bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wdfy4-deficiency reveals a critical role for cross-presentation in anti-viral and anti-tumor responses
Authors: Theisen Derek J , Davidson Jesse T , Briseño Carlos G , Gargaro Marco , Lauron Elvin J , Wang Qiuling , Desai Pritesh , Durai Vivek , Bagadia Prachi , Brickner Joshua R , Beatty Wandy L , Virgin Herbert W , Gillanders William E , Mossamaparast Nima , Diamond Michael S , Sibley L David , Yokoyama Wayne , Schreiber Robert D , Murphy Theresa L , Murphy Kenneth M 
Published: January 2023

Abstract
Cross-presentation allows for the presentation of exogenous viral and tumor antigens to CD8+ T cells by XCR1+ classical dendritic cells (cDC1s). Previously, the role of cross-presentation in cytotoxic T cell responses in vivo was unclear due to the lack of mouse models specifically deficient in cross-presentation. We developed a CRISPR-Cas9 screen to find novel regulators of cross-presentation and found that the protein WDFY4 is essential for cross-presentation of cell-associated antigens but not for direct presentation or presentation on MHCII. WDFY4-deficient mice had normal cDC1 development and were able to survive infections with Toxoplasma gondii through production of IL-12. However, WDFY4-deficient mice failed to prime CD8+ T cells to viral antigens and were completely unable to control immunogenic tumors. WDFY4 interacts with proteins related to vesicular formation and trafficking such as clathrin and HSP90ab1 and localizes near the cell surface, suggesting its involvement in vesicular targeting after antigen uptake during cross-presentation.
High GILT expression and an active and intact MHC class II antigen presentation pathway are associated with improved survival in melanoma
Authors: Hastings Karen , Meador Lydia , Menon Hari , Lu Yih-Kaung , Brill Jacob , Cui Haiyan , Roe Denise J. , DiCaudo David J. , Buetow Kenneth H. 
Published: January 2023

Abstract
The MHC class I antigen presentation pathway in melanoma cells has a well-established role in immune-mediated destruction of tumors. However, the clinical significance of the MHC class II antigen presentation pathway in melanoma cells is less clear. In antigen presenting cells, gamma-interferon-inducible lysosomal thiol reductase (GILT) is critical for MHC class II-restricted presentation of multiple melanoma antigens. While not expressed in benign melanocytes of nevi, GILT and MHC class II expression is induced in malignant melanocytes in a portion of melanoma specimens. Analysis of The Cancer Genome Atlas (TCGA) cutaneous melanoma dataset showed that high GILT mRNA expression was associated with improved overall survival. Expression of IFN-γ, TNF-α, and IL-1β was positively associated with GILT expression in the TCGA melanoma specimens. These cytokines were capable of inducing GILT expression in melanoma cells in vitro. GILT protein expression in melanocytes was induced in halo nevi, which are nevi undergoing immune-mediated regression, and is consistent with the association of GILT expression with improved survival in melanoma. To explore potential mechanisms of GILT’s association with patient outcome, we analyzed the mRNA expression pattern in the MHC class II antigen presentation pathway. In contrast to healthy skin where the MHC class II pathway was nearly uniformly expressed and intact, there was substantial variation in the MHC class II pathway of the TCGA melanoma dataset. Both an active and intact MHC class II pathway were associated with improved overall survival in melanoma. These studies support a role for GILT and the MHC class II antigen presentation pathway in melanoma outcome.
Comprehensive Immunopeptidome Analysis of I-Ab-bound peptides from Thymus and Splenic B cells in C57BL/6 mice
Authors: Nanaware Padma Pandurang , Stern Lawrence J 
Published: January 2023

Abstract
Antigen presentation in the thymus is central to selection of CD4 and CD8 T cells. Despite postulated roles for differential central and peripheral antigen presentation pathways for MHC-I and MHC-II, comprehensive immunopeptidome analysis of the thymus has not been reported. Advances in mass spectrometry (MS) technology now allow analysis of the MHC-presented peptidomes of tissue samples containing small numbers of antigen-presenting cells. To map the immunopeptidome in the thymus of C57/BL6 mice presented by I-Ab, we used immunoaffinity coupled to MS. We identified &gt;1000 peptides using a conventional data-dependent acquisition strategy (DDA). We compared the immunopeptidome of thymus to that of the splenic B cells. Some of the core epitopes were unique to thymus, and some were unique to splenic B cells, although most were shared. We observed differences in the general characteristics of the peptidomes presented by thymus and splenic B cells, including length distribution and hydrophobicity. To help understand the impact of the hydrophobicity differences, we selected 57 peptides representative of thymic-derived, splenic B-derived, or shared peptidomes, and studied their binding affinity to IAb. Results suggest that the pool of peptides presented by I-Ab in thymus has lower MHC binding than does the pool presented by splenic B cells. We are exploring a data-independent acquisition strategy (DIA) for quantitative comparison of peptides identified in thymus and splenic B cells to further characterize antigen presentation differences in thymus and periphery.
VSV-primed CD8+ T cells suppress autoreactive germinal centers
Authors: Kole Hemanta K , Scott Bethany , Crampton Steve , Sule Gautam , Deane Jonathan , Bolland Silvia 
Published: January 2023

