bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of highly preserved gene co-expression module groups among multiple isolated CD4+ cellular sample datasets contribute to the elucidation of cell-type specific systemic lupus erythematosus bio-signatures in humans
Authors: Geraci Nicholas S. , Catalina Michelle , Heuer Sarah , Robl Robert , Lipsky Peter E. , Grammer Amrie C. 
Published: January 2023

Abstract
Gene expression profiles from three CD4+ T cell lupus datasets were assessed by weighted gene co-expression network analysis (WGCNA) to identify a consistent 65 gene module. Enrichr assessment of functional molecular pathways indicates that this module includes TCR signaling, DNA synthesis, proliferation and apoptosis. GAGE evaluation of this CD4+ T cell gene signature compared with SLE whole blood, PBMC, kidney, synovium, and skin revealed that this CD4+ T cell gene signature was consistently enriched in all datasets tested. Since the mechanisms underlying tissue pathology in SLE are not completely understood, gene expression profiles from lupus affected skin, synovium, and kidney were analyzed for commonalities. Notably, the majority of lupus tissue DE genes were detected in more than one tissue and 439 were differentially expressed in all tissues. Curated STRING-based interaction analysis of these 439 DE genes identified a number of functions and pathways that were commonly activated in all four tissues such as T cell signaling and Interferon Signaling Genes. Curated STRING-based interaction analysis of the up-regulated genes in at least three of the four tissues identified several additional cellular and molecular processes, including T cell adhesion, DNA damage response and cell proliferation. These results indicate that common cellular and molecular pathways involving T cells can be identified in all affected lupus tissues, implying that related processes might be involved in the pathology of multiple organs in this autoimmune disease.
Targeting transcription cofactor OCA-B specifically blocks pancreatic T cell infiltration, cytokine production and elevated glucose in the NOD mouse model of type-1 diabetes (T1D)
Authors: Tantin Dean R. , Kim Heejoo 
Published: January 2023

Abstract
Type 1 Diabetes (T1D) is an autoimmune disease in which the host immune system is misdirected towards antigens associated with beta cells of the endocrine pancreas. In CD4 T cells, OCA-B (Pou2af1/OBF-1/Bob.1) promotes memory T cell function via the maintenance of poised gene expression states at multiple direct immunomodulatory target genes (e.g. Il2, Il21, Ifng, and Il2ra). OCA-B ensures poised gene expression states by recruiting the histone lysine demethylase Jmjd1a/Kdm3a. OCA-B is not expressed in naïve CD4 T cells, but becomes stably expressed upon stable antigen exposure. Memory T cell phenotypes can promote autoimmunity (including T1D), even in cases of persistent self-antigens. Consistently, OCA-B levels are strongly elevated in central memory CD4 T cells, but are even more elevated in islet-reactive, pancreas-infiltrating CD4 T cells in T1D. GWAS studies associate human polymorphisms in binding sites for Oct1, the transcription factor with which OCA-B docks, in autoimmunity generally and T1D in particular. Using a rationally-designed peptide inhibitor of OCA-B downstream effector function, we observe robust improvement in glucose levels in NOD mice genetically pre-disposed to T1D. In contrast, control peptides have no effect. The therapeutic benefit is associated with reductions in pancreatic-infiltrating CD4 and CD8 T cell numbers and cytokine production. In contrast, T cell numbers in pancreatic lymph nodes (PLNs) are normal, suggesting that non-self-directed immune function is largely intact. Our results show that OCA-B promotes pro-inflammatory T cell phenotypes needed in T1D and that it can be targeted pharmacologically.
Autoreactive and immunization-induced follicular helper T cells have opposite glucose and glutamine requirements
Authors: Choi Seung-Chul , Titov Anton , Abboud Georges , Morel Laurence 
Published: January 2023

