphatases activity and phosphorylation (e.g. SHP-1). The question was always whether these changes are occurring also uniformly in T cell or there are differences between the various subpopulations (naive to the continuum of memory T cells). Our studies indicate that there are changes according to the subpopulations and that basal hyper-phosphorylation status we observe may be explained by signaling crosstalks. We also observed that there is a resemblance between naïve and TEMRA T cells, which differ much from CM and RM cells. In conclusion the different T cell subpopulations may have very specific changes distinguishing them from each other. This needs further investigations in relation to their functions.
Inhibition of T cell activation by Borrelia burgdorferi
Authors: Whiteside Sarah , Snook Jeremy P , Ma Ying , Weis John H , Williams Matthew A , Weis Janis J 
Published: January 2023

Abstract
Infection with the spirochete B. burgdorferi induces both innate and adaptive immune responses, which coordinate to control disease progression. Previous studies have demonstrated that Borrelia specific antibodies are critical to the control and resolution of infection. The antibody response is characterized by T cell-independent recognition of numerous B. burgdorferi lipoproteins, which contribute to protection from subsequent challenge. In contrast, the role of T cells in protective vs. disease modulating responses to B. burgdorferi infection is poorly understood. The failure to identify protective T cell epitopes of B. burgdorferi in both mice and humans has limited this line of investigation. We have identified bystander activation of CD4+ and CD8+ T cells during infection, a feature that may obscure the identification of antigen-specific T cell responses. Paradoxically, we have also identified a novel modulatory activity in B. burgdorferi that suppresses activation and proliferation of both CD4+ and CD8+ T cells. Suppression can be demonstrated in naïve cells from wild type and SMARTA TCR transgenic mice, indicating the ability to override antigen specific and potentially protective immune responses. Our results are consistent with those of Elsner et al., indicating that B. burgdorferi infection results in temporary immunosuppression of the host. Experiments are ongoing to identify potential molecular mechanisms of suppression.
Quantitative proteomics to predict functional consequences of ubiquitylation events during T cell stimulation
Authors: O’Leary Claire E , Ding Hua , Spruce Lynn , Fazelinia Hossein , Seeholzer Steven , Oliver Paula M 
Published: January 2023

Abstract
The post-translational attachment of ubiquitin to cellular proteins can alter protein function and half-life, thereby profoundly impacting cell signaling and fate decisions. New proteomics-based techniques have been developed that have the potential to reveal relationships between ubiquitylation and protein fate. Here, we assess the feasibility and scalability of using quantitative proteomic approaches to identify ubiquitylated proteins in primary T cells in a high throughput manner. Furthermore, we sought to identify TCR-dependent changes in protein ubiquitylation. We utilized immunoprecipitation of ubiquitin remnant peptides (peptides with modified lysine residues) and quantitative mass spectrometry to quantify changes in protein-specific ubiquitylation in CD4+ T cells stimulated via the TCR compared to resting T cells. Our analysis identifies thousands of modified lysines in primary T cells, and reveals dynamic changes in ubiquitylation of hundred of proteins, including key signaling transducers, during TCR stimulation. We then performed whole cell proteomic analysis to quantify changes in relative protein abundance during T cell activation. By comparing changes in ubiquitylation with changes in protein abundance in stimulated CD4+ T cells, these data can be used as a resource to predict the consequences of TCR-induced protein ubiquitylation. This work establishes ubiquitin remnant profiling and whole proteome analysis as important techniques for global analysis of ubiquitylation in primary T cells.
The transcription factor IRF8 regulates natural killer cell development and response to cytomegalovirus infection
Authors: Adams Nicholas M , Rapp Moritz , Sun Joseph Chai-Yuen 
Published: January 2023

