bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of anti-inflammatory alveolar macrophages associates with lung inflammation in untreated HIV infection
Authors: Neff Charles Preston , Logue Eric C , Siebert Janet , Görg Carsten , Fiorillo Suzanne , Twigg Homer L , Campbell Thomas B. , Fontenot Andrew P , Palmer Brent E 
Published: January 2023

Abstract
HIV-1 is associated with infectious and noninfectious lung disease, both of which are exacerbated by cigarette smoke. Alveolar macrophages (AMs) are the most prominent immune cell in the alveolar space. These cells play an important role in clearing inhaled pathogens and regulating the inflammatory environment, however, how HIV infection impacts AM function is not well understood, in part due to their autofluorescent properties. The aim of this study was to evaluate the impact of HIV infection on AMs. Utilizing Time of Flight Mass Cytometry (CyTOF) and RNAseq we characterized macrophages from bronchoalveolar lavage (BAL) of HIV-infected and uninfected smokers and nonsmokers. We found that the frequency of alternatively activated AMs, defined by expression of CD163 and CD206, was decreased, while CD163-CCR7+ AM were increased in HIV infection. This phenotype was associated with increased levels of inflammatory cytokines and macrophage activation. While the inflammatory state of macrophages was not impacted by cigarette smoke, other markers such as TLR4 and CXCR4, which are associated with heightened inflammatory response to bacterial products and HIV infection, were altered with smoking. These findings suggest that HIV infection is associated with an increase in pro-inflammatory and depletion of anti-inflammatory AMs, which along with cigarette smoke-induced TLR4 and CXCR4 expression contributes to increased inflammation in the lung. Furthermore, this study demonstrates that CyTOF is a reliable method for immunophenotyping highly autofluorescent cells isolated from the bronchoalveolar lavage of cigarette smokers.
Hepatocytes engulf and rapidly silence coxsackievirus, protecting the host against systemic viral pathology
Authors: Kimura Taishi , Flynn Claudia T , Whitton J Lindsay 
Published: January 2023

Abstract
Liver has many biological functions, including (but by no means limited to) the removal, from the blood, of various pathogenic organisms. This phenomenon has been best-studied for bacteria, and is thought to be mainly mediated by Kupffer cells and sinusoidal endothelial cells; these cells, too, have been implicated in clearance of some viruses. However, to date, hepatocytes - which constitute ~90% of the liver’s biomass - have been thought to be bystanders in this activity. Herein we show that hepatocytes directly protect the host against type B coxsackieviruses (CVBs) by engulfing, then rapidly silencing, these pathogens. Novel CARHEP KO mice, which carry a hepatocyte-specific deletion of the coxsackievirus-adenovirus receptor (CAR), are unable to capture circulating CVB3, leading to a dramatic early rise in blood-borne virus, followed by markedly-elevated morbidity, mortality, and increased viral load. The enhanced pathogenicity in CARHEP KO mice occurs despite the production of abundant type I interferon (T1IFN), which is derived from plasmacytoid dendritic cells (pDCs). In addition, we show that in genetically-intact (wild type; WT) mice, the rapid hepatocyte silencing of trapped virus is dependent on IRF1; in its absence, CVB3 undergoes efficient productive replication in hepatocytes and, as a result, virus titers in all tested extrahepatic tissues are several logs higher than in WT animals. In summary, hepatocytes act as a trap for CVBs, internalizing the viruses and reducing systemic viral burden, and thereby protecting the host from systemic disease.
ThG cells: a distinct T helper cell subset expressing GM-CSF, TNF, and IL-2, but not Th lineage-specific cytokines
Authors: Rasouli Javad , Casella Giacomo , Zhang Weifeng , Xiao Dan , Zhang Guang-Xian , Ciric Bogoljub , Rostami Abdolmohamad 
Published: January 2023