Abstract
Pathogenic infections are important environmental modifiers of autoimmune disease as they can alter the immune system in a way that either promotes or reduces autoimmune responses. We tested the effect of infection with vesicular stomatitis virus (VSV) on the FcγR2B−/− (R2) mouse strain that spontaneously develops lupus disease. Infecting FcγR2B−/− mice with live VSV reduces autoantibody levels and inflammatory pathology and prolongs survival. We showed that VSV-mediated protection can be transferred in a CD8 cell adoptive transfer experiment. After further testing the transfer of various CD8 T cell subsets, we have identified CD8+CD122+NKG2D+ cells as mediator in VSV-induced Lupus amelioration. RNA Sequencing data for gene expression profiles among various CD8 subsets, indicate that the protective cells express higher level of genes linked to memory phenotype. Our working hypothesis is that the viral infection may induce the expansion of long lived CD8 populations that regulate the antibody response.
In support of the idea we initiated to identify the target of the VSV-primed CD8 T cells in vivo. We examined the effect of VSV-primed CD8 T cells on the immune phenotypes of recipient R2 mice at the initial stages, e.g. after 1, 2 or 3 weeks of transfer. Interestingly, we found that Tfh and germinal center B cells are significantly reduced after three weeks of VSV-CD8 transfer. Thus, the protective CD8 T cells from VSV-infected mice might target autoreactive germinal center to regulate the antibody response. How VSV-CD8 T cells might control germinal center & why it takes about 3 weeks for controlling is under investigation.
Induction of Regulatory B Cells by Bacterial DNA in the Gut Microbiota at Early Age is Beneficial in Lupus-prone Mice
Authors: Mu Qinghui , Swartwout Brianna , Cabana-Puig Xavier , Grieco Joe , Cecere Thomas E , Luo Xin M 
Published: January 2023

Abstract
SLE is a complex autoimmune disorder with no known cure. We previously reported that oral vancomycin treatment of female MRL/lpr mice during active disease (9 to 15 weeks of age) could significantly ameliorate disease symptoms. However, when vancomycin treatment was initiated from an earlier age (from 3 to 15 weeks), the beneficial effect was not observed. Strikingly, mice given vancomycin during the pre-disease stage (from 3 to 8 weeks) exhibited exacerbated lupus disease. As vancomycin works by removing parts of the gut microbiota, we hypothesized that the regulatory immunity induced by gut microbiota at early age is essential in hammering lupus disease development in MRL/lpr mice. To test the hypothesis, we analyzed diverse regulatory cell types from the mice receiving vancomycin from 3 to 8 weeks of age. Regulatory B (Breg) cells, in particular, were found to be reduced in both the percentage and absolute number in multiple lymphoid organs. Importantly, adoptive transfer of Breg cells at 6–7 weeks of age to long-term vancomycin-treated mice improved lupus-like symptoms. This clearly indicates that Breg cells, inducible by vancomycin-sensitive gut microbiota, plays an important role in suppressing lupus disease initiation and progression. We next sought to determine Breg inducers in the gut microbiota. The serum level of bacterial DNA was found to be significantly lower in mice treated with vancomycin. More importantly, early administration of bacterial DNA reproduced the beneficial effect seen in the Breg adoptive transfer experiment. Together, these results suggest an important protective mechanism against lupus initiation that involves bacterial DNA in the gut microbiota and the induction of Breg cells.
Linking diet, gut microbiota and autoimmunity: A phytoestrogen diet alters the gut microbiota and influences Experimental Autoimmune Encephalomyelitis (EAE)
Authors: Freedman Samantha N , Shahi Shailesh , Zarei Kasra , Gupta Arnav , Guseva Natalya , Bossler Aaron , Legge Kevin L , Mangalam Ashutosh K 
Published: January 2023

