bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial DNA Mediated Protection from Systemic Lupus Erythematosus
Authors: Oakland David N , Appiah Michael , Zhu Jing , Lipsky Peter , Luo Xin M 
Published: August 2023

Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with no known cure. Current therapies primarily rely on symptom control with corticosteroids, however these therapies carry many adverse effects. In recent decades, the gut microbiome has gained appreciation as a major immunomodulator of autoimmune disease. Toll-like receptor 9 (TLR9) is known to interact with microbial DNA readily provided by the gut microbiota. Polymorphisms of TLR9 have been implicated in increased susceptibility to SLE, and overexpression of the receptor has been shown to be protective in mice. Agonization of TLR9 with bacterial DNA (bDNA) could provide a passive immunity to lupus and other autoimmune conditions without the side effects of corticosteroids.
We previously showed that in vivo administration of bDNA was protective against lupus in mice, however the mechanism behind this protection was unknown. In vitro stimulation of lupus prone splenocytes showed increased production of IL-10, a potent anti-inflammatory cytokine, along with an increase in IL-6, a cytokine known to induce the proliferation of IL-10 producing B cells and antibody producing plasma cells. This phenomenon is dependent on TLR9 expression, but expression of TLR9 on either B cells or dendritic cells is sufficient to increase IL-10. However, TLR9 activation on B cells may cause an increase in IL-10 with a less dramatic increase in IL-6, which may lead to a more beneficial, anti-inflammatory profile as a potential therapeutic.
Our results suggest bDNA as a possible anti-inflammatory avenue of autoimmune management that avoids the use of corticosteroids. Future studies will focus on B cell targeted delivery of bDNA that promotes IL-10 without the side effect of increasing IL-6.
Human gut commensals support development of ocular autoimmunity in retina-specific T cell receptor transgenic mice
Authors: Zhang Amy , Horai Reiko , Jittayasothorn Yingyos , Badger Jonathan H , Nagarajan Vijayaraj , Murphy Caitlin Elizabeth , Yuan Wuxing , O’hUigin Colm , Honda Kenya , Caspi Rachel 
Published: August 2023

Abstract
Autoimmune uveitis is a major cause of blindness, in which intraocular inflammation is driven by T cells that target the neuroretina. In a mouse model of spontaneous autoimmune uveitis (R161H), retina-specific T cells are primed in the gut through their transgenic TCR, and trigger disease. To support the relevance to human disease, we examined the development of uveitis and its association with gut microbiota in gnotobiotic R161H mice colonized with gut flora from healthy human donors. We then performed fecal metagenomic sequencing, gut immunophenotyping by flow cytometry and disease monitoring. Our results indicate that human gut commensals support development of autoimmunity in the spontaneous uveitis model. Human flora mice compared to SPF mice harboring normal mouse flora displayed altered intestinal effector and regulatory CD4 T cell profiles, and had decreased fecal metabolites including microbe-derived short chain fatty acids. Microbiome analyses showed that human flora mice retained a distinct but simplified gut microbial community compared to their original donor sample. Mice with high disease scores appeared to harbor more diverse gut flora than those with low scores. Verrucomicrobia, Actinobacteria, and Fusobacteria were enriched in mice with high disease scores, whereas Firmicutes appeared enriched in mice with low disease scores. In-vivo association studies are underway to examine the ability of candidate microbes to modulate autoimmune uveitis. These findings suggest that some taxa of human commensals may have enhancing or suppressive effects on the development of ocular autoimmunity. These candidate microbes can be explored as targets or as probiotics for therapeutic use.
Benzo[a]pyrene exposure reduces cell-type diversity in lupus-prone mice
Authors: Zhu Runqi , Kennicott Kameron , Liang Yun 
Published: August 2023