Abstract
The diversity of human antigen-experienced (CD45RA−) CD4+ T cells in the blood has not been fully elucidated. Using single cells RNA-seq and high-dimensional single-cell mass cytometry (CyTOF), we identified eight distinct populations of CD45RA−CD4+ T cells in peripheral blood of healthy donors. In addition to Tregs and established Th lineages, we also identified a distinct population of T cells that expressed GM-CSF, but lacked expression of master transcription factors and signature cytokines of other Th cell lineages. These cells, which we tentatively designated “ThG”, co-expressed GM-CSF, IL-2, TNF, IL-3 and CCL20. ThG cells had a stable phenotype and were highly encephalitogenic. Similar to Th17 cells, ThG cells switched their phenotype to Th1 in response to IL-12. T-bet was not required for ThG development, but it was required for their encephalitogenicity. Analogous to other Th cells, ThG cells had a tendency to eventually cease GM-CSF expression without other major changes in their phenotype, which clearly opens the possibility that GM-CSF− ThG cells actually exist.
The effects of α-MSH on epidermal γδ T cell activation and function
Authors: Darby Taylor , Jameson Julie M 
Published: January 2023

Abstract
The hair follicle is a site of immune privilege that, when disrupted, results in the autoimmune disorder alopecia areata. Although there are a variety of cell types that reside near the hair follicle and may be involved in the initiation of alopecia areata, few studies have focused on γδ T cells. γδ T cells are resident in epithelial tissues where they normally play roles in inflammation and wound healing. Alpha-melanocyte-stimulating(α-MSH) is an immunoregulator locally produced within the hair follicle. α-MSH ensures the immune system is suppressed during anagen phase (growth phase) and restored during catagen phase (resting phase). The effects of α-MSH on epidermal γδ T cells via MC1R, one of five melanocortin receptors, is unknown. We therefore purified primary epidermal γδ T cells to investigate the immunomodulatory effects of α-MSH. Flow cytometry and the Luminex platform were used to compare changes in MC1R expression levels and cytokine production in response to α-MSH. Here we show that resting epidermal γδ T cells express MC1R, and TCR stimulation increases MC1R expression. Upregulation of MC1R expression is augmented further by stimulation with α-MSH. Epidermal γδ T cells significantly upregulate immunostimulatory cytokines when stimulated with anti-CD3, but cytokine production did not significantly change with the addition of α-MSH. Additional findings suggest that α-MSH instead plays a role in MC1R regulated pathways such as DNA repair and cell survival. This study begins to delineate the mechanisms by which α-MSH impacts γδ T cell function and leads to the disruption of immune privilege that occurs in alopecia areata.
Decoding patterns of macrophage TNF production to model NF-κB dynamics and cell-cell communication
Authors: Cruz J. Agustin , Gottschalk Rachel A. , Lee Robin E.C. 
Published: January 2023

Abstract
Immune and stromal cells communicate through cytokines to initiate intracellular signaling, gene expression, and a multifaceted immune response. Cytokine signaling coordinates the dynamics of intracellular pathways that regulate inflammation. Immune and stromal cells both produce and respond to tumor necrosis factor-alpha (TNF), mediating inflammation and enabling communication between these compartments. The inflammatory role of TNF, activating the nuclear factor-κB (NF-κB) signaling and mitogen-activated protein kinase (MAPK) pathways, is well known. However, the effect of varying the time and amplitude patterns of TNF production in neighboring immune and stromal cells has not been systematically studied. Moreover, little is known about how time and amplitude patterns of an inflammatory signal input impact the nature of inflammatory responses. To study this relationship between production and response to TNF and its role in the dynamics of TNF-dependent NF-κB and MAPK signaling, we are using a systems immunology approach. Specifically, we are experimentally determining the patterns of TNF produced by human macrophages stimulated with heat-killed bacteria and characterizing the effect of these TNF stimulation patterns in the dynamics of NF-κB and MAPK responses in human cell lines. Additionally, we will use these experimental results to calibrate our deterministic 2 feedback with competitor (D2FC) mathematical model and model the dynamics of NF-κB signaling. Findings from this research will likely apply to other cytokine and signaling pathways, contributing to understanding the integration of time varying cytokine stimuli.
De novo T cell development in humans favors the early formation of memory phenotype cells: insights from SCID-X1 patients treated with gene therapy
Authors: Boi Shannon Kathryn , Abdelsamed Hossam Aly , Mamcarz Ewelina ,   LVXSCID-ND Clinical Group, Gottschalk Stephen , Youngblood Benjamin A 
Published: January 2023