Abstract
Both glycolysis and mitochondrial oxidative metabolism are elevated in CD4+ T cells from lupus-prone mice, and metabolic inhibitors targeting both of these pathways normalized lupus T cell functions in vitro and reverted disease in mice. Here, we showed that inhibiting glucose metabolism with 2-deoxy-D-glucose (2DG) results in a drastic reduction of follicular helper T (TFH) cell frequency in lupus-prone B6.Sle1.Sle2.Sle3 (TC) mice. However, treatment of TC mice with 2DG had little effect on the production of antibodies or the expansion of TFH cells following immunization with a nominal antigen of T-cell-dependent (TD) humoral responses, and no effect on the frequency of influenza virus-specific TFH cells induced by immunization with PR8 influenza virus. Thus, TFH cells supporting the production of autoantibodies are different from TFH cells providing protective humoral immunity against pathogens. The specific metabolic signature from autoimmune TFH cell is significantly different compared with exogenous antigen-specific TFH cells. Further results obtained with gene expression analysis and treatment with metabolic inhibitors indicated that autoreactive TFH cells depend on glucose metabolism, while exogenous antigen-specific TFH cells are more glutamine-demanding. Overall, our results predict that targeting TFH cellular metabolism provides an effective and safe therapeutic approach for systemic autoimmunity by eliminating autoreactive TFH cells.
Stromal cell-derived factor-1 (CXCL12) activates integrins by direct binding to an allosteric ligand-binding site (site 2) of integrins without CXCR4.
Authors: Takada Yoshikazu , Fujita Masaaki , Davari Parastoo , Takada Yoko K. 
Published: January 2023

Abstract
Leukocyte arrest on the endothelial cell surface during leukocyte extravasation is induced by rapid integrin activation by chemokines. We recently reported that fractalkine induces integrin activation without its receptor CX3CR1 through binding to the allosteric site (site 2) of integrins. Peptides from site 2 bound to fractalkine and suppressed integrin activation by fractalkine. We hypothesized that this is not limited to membrane-bound fractalkine. We studied if stromal cell-derived factor 1 (SDF1), another chemokine that plays a critical role in leukocyte arrest, activates integrins through binding to site 2. We describe here that (1) SDF1 activated soluble integrin αvβ3 in cell-free conditions, suggesting that SDF1 can activate αvβ3 without CXCR4; (2) site 2 peptide bound to SDF1, suggesting that SDF1 binds to site 2; (3) SDF1 activated integrins αvβ3, α4β1, and α5β1 on CHO cells (CXCR4-negative) and site 2 peptide suppressed the activation; (4) A CXCR4 antagonist AMD3100 or pertussis toxin did not affect the site 2-mediated integrin activation by SDF1; (5) Cell-surface integrins were fully activated in 1 min (much faster than activation of soluble αvβ3) and the activation lasted at least for 1 h. We propose that the binding of SDF1 to cell-surface proteoglycan facilitates the allosteric activation process; (6) Mutations in the predicted site 2-binding site in SDF1 suppressed integrin activation. These results suggest that SDF1 (e.g., presented on proteoglycans) can rapidly activate integrins in an allosteric manner by binding to site 2 in the absence of CXCR4 or other GPCR. The allosteric integrin activation by SDF1 is a novel target for drug discovery.
Interleukin-33 modulates human natural killer cell responses
Authors: Ohayon David E. , Ali Ayad , Alarcon Pablo C. , Krishnamurthy Durga , Osterburg Andrew R. , Borchers Michael T. , Waggoner Stephen N. 
Published: January 2023

Abstract
Interleukin-33 (IL-33) promotes type 2 cytokine responses in CD4 T cells, granulocytes, and innate immune lymphocytes. Although type 1 (IL-12) and type 2 (IL-33) cytokines are classically thought to counterbalance one another, a combination of IL-12 and IL-33 paradoxically promotes profound expression of type 1 effector cytokines, interferon gamma (IFN-γ), tumor necrosis alpha (TNF-α), and granulocyte-macrophage colony-stimulating factor (GM-SCF), when administered to human natural killer (NK) cells. Mechanistically, IL-33 stimulates potent mitogen-activated protein kinase (MAPK) p38 in human NK cells, but has no impact on IL-12-induced signal transducer and activator of transcription 4 (STAT4) phosphorylation. Importantly, pharmacological inhibition of p38 MAPK significantly reduced IFN-γ and TNF-α release by IL-12 and IL-33 stimulated NK cells. Even in the absence of IL-12, IL-33 could synergize with other type 2 cytokines like IL-27 or IL-4 to trigger high expression levels of IFN-γ. The altered sensitivity of NK cells to type 1 and 2 cytokines in the presence of IL-33 may have important consequences in diseases associated with mixed cytokine milieus, including cases of severe asthma exacerbated by respiratory viral infection.
Defining IL-2 mediated regulation of Il9 activation using knock-in reporter mice
Authors: Kharwadkar Rakshin P. , Ulrich Benjamin Joseph , Kaplan Mark H. 
Published: January 2023