Abstract
The etiology of multiple sclerosis (MS) involves genetic predisposition and an unknown environmental trigger. The gut microbiome may be an environmental contributing factor. Previously, we have shown that certain gut bacteria especially those with ability to metabolize phytoestrogen are less abundant in MS patients compared to healthy individuals. We hypothesize that phytoestrogen metabolism via microbial flora induces an anti-inflammatory state in the intestine. Therefore their reduced levels might predispose to disease development and/or severity. To test this, we placed C57Bl/6 mice on a diet with or without phytoestrogens and induced Experimental Autoimmune Encephalomyelitis (EAE), an experimental model of MS. We observed that mice on a phytoestrogen diet developed milder disease compared to those on a phytoestrogen free diet; a phenomenon dependent on the presence of phytoestrogen-metabolizing bacteria in the gut. We also found that a phytoestrogen diet alters the gut microbiota compared to a phytoestrogen-free diet with the gut microbiota of phytoestrogen group closely resembling the gut microbiota of healthy individuals. The gut microbiota of mice on a phytoestrogen-free diet closely resembles the gut microbiota of MS patients. Furthermore, mice on a phytoestrogen-diet exhibit an altered immune profile in the colonic lamina propria and mesenteric lymph nodes. Finally, we found that phytoestrogen-metabolites altered the cytokine-producing function of human colonic epithelial cells in vitro. Our results suggest that dietary phytoestrogen metabolites produced by commensal bacteria can alter the phenotype and function of the intestinal immune system, which may influence central nervous system autoimmunity.
Dysbiosis reprograms the differentiation of thymus-derived regulatory T cells
Authors: Wang Ke , Yang Bi-Huei , Fu Wenxian 
Published: January 2023

Abstract
Foxp3+ regulatory T (Treg) cells can be developed from the thymus (tTreg) or induced in the peripheral tissues (pTreg). While abundant literature has reported that gut microbiota and derived metabolites profoundly influence the generation and abundance of pTreg cells, whether these environmental cues also affect tTreg cells remains poorly understood. Our previous work has defined tTreg cells in peripheral organs into three distinct subsets, exhibiting different profiles of differentiations and functions. We here report that intestinal tTreg cells exhibited a "reversed” phenotype of differentiation in antibiotic (Abx) treated mice. This "dedifferentiation” was mediated by gut microbiota because cohousing Abx treated mice with untreated mice rectified this abnormal phenotype. In addition, we found that dysbiosis altered Treg's cytokine dependence for their maintenance and survival. Thus, gut microbiota have a critical role in shaping the differentiation and functional programs of tTreg cells.
This work is supported by NIH DK114427, AI139753 (to W.F.)
Heightened levels of antimicrobial response factors in patients with systemic lupus erythematosus
Authors: Ayyappan Prathapan , Harms Robert Z , Buckner Jane H , Sarvetnick Nora E 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disorder characterized by immune system abnormalities and severe inflammation leading to multi-organ damage. Compromised gut permeability and microbial translocation is suggested to be associated with SLE. The objective of this study was to assess whether SLE subjects have increased systemic exposure to bacteria. Plasma from 30 SLE patients and 30 age and sex matched healthy controls were assessed for a series of clinically relevant antimicrobial response factors (ARFs) including sCD14, EndoCAbs, LBP, lysozyme, CXCL16, FABP2, galectin-3, and LL-37. The levels of sCD14 (P&lt;0.0001), lysozyme (P&lt;0.0001) and CXCL16 (P=0.001) were significantly elevated in SLE subjects compared to healthy controls. sCD14 exhibited a positive correlation with SELENA-SLEDAI score. EndoCAbs are antibodies directed against the endotoxin core of LPS. Interestingly, the ratio of EndoCAb IgM:total IgM was significantly decreased in SLE (P=0.006) and this ratio was negatively correlated with sCD14 levels (P=0.030, r=-0.396). We observed significant positive correlations between lysozyme levels and sCD14 (r=0.499, P=0.005), LBP (r=0.434, P=0.016), and FABP2 (r=0.396, P=0.030). Levels of CXCL16 was also positively correlated with the levels of sCD14 in SLE cohort (r=0.551, P=0.001). Moreover, Galectin-3 levels also positively correlated with lysozyme (r=0.447, P=0.013), sCD14 (r=0.425, P=0.019), and LBP (r=0.416, P=0.022). Overall, these changes in the levels and relationships between ARFs link microbial exposure and SLE. Thus, our study results are relevant to clinical SLE that will help to define better therapeutic strategies for SLE patients.
Aberrant MDA5 signaling and IFN-β synthesis elicit protection from Coxsackievirus-accelerated Type 1 diabetes
Authors: Blum Samuel I , Burg Ashley R , Chen Yi-Guang , Tse Hubert Ming 
Published: January 2023