Abstract
We recently reported that treatment of SCID-X1 infants (X-linked severe combined immunodeficiency) with autologous bone marrow expressing the corrected IL2RG resulted in reconstitution of T, B, and NK cells (Mamcarz et al., NEJM. 2019). Longitudinal observation of these patients undergoing immune reconstitution affords the unique ability to study human T cell development in real time. Accordingly, we observed that during the first few weeks of reconstitution, T cells egressing early into the peripheral blood were primarily demarcated by CD45RO+ expression, a memory phenotype. After establishing memory-like cells, CCR7+CD45RO− naive T cells appeared, and both populations continued to increase in absolute counts over time. Phenotypic analysis of CD45RO+ cells demonstrated an enrichment of NKG2A+ memory-like phenotype (MP) T cells. Moreover, epigenetic analysis by DNA methylation profiling of CD45RO+ cells exhibited a hybrid state of naïve and effector programs among the memory population. Culture of isolated MP T cells in IL-12/IL-18 from SCID-X1 patients resulted in expression of IFNg in an antigen-independent manner. Collectively, these data suggest that MP T cells develop early in humans and are endowed with the capacity to rapidly elicit effector cytokines in an antigen-independent manner.
Monoallelic and monogenic Tcrb assembly enforced by Vβ recombination signal sequences and physiological roles for Tcrb repertoire and allelic exclusion
Authors: Wu Glendon S , Bassing Craig 
Published: January 2023

Abstract
Monoallelic expression of antigen receptor (AgR) genes is assumed to be critical for the proper selection and function of T and B lymphocytes. V(D)J recombination of Tcrb, Igh, and Igk loci is regulated such that most cells assemble and express functional AgR genes from one allele (allelic exclusion). The V gene segment recombination signal sequences (RSSs) of Tcrb and Igh loci are weak and have been proposed to mediate monoallelic V-to-DJ recombination. To test the role of Vβ RSSs in promoting Tcrb allelic exclusion, we created and studied mice harboring replacements of the DJCβ-distal V2 and -proximal V31 RSSs with the stronger 3′Dβ1 RSS. Here, we show a substantial role for weak Vβ RSSs in limiting: Vβ recombination frequency, biallelic functional Vβ-to-DJβ recombination and biallelic TCRβ expression, and dual TCRβ chain expression encoded by a single Tcrb allele. Our data indicate that weak Vβ RSSs limit Vβ recombination to promote monogenic Tcrb assembly in the time window before feedback inhibition halts Vβ recombination. Given that AgR allelic exclusion is most stringently applied to Tcrb and Igh, whose assembly and expression drives cellular proliferation, we hypothesized that mechanisms directing monoallelic induction of RAG double strand breaks (DSBs) evolved at Tcrb and Igh loci in part to suppress DSBs from entering S phase and forming oncogenic AgR translocations. We find that p53D/D mice with V2 and V31 RSS replacements succumb more rapidly to thymic lymphomas than their p53D/D counterparts, which is consistent with our model. As Vβ RSS replacement mice exhibit dramatic shifts in the Vβ repertoire, we also have begun using them to test relationships between Vβ repertoire and host defense.
Thymic epithelial miR-155 promotes regulatory T cell development through safeguarding medullary thymic epithelial cell maturation
Authors: Dong Jiayi , Warner Lindsey M. , Lin Ling-Li , Chen Mei-Chi , O’Connell Ryan M , Lu Li-Fan 
Published: January 2023

Abstract
During thymocyte development, medullary thymic epithelial cells (mTECs) provide appropriate instructive cues in the thymic microenvironment for not only negative selection but also the generation of regulatory T (Treg) cells. Here, we identify that miR-155, a microRNA whose expression in Treg cells has previously been shown to be crucial for their development and homeostasis, also contributes to thymic Treg (tTreg) cell differentiation by promoting mTEC maturation. Mechanistically, we show that RANKL stimulation induces expression of miR-155 to safeguard the thymic medulla through targeting multiple known and previously uncharacterized molecules within the TGFβ signaling pathway, which is recognized for its role in restricting the maturation and expansion of mTECs. Our work uncovers a miR-155-TGFβ axis in the thymic medulla to determine mTEC maturity and, consequently, the quantity of tTreg cells and suggests that miR-155 ensures proper tTreg cell development in both cell-intrinsic and -extrinsic manners.
In vitro and in vivo modulation of Hematopoietic Stem Cell (HSCs) differentiation into T and B cells by poly dispersed acid-functionalized single-walled carbon nanotubes (AF-SWCNTs)
Authors: MIA MD. BABU , SAXENA RAJIV KRISHNA 
Published: January 2023

Abstract

Background
AF-SWCNTs are known to have significant effect on the immune function. There is not much information available on the effect of carbon nanotubes (CNTs) on the differentiation of the HSCs. In the present study we have focused on studying the modulatory effects of AF-SWCNTs on the differentiation of HSCs into T & B cells.