Abstract
T cells are critical regulators of inflammatory disease and immunity. CD4+ T helper cells develop into various subsets that are specialized in secretion of particular cytokines and mediate restricted types of inflammation. One of these subsets, IL-9 secreting Th9 cells, have proven to be effective in clearing helminthic infections and in tumor immunotherapy. Inappropriate Th9 activity has also been associated with colitis and atopic inflammation. While IL-4 and TGF-β are primary cytokines required for Th9 differentiation, other stimuli, including an IL-2/STAT5 pathway, are necessary for acute activation. Recent studies have reported a reduction in IL-9, when differentiated Th9 cells are stimulated in the absence of exogenous IL-2. This implies that IL-2 plays an important role in modulating IL-9 expression in Th9 cells, in a paracrine manner. Using two distinct IL-9 reporter mice, one with a reporter knocked-in to the first Il9 exon and the other with a downstream IRES-reporter, we noted that exon 1 disruption results in reduced allele expression. Specifically, the allele is no longer responsive to IL-2. This is correlated with diminished STAT5 binding near the promoter, suggesting novel effects of the first exon on cytokine responsiveness of the allele. In ongoing studies we will more precisely map STAT5 binding across the promoter and the 5-prime end of the Il9 gene to define how gene regulation and cytokine responsiveness might be exploited to control IL-9-dependent immune responses.
Signals that induce IL-10 production by peripheral regulatory T cells
Authors: Dean Emma C. , Moseley Carson E. , Hatton Robin D. , Pham Duy , Weaver Casey T. 
Published: January 2023

Abstract
Inflammatory bowel disease (IBD) is an immune-mediated disease of the intestinal tract caused by chronic inflammation that can be relapsing and remitting. This inflammation leads to flares that often require patients to be treated with life-long biologic therapy. Interleukin 10 (IL-10) is an immunosuppressive cytokine produced by effector T cells, especially regulatory T cells (Tregs), to limit inflammatory responses to both foreign and self-antigens. Although IL-10-producing peripheral Tregs (IL-10+ pTregs) are thought to play a mitigating role in murine models of colitis, signals that control transcriptional regulation of the Il10 locus are not well understood. Here, we have examined cytokine and non-cytokine signals that enhance the induction of IL-10+ pTregs in vitro and in vivo. We find that in vitro a mix of inflammatory cytokines acting in concert with IL-2 and on-going TGFβ signaling induce the production of Foxp3+IL-10+ pTregs from Foxp3+IL-10- precursors. Ongoing studies are directed at extending these findings to the in vivo induction of IL-10-producing pTreg cells, and examining the ability of these cells to curb intestinal inflammation driven by aberrant effector T cell responses against the intestinal microbiota. Ultimately, we hope that by identifying signals to amplify our target population, we can perform genomic analyses to better decipher what modulates the transcriptional landscape of the Il10 locus, and identify novel immune therapies for patients with IBD.
Aire is not essential for regulating autoimmune pathology in mice transgenic for human autoimmune-disease associated MHC class II genes HLA-DR2b and HLA-DR4.
Authors: Nalawade Saisha A. , Ji Niannian , Kraig Ellen , Forsthuber Thomas 
Published: January 2023

Abstract
The human MHC class II molecules HLA-DR2b (DRB1*1501) and HLA-DR4 (DRB1*0401) are strongly linked to increased susceptibility to autoimmune diseases, such as multiple sclerosis (MS) and rheumatoid arthritis (RA). However, their contribution to disease pathogenesis is not completely understood. Conceivably, autoimmune disease-associated HLA alleles could shape the repertoire of pathogenic T cells via central or peripheral tolerance. The ectopic expression of tissue-specific antigens promoted by the autoimmune regulator (AIRE) is thought to play a critical role in central tolerance. Aire knockout mice (Aire−/−) develop spontaneous autoimmune pathology characterized by multi-organ lymphocytic infiltrates. Aire deficiency in humans causes multi-organ autoimmune conditions observed in autoimmune polyendocrinopathy syndrome type 1 (APS I). We wanted to investigate whether lack of Aire expression promoted spontaneous MS- or RA-like autoimmune pathology in HLA-DR2b or HLA-DR4 transgenic (tg) mice. We observed that Aire-deficiency modestly enhanced experimental autoimmune encephalomyelitis (EAE) in HLA-DR tg mice, but did not lead to spontaneous neuroinflammation or arthritis. Our results suggest that Aire has a mild and non-essential effect in restraining the autoimmune response in the context of autoimmune disease-associated human HLA alleles.
The effect of Ebola Virus secreted glycoprotein on activated macrophages.
Authors: Bradley Jillian Helena , Shapiro Lindsey , Hitchcock Clara , Kulis Dakota , Needell Lauren , Henry Nathan , Gregg Randal K. 
Published: January 2023