Abstract
Viral infections can trigger the synthesis of proinflammatory cytokines and free radicals that contribute to pancreatic β-cell destruction leading to Type 1 diabetes (T1D). We previously demonstrated that Coxsackievirus B3 (CB3) infection of Non-Obese Diabetic (NOD) mice can accelerate T1D, due to the induction of antiviral signaling pathways including melanoma differentiation-associated protein 5 (MDA5). SNPs within Ifih1, the gene encoding for MDA5, is associated with T1D pathogenesis, but the molecular mechanism contributing to innate immune dysregulation is not known. We hypothesized that attenuated MDA5 expression and signaling can delay diabetogenic viral-accelerated T1D. We generated NOD mice mutated in Ifih1 that displayed a loss in MDA5 expression (NOD.Ifih1-m1) or an in-frame deletion in the helicase domain that decreased MDA5 synthesis (NOD.Ifih1-m4). Interestingly, CB3-infected NOD and NOD.Ifih1-m1 mice displayed virus-accelerated T1D, but NOD.Ifih1-m4 (n=9 per group) mice were significantly delayed in both spontaneous and CB3-accelerated T1D (p=0.0036 and p=0.0004, respectively). CB3-infected NOD.Ifih1-m4 mice exhibited a 4-fold decrease in pancreas IFN-β levels and may partly explain the delay in CB3-induction of T1D. The Ifih1-m4 mutation did not compromise pancreatic viral clearance, and this was complemented by a ~34% and ~32% reduction in pancreas-infiltrating CD8 T cells and activated macrophages (F4/80+, I-Ag7+), respectively, in comparison to CB3-infected NOD mice. The protective Ifih1-m4 mutation may establish an acute level of IFN-β and islet-infiltrating lymphocytes to inhibit CB3 replication without mediating bystander activation and virus-accelerated autoimmune diabetes.
Synergetic effect of an autoantigen CII and a mycoplasma superantigen on the onset and development of autoimmune arthritis in mice
Authors: Mu Hong-Hua , Jiang Shaowei , Wang Xingqiong , Meaney Connor , Wang Jingyi 
Published: January 2023

Abstract
An infection can amplify an autoimmune disease by either exacerbating an ongoing disorder, including a relapse, or by leading to chronic progressive disease. We have been studying a mouse autoimmune arthritis induced by M. arthriditis. M. arthritidis produces a potent superantigen (SAg) MAM, which is shown to be partially responsible for the chronic autoimmune arthritis. Although the MAM clearly plays a role in disease induced by live M. arthritidis, MAM alone does not induce overt disease. It does alter the immune system rendering mice more susceptible to disease that caused by other autoimmune agents such as type II collagen (CII). A key question however is how do CII and MAM act together in the host to initiate inflammation and then an autoimmune arthritis? MAM was injected into mice convalescing from CIA or mice suboptimally immunized with CII. In contrast to controls, MAM caused an exacerbation of arthritis in mice that were recovering from CIA. MAM also triggered arthritis onset in mice that had been immunized with CII up to 71 days previously. Injection of MAM during the onset phase of CIA also triggered and enhanced the severity of arthritis in mice given low doses of CII. We also tested the CII-specific immune responses in mice injected with CII alone and also to the mixtures of the CII and MAM. The T cell profile analysis demonstrated that MAM significantly promoted IL-17 and IFNg following exposure to CII in vivo. Of particular interest was that MAM-enhanced IL-17 can stimulate synoviocytes to release a spectrum of chemokines, CXCL1, CXCL2, CXCL12, CCL2 and CCL5, and attracted inflammatory leukocytes. Thus, the results suggest MAM can serve as an enhancer and a trigger by activating inflammatory responses to other bioactive molecules, i.e. CII.
Novel role of T cells to induce development of proliferative plasmablasts in systemic lupus erythematous
Authors: Ojo Oluwagbemiga A , Liu Shanrun , Wu Qi , Yang PingAr , Crossman David K , Chatham Winn , Hsu Hui-Chen , Mountz John D 
Published: January 2023