Methods
Single-walled CNTs were acid-functionalized by treating with concentrated sulfuric & nitric acid; thus, tagged with Alexa Fluor 633 to get fluorescent AF-SWCNTs (FAF-SWCNTs). To study internalization, magnetic beads enriched C57bl/6 mouse bone marrow (BM) HSCs (Lin− Sca1+cKit+) were incubated with FAF-SWCNTs & studied using flow cytometry & confocal microscopy. HSCs were cultured with a cocktail of cytokines to induce differentiation to T & B cells, in (+/−) AF-SWCNTs & monitored by live cell imaging. For in vivo ontogenesis study, mice were lethally irradiated (gamma irradiation) & reconstituted using syngeneic BM cells pretreated (+/−) AF-SWCNTs. At different time points, appearance of T & B cells in the spleen was monitored.

Results
Our results indicate that HSCs internalized significant amounts of FAF-SWCNTs in vitro that remained essentially localized in cytoplasm. Differentiation of cytokines stimulated HSCs to T & B cell was significantly suppressed by AF-SWCNTs. Results of our in vivo experiments indicated that after 17th day of BM transplantation, significant numbers of T & B cells appeared in the reconstituted mouse spleen. However, when AF-SWCNTs pretreated BM cells used to reconstitute irradiated mice, significant decline in both of their percentage & absolute recovery was noted. These results indicate that CNTs may significantly modulate the differentiation of HSCs into lymphocytes.
Redox regulation of autophagy in thymic stromal cell function
Authors: Semwal Manpreet Kaur , Hester Allison K , Xiao Yangming , Udeaja Chioma , Venables Thomas , Griffith Ann V 
Published: January 2023

Abstract
T lymphocytes develop in the thymus, where mutually inductive signaling between lymphoid progenitors and thymic stromal cells (TSCs) directs the progenitors along a well-characterized program of differentiation. However, the biology of the TSCs comprising the lymphopoietic thymic microenvironment remains relatively under-characterized because stromal cells are rare and difficult to isolate. Using a deconvolution technique to study gene expression essentially in situ, we previously identified a deficiency in the H202 quenching enzyme catalase (CAT) in TSCs, and found that CAT deficiency results in high H202 levels in this population, eventually leading to thymic atrophy. Our current studies address the possibility that high H202 levels serve physiological functions in TSCs in the young, steady state thymus. TSCs exhibit high basal levels of autophagy at the steady state, which is critical for self-antigen presentation and T cell selection. The mechanisms governing high basal autophagy in TSCs are unknown, however autophagy is induced by many stressors, including high H202 levels. Our data indicate that catalase overexpression targeted to mitochondria in transgenic mice (mCAT Tg) results in diminished autophagy in TSCs and causes diminished negative selection in the thymus, eventually leading to autoimmunity. The effects on negative selection in mCAT Tg mice are rescued by increased basal autophagy on the beclin 1 knock-in (Becn1F121A/F121A) background. Our results suggest that the high basal autophagy level required in TSCs for T cell negative selection is promoted by physiologically low levels of catalase expression in the steady state thymus.
A transition from MYC to MYCL dominance identifies early specification events during the development of IRF8-dependent dendritic cell subsets
Authors: Anderson David A , Murphy Theresa L , Murphy Kenneth M 
Published: January 2023