Abstract
During Ebola virus (EBOV) infection, secreted glycoprotein (sGP) and viral protein 40 (VP40) are found in large quantities in the serum of infected animals. Studies suggest that sGP only provides passive immunity by serving as a decoy to anti-EBOV antibodies, and no role for soluble VP40 has been determined. Using an in vitro model incorporating treatment of THP-1 macrophages with recombinant EBOV sGP and recombinant VP40, we examined the impact of the viral proteins upon key macrophage functions.
Treatment with sGP inhibited macrophage production of pro-inflammatory cytokines (TNFα and IL-6) while the yield of anti-inflammatory cytokine (IL-10) remains unaltered. In contrast, VP40 seems to increase the production of pro-inflammatory cytokines. Furthermore, sGP affected only the function of activated macrophages and not the polarization. Phagocytic capacity was unaffected by sGP. Interestingly, the migratory ability of macrophages was diminished by sGP, and cell viability was increased, potentially due to a decrease in expression of CD11b, a vital macrophage integrin. Thus, the results suggests that while EBOV VP40 increases anti-viral immunity, EBOV sGP may operate to diminish functional contributions of non-infected macrophages for the purpose of increasing the potential viral dissemination between macrophages.
Previously macrophages were activated utilizing a TLR4 agonist, LPS. TLR2 agonist zymosan, TLR3 agonist HMW Poly (I:C), TLR7 agonist imiquimod, and TLR9 agonist Class C CpG were examined. Further directions include determining the mechanism behind the inhibition and the specific TLR pathway molecules that are affected by sGP treatment.
A new malaria killer: Fc receptor gamma chain and PLZF identify NK cell subsets that correlate with reduced Plasmodium falciparum parasitemia and increased antibody dependent cellular cytotoxicity against opsonized infected RBCs.
Authors: Hart Geoffrey T. , Tran Tuan , Theorell Jakob , Arora Gunjan , Crompton Peter , Bryceson Yenan , Long Eric O. 
Published: January 2023

Abstract
Plasmodium falciparum (P.f) infection is a major cause of morbidity and mortality world-wide where symptoms and death occur as a result of the blood stage of the P.f. life cycle. To date, there is no effective blood stage malarial vaccine. Natural Killer (NK) cells are key players in the control of hematopoietic cancers and viral infections, however their role in blood stage malaria is unknown. We undertook a comprehensive analysis of NK cell phenotype and function in a cohort of subjects from a malaria clinical study in Mali, Africa. Using an unbiased analysis of different NK cell subsets, we found three major findings: 1. Fc receptor gamma chain (−) or PLZF (−) NK cells correlate with reduced parasitemia 2. Fc receptor gamma chain (−) NK cells correlate with protection from malaria symptoms 3. Fc receptor gamma chain (−) NK cells are enhanced for antibody dependent cellular cytotoxicity (ADCC). Antibodies are known to be protective in malaria, however the mechanism of this protection is still being elucidated. We hypothesized Fc receptor gamma chain (−) NK cells may be clearing opsonized, malaria-infected RBCs in vivo via ADCC. We show that Fc receptor gamma chain (−) NK cells specifically release lytic granules in response to opsonized, infected RBCs. This work indicates the host may increase the number of Fc receptor gamma chain (−) NK cells to aide in clearance of infected RBCs through ADCC. Because the antigens on the surface of infected RBCs are different than the invading parasite, these results could improve the identification of effective targets for blood stage vaccines.
Meningeal inflammation drives long-term engraftment by monocytes that impair CNS immunity
Authors: Rua Rejane , Lee Jane , Silva Alex , Dragan Maric , Johnson Kory , McGavern Dorian B. 
Published: January 2023