Abstract
While research on human SLE and mouse models of lupus have focused on mechanisms of B cell tolerance loss, these efforts have been complicated by multiple networks of immune regulatory genes, thereby impeding current understanding of the development of autoantibody producing B cells in SLE. We applied an unsupervised single cell RNA-seq (scRNA-seq) approach to determine the network and pathways-associated with the development of plasmablasts (PBs) in SLE. PBs were isolated as CD19+CD21−IgD−CD27hiCD38hi cells from PBMCs of SLE patients (n=3). A high-throughput scRNA-seq was carried out using a droplet-based 10x Chromium approach (~ 2,000 cells per sample). We identified two populations of PBs based on the expression of MKI67 encoding for Ki67, a nuclear protein associated with cellular proliferation. Representative genes elevated in MKI67+ PBs included cell cycle related genes as well as TNFR2. Gene ontology analysis further suggest that TNFR2+ B cells expressed increased levels of genes that are associated with cell cycle G1/S transition, DNA synthesis and elongation, and replication. Flow cytometry analysis identified TNFR2+ B cells as a population of antibody secreting cells expressing higher levels of CD86, CD11c, and CD38 but lower levels of CD20. As both CD86 and CD11c poise B cells to receive T-cell help, our studies suggest that T-cell stimulation enables development of cycling PBs in SLE. The strong association of TNFR2 with cell cycle genes in PBs suggest that blockade of TNFR2 may be a novel strategy to inhibit PB proliferation and differentiation.
Ikaros mutations can bypass the requirement for second co-stimulatory signal and lead to break of B-cell tolerance
Authors: Schjerven Hilde , Rodriguez Princess D , Howell William , Vestbostad Johanne , Frietze Seth , Schjerven Hilde 
Published: January 2023

Abstract
Autoimmunity is thought to arise due to a combination of genetic and environmental factors. IKZF1, encoding the Zinc finger (ZnF) transcription factor Ikaros, is implicated in human autoimmunity through GWAS and recent discovery of germline IKZF1 mutations in patients with autoimmune diseases. We have previously created mouse models with targeted deletions of Ikaros DNA-binding ZnF1 or ZnF4, and recently found that mice lacking Ikaros ZnF4 (Ik-dF4) displayed very high levels of autoreactive antibodies and elevated levels of the autoimmunity-associated cytokine IL-6 in serum at young age, while mice lacking ZnF1 did not. Furthermore, ex vivo stimulation of peripheral B cells with anti-IgM (aIgM) +/− CD40L revealed that Ik-dF4 B cells responded to BCR-stimulation alone (aIgM), while wt B cells required a second co-stimulatory signal (CD40L). To understand the underlying mechanism, we performed transcriptome profiling of these stimulated wt and Ik-dF4 B cells. Overall, the Ik-dF4 B cells displayed the same pattern of gene-expression changes as wt B cell upon activation by both signals (aIgM + CD40L). Further analysis revealed a set of genes selectively altered upon aIgM alone in Ik-dF4 B cells, and another set of genes that were aberrantly expressed in Ik-dF4 B cells at baseline. Pathway analysis suggest candidate mediators, and we have initiated functional studies. Preliminary results indicate that a small molecule inhibitor can block the aberrant activation with aIgM alone in Ik-dF4 B cells, while displaying only partial inhibition of the normal two-signal activation. Studies are actively ongoing to confirm these preliminary findings, and we will present our results to date at the meeting for how Ikaros regulates B cell tolerance.
Natural Killer Cell Re-Modeling of the Extra-Cellular Matrix by the Degradation of Hyaluronan: Potential Role in Type 1 Diabetes
Authors: Fuchs Bryce E , Wall Valerie , Kang Inkyung , Workman Gail , Evanko Stephen , Wight THomas , Long Sarah Alice 
Published: January 2023

Abstract
Natural Killer (NK) cells have been shown to contribute to early insulitis during development of Type 1 Diabetes (T1D). We previously identified increased Hyaluronan (HA) deposition within inflamed pancreatic islets, indicative of remodeling of the extra cellular matrix (ECM) of which HA is a component. NK cells express CD44, a ligand for HA, and granzymes known to facilitate extravasation through the ECM. Thus, we asked whether NK cells may directly interact with the ECM, potentially contributing to HA modification in pancreatic islets. Isolated NK cells activated with IL-12, IL-15, and IL-18 up-regulated Has3, CD44, and Hyal1: genes related ECM re-modeling suggesting that NK cells may act upon the ECM. To test NK-ECM interactions, we used a co-culture system of stimulated NK cells and HA producing fibroblasts. We found down-regulation of Hyaluronidases Hyal1 and Hyal2 and up-regulation of HA Synthases Has1 and Has2. These results are consistent with NK cell modulation of ECM, that was also indicated by depletion of the fibroblast cell layer. Comparatively, CD4 and CD8 T cells did not show depletion of the cell layer and differed in the degree and composition of ECM related transcripts. Together, these data suggest that NK cells play a critical role in ECM re-modeling; this NK-ECM interaction may contribute to pancreatic inflammation in the setting of T1D.