Abstract
Early work defined the common dendritic cell progenitor, or CDP, as a clonogenic population that gives rise to pDCs, cDC1s, and cDC2s. It was recently shown that pDC and cDC1 specification can occur within the CDP. Defining phenotypic and transcriptional heterogeneity within the CDP can thus be used to refine our understanding of the gene regulatory network that controls DC development. Using scRNA-Seq and in vivo reporter analysis, we identified populations with mutually exclusive expression of Myc and Mycl. We found that Myc-expressing cells develop into all DC subsets when cultured in Flt3L. Alternatively, Mycl-expressing cells develop into cDC1s and pDCs, but not cDC2s. Therefore, we asked whether Mycl expressing CDPs represent a clonogenic, bipotent progenitor of cDC1s and pDCs. Consistent with work that showed sustained expression of Mycl in differentiated populations of pDCs and cDC1s, we were able to exclude pDC and cDC1-specified populations on the basis of subset-specific marker expression. However, a population of Mycl-expressing CDPs that did not express subset specific markers remained. When purified and cultured in vitro, this rare population gives rise to both pDCs and cDC1s. These results indicate that Mycl expression marks a putative, common progenitor of pDCs and cDC1s that excludes cDC2 potential. These results are consistent with recent work that demonstrated a shared dependence of pDC and cDC1 specification on a distal enhancer of Irf8. Along these lines, we find that the transition from MYC to MYCL dominance in pDCs is disrupted in Irf8−/− mice. We have thus identified Myc and Mycl as targets of the gene regulatory network that controls DC development.
Interleukin-15 bridges astrocyte-microglia crosstalk and exacerbates brain injury following intracerebral hemorrhage
Authors: Shi Samuel , Li Yu-Jing , Shi Kaibin , Wood Kristofer , Ducruet Andrew F , Liu Qiang 
Published: January 2023

Abstract

Background and Purpose
Microglia are among the first cells to respond to intracerebral hemorrhage (ICH), but the mechanisms that underlie their activity following ICH remain unclear. Interleukin (IL)-15 is a proinflammatory cytokine that orchestrates homeostasis and the intensity of the immune response following central nervous system inflammatory events. The goal of this study was to investigate the role of IL-15 in ICH injury.

Methods
Using brain slices of ICH patients, we determined the presence and cellular source of IL-15. A transgenic mouse line with targeted expression of IL-15 in astrocytes was generated to determine the role of astrocytic IL-15 in ICH. The expression of IL-15 was controlled by a glial fibrillary acidic protein promoter (GFAP-IL-15tg). ICH was induced by intraparenchymal injection of collagenase or autologous blood.

Results
In patients with ICH and wild type mice subjected to experimental ICH, we found a significant upregulation of IL-15 in astrocytes. In GFAP-IL-15tg mice, we found that astrocyte-targeted expression of IL-15 exacerbated brain edema and neurological deficits following ICH. This aggravated ICH injury in GFAP-IL-15tg mice is accompanied by increased microglial accumulation in close proximity to astrocytes in perihematomal tissues. Additionally, microglial expression of CD86, IL-1β, and TNF-α is markedly increased in GFAP-IL-15tg mice following ICH. Furthermore, depletion of microglia using a colony stimulating factor 1 receptor inhibitor diminishes the exacerbation of ICH injury in GFAP-IL-15tg mice.

Conclusions
Our findings identify IL-15 as a mediator of the crosstalk between astrocytes and microglia that exacerbates brain injury following ICH.
Mechanisms of anti-NMDAR Antibody Mediated Damage to the Fetal Brain
Authors: Carroll Kaitlin , Kowal Czeslawa , Diamond Betty 
Published: January 2023

Abstract
Mothers with systemic lupus erythematosus (SLE) have an increased frequency of children with learning disorders and autism spectrum disorder (ASD) which associates with maternal anti-DNA antibodies, indicating that in utero exposure to autoantibodies may lead to neurodevelopmental alterations. A subset of anti-dsDNA antibodies present in 40% of SLE patients has been shown to cross-react with the N-methyl D-aspartate receptor (NMDAR) excitatory neuronal receptor. Immunizing mice with these antibodies (DNRAbs) causes morphological neurodevelopmental alterations and persistent behavioral and neurocognitive abnormalities in male offspring, as well as the death of a high proportion (~40%) of female fetuses due to their earlier expression of the GluN2A NMDAR subunit. The brains of the fetuses from DNRAb+ dams display increased neuronal apoptosis and thinned cortical plates, indicating alterations in neuronal migration. Male offspring of DNRAb+ dams exhibit delayed reflex acquisition, cognitive impairments in fear extinction and novel object recognition, and decreased overall cortical volume. These results parallel the substantially higher proportion of male children born to women with SLE, as well as the higher rate of developmental disorders in these children. Current studies are addressing the mechanisms of this antibody-mediated damage and whether these offspring exhibit characteristics of ASD.