Abstract
Tissue-resident macrophages have an embryonic origin and can be replenished by blood monocytes in some tissues during adulthood. Under steady-state conditions, infiltrating monocytes can share phenotypic and genotypic features with their embryonically-derived counterparts. However, little is known about the properties of monocytes/macrophages that establish tissue residency after an inflammatory challenge. The meninges of the central nervous system (CNS) are populated by a dense network of specialized macrophages that serve as immune sentinels. Following infection by lymphocytic choriomeningitis virus (LCMV), these resident macrophages become activated by innate inflammatory cytokines, acquire viral antigens, and are targeted by infiltrating cytotoxic T lymphocytes (CTL), which leads to their depletion. Innate cytokines and chemokines released by CTL also promote a massive recruitment of inflammatory monocytes from the periphery. Surprisingly, these infiltrating monocytes engraft the meningeal niche and remain in situ several months after viral clearance. This leads to significant phenotypic and functional changes in meningeal immunity – a defect that can be partially restored by blocking IFNγ signaling. Importantly, macrophages that establish residency in the meninges after an inflammatory event are deficient in bacterial and immunoregulatory sensors, which impedes their ability to detect pathogens and dampen subsequent meningeal immune responses. Collectively, these data indicate that monocytes can engraft the meninges after an inflammatory challenge and contribute to long-term alterations in CNS immunity.
Modulation of Xanthine metabolism ameliorates inflammation and accelerates diabetic wound healing
Authors: Joshi Amrita , Kimball Andrew , Schaller Matthew , denDekker Aaron , Burant Charles , Kunkel Steven L. , Gallagher Katherine 
Published: January 2023

Abstract
Wound healing in diabetic patients is impaired because of dysregulated innate immune response that results in a chronic inflammatory state. It has been shown by our group and others that metabolites can contribute to a state of chronic inflammation in diabetic tissues. In a murine model of Type-2 diabetes (diet-induced obese mice; DIO), we assessed role of uric acid in driving macrophage-mediated inflammation and delayed wound healing. Using liquid chromatography-mass spectrometry, we show that macrophages from DIO mice have reduced levels of xanthine, a precursor in the uric acid pathway. Xanthine is converted to uric acid via Xanthine oxidase/dehydrogenase (XOR) encoded by the Xdh gene. DIO macrophages express higher levels of Xdh and increased levels of uric acid, suggesting increased XOR activity. Further, exogenous addition of uric acid led to increased production of IL-1β by macrophages. Importantly, pharmacologic inhibition of XOR with Allopurinol resulted in reduced levels of IL-1β expression by macrophages. In order to examine this in vivo, DIO mice were treated with Allopurinol leading to significantly improved wound healing. In summary, our data suggest that the xanthine metabolic pathway can be targeted therapeutically to accelerate wound healing in diabetic patients.
Human NKG2D ligand regulation of Natural Killer cell function and its implications in Cancer and Inflammation
Authors: Dhar Payal , Wu Jennifer 
Published: January 2023

Abstract
NKG2D is an activating lymphocyte receptor which plays an essential role in stimulating immune responses against tumors. The importance of ligand-induced activation of NKG2D in controlling tumor growth has been well established in various animal models. Amongst diverse NKG2D ligands, MHC I chain related molecule MICA/B is expressed most prevalently in human cancers, but absent in rodents. Proteolytically shed-form of MICA/B (sMIC) has been shown to correlate with advanced cancer stages in patients. Previous studies in our lab using two humanized bi-transgenic mice, one expressing native ligand (TRAMP/MICB) and alternatively expressing shedding-resistant mutant (TRAMP/MICB.A2) revealed opposite roles of the two forms of MIC ligand in tumor immunity. Mice with high levels of sMIC exhibited augmented tumor progression, whereas mice expressing MICB.A2 in tumors enjoyed tumor-free survival; raising an intriguing question of why do these similar forms of MIC have different effects on tumor immunity. To address this, we investigated the signaling events and functional outcomes in NK cells upon stimulation by the two forms of ligands. Co-culture studies of NK cells with tumor cells expressing sMICB and MICB.A2 revealed elevated pro-inflammatory cytokine production by NK cells upon stimulation with sMICB. In contrast, NK cells stimulated with MICB.A2 displayed enhanced expression of cytotoxicity mediators and signaling molecules of cytotoxicity pathway. This suggests that sMICB may polarize the NKG2D signaling pathways with preferential activation of inflammatory cytokine pathways. Our data has uncovered a potential mechanism by which sMIC promotes tumor progression and endorses sMIC as a viable target for cancer immunotherapy.