Abstract
Interferon regulatory factor 8 (IRF8) is a transcription factor critical for specifying monocyte and dendritic cell lineage fate and for directing B cell development, yet its function in natural killer (NK) cells is not understood. NK cells are innate lymphocytes that develop in the bone marrow and are capable of antigen-specific clonal proliferation. We observe in mixed bone marrow chimeric mice that despite a prevalent NK progenitor (NKP) population compared to wild-type, peripheral Irf8−/− NK cells exhibit proper maturation and full functionality. However, using an adoptive transfer system, we demonstrate that IRF8 is indispensable for robust expansion of NK cells in response to mouse cytomegalovirus (MCMV). Consistent with this finding, Ly49H+ NK cells upregulate Irf8 transcript during the early stages of MCMV infection. Furthermore, the Irf8 locus is dynamically regulated upon activation, showing extensive STAT4 binding at promoter and enhancer regions, and upregulation of the activating epigenetic marks H3K4me3 and H3K4Ac27. Thus, our work elucidates the functional contribution of IRF8 during NK cell development and antiviral responses.
Regulation of cytotoxic T cell and germinal center B cell responses by the c-MYC-AP4 transcription factor cascade
Authors: Chou Chun Jim , Pinto Amelia K , Persaud Stephen P , Verbaro Daniel J , Tonc Elena , Holmgren Melanie , Cella Marina , Allen Paul M , Colonna Marco , Bhattacharya Deepta , Diamond Michael S , Egawa Takeshi 
Published: January 2023

Abstract
The process of amplifying immune responses by expanding a pool of antigen-specific cells, termed clonal expansion, is an important feature of the adaptive immunity. Whereas clonal expansion of cytotoxic T lymphocytes is required for complete eradication of pathogens in tissues, proliferation of B lymphocytes in the germinal centers is critical for generating a diverse immunoglobulin gene repertoire from which protective antibody carrying multiple mutations can arise. While the proto-oncogene c-MYC is absolutely required for the activation and cell cycle initiation in lymphocytes, its expression is temporally restricted. Activated lymphocytes, however, continue to proliferate after c-MYC levels decay to maximize clonal expansion. It remains unknown how lymphocytes sustain their proliferative program in the absence of c-MYC. We demonstrated that the c-MYC-inducible transcription factor, AP4, is required for sustained expansion of antigen-specific lymphocytes. Mice lacking AP4 in T cells exhibit diminished cytotoxic T cell responses and succumb to West Nile virus infection due to uncontrolled viral replication in the central nervous system. Furthermore, conditional deletion of AP4 in B lymphocytes impaired germinal center growth. These mice failed to control chronic viral infection due to blunted neutralizing antibody responses. ChIP-seq and gene expression analyses revealed a significant overlap between AP4 and c-MYC regulated genes. Thus, the c-MYC-AP4 transcription factor cascade is a general module utilized by activated lymphocytes to maximize immune responses.
The Notch signaling pathway: a new mastor regulator of effector CD8 T cell differentiation
Authors: Duval Frédéric Antoine , Mathieu Mélissa , Daudelin Jean-François , Labrecque Nathalie 
Published: January 2023

Abstract
Following an infection, naïve CD8 T cells expand and differentiate into effectors able to eliminate the pathogen. At the peak of the response, two major populations of effectors are distinguishable: short-lived effector cells (SLECs) meant to die by apoptosis and memory precursor effector cells (MPECs) destined to survive as memory cells that confer long-term protection. We postulated that the Notch signaling pathway, known for its role in cellular differentiation and binary cell fate choice, acts as a key player in the MPEC/SLEC differentiation choice. To elucidate the role of Notch signalling, we have analyzed CD8 T cell response in mice lacking or not the expression of Notch1 and Notch2 in mature CD8 T cells. Following infection with Listeria or vaccination with antigen-pulsed dendritic cells, Notch deficiency drastically diminished SLEC generation and affect cytokines production without impairing CD8 memory T cell generation. Interestingly, altered SLEC differentiation occurs despite normal expression of the transcription factors, T-bet and Blimp-1, known to be necessary for SLEC differentiation. Moreover, the reduced generation of SLECs in absence of Notch signaling correlated with defective expression of CD25 by effectors. However, restoration of CD25 expression along with daily IL-2 complementation in Notch1/2-deficient T cells did not correct SLEC differentiation. These results suggest either that Notch regulates the expression of new players involved in SLEC differentiation or Notch signaling collaborates with already known actors of SLEC differentiation such as T-bet or Blimp-1. The identification of the genes regulated by Notch should help to reveal its role in CD8 T cell response.