Abstract
Studies indicate that genetic factors only account for approximately thirty percent of all autoimmune diseases, while the rest of autoimmune pathogenesis is attributed to environmental factors including toxic chemicals, dietary components, and infections. To understand if and how toxic chemicals trigger autoimmunity, we investigated the effect of benzo[a]pyrene (BaP) exposure on the development of autoimmune phenotypes in the lupus-prone MRL/MpJ strain. Since BaP is a polycyclic aromatic hydrocarbon commonly found in byproducts of industrial incineration, motor vehicle emissions and cigarette smoke, we subjected mice to skin plus lung exposure to BaP over the course of 8 weeks before lupus onset. BaP treatment resulted in total body weight loss in male mice, while marginal changes in anti-dsDNA levels occurred. Multi-organ analyses of BaP-treated and control MRL mice suggested that kidney is a major organ directly affected by the metabolism of benzene-containing compounds, with increased expression of BaP-target genes including Cyp4b1 and Hao2. Intriguingly, spatial transcriptomic data showed that BaP caused drastic reduction in cell type diversity in both kidney and spleen of MRL mice. In addition, BaP exposure triggered C3 deposit in a more severe manner in the kidney of male MRL mice compared to female. Collectively, our results show that BaP exposure reduces cell type diversity in lupus-prone mice before disease onset, and stimulates sex-biased molecular pathways which may help explain the increased likelihood of end organ damage in males with lupus.
Clonally Expanded Cytotoxic CD8+ T cells Target Citrullinated Antigens In ACPA+ Rheumatoid Arthritis
Authors: Moon Jae Seung , Younis Shady , Sharpe Orr , Rao Navin L , Carman Julie A , James Eddie A , Buckner Jane H , Deane Kevin D , Holers V Michael , Donlin Laura T , Davis Mark M , Robinson William H 
Published: August 2023

Abstract
The immune mechanisms that mediate synovitis and joint destruction in rheumatoid arthritis (RA) remain poorly defined. Although increased levels of CD8+ T cells have been described in RA, their role in pathogenesis remains unclear. Here we perform single cell transcriptome and T cell receptor (TCR) sequencing of CD8+ T cells derived from anti-citrullinated protein antibodies (ACPA)+ RA blood. We identify GZMB+CD8+ subpopulations containing large clonal lineage expansions that express cytotoxic and tissue homing transcriptional programs, while a GZMK+CD8+ memory subpopulation comprises of smaller clonal expansions that express effector T cell transcriptional programs. We demonstrate RA citrullinated autoantigens presented by MHC class I activate RA blood-derived GZMB+CD8+ T cells to expand, express cytotoxic mediators, and mediate killing of target cells. We also demonstrate that these clonally expanded GZMB+CD8+ cells are present in RA synovium. These findings suggest that cytotoxic CD8+ T cells targeting citrullinated antigens have a role in contributing to synovitis and joint tissue destruction in ACPA+ RA.
The study was supported by following grants: National Institutes of Health grant R01 AR063676, U19 AI110491, R01 AR078268, and Janssen Biotech, Inc.
Distinct phenotypes of rare autoreactive and virus-reactive CD8+ T cells revealed through novel clustering algorithm
Authors: Kus Anna , Wiedeman Alice , Long Alice 
Published: August 2023

Abstract
Antigen-specific cells are implicated in the development and progression of disease in autoimmunity, infectious disease, and cancer, and are an attractive target for therapies. While robust detection of antigen-specific cells is possible with tetramer and activation-induced marker assays, extensive characterization of these cells remains challenging due to their rarity. Here we present a novel computational tool, DISCOV-R, that enables deep phenotyping of rare antigen-specific cells through unbiased clustering of a parent population into subsets defined by expression of phenotyping markers and overlaying the antigen-specific population. Using this tool with 35-parameter mass cytometry (CyTOF) along with class I MHC-tetramer assays, we identified phenotypes enriched among rare islet autoantigen-reactive and chronic virus-reactive CD8+ T cells when compared to total CD8+ T cells from 46 type 1 diabetics. CD8+ T cells were clustered based on expression of 24 phenotypic markers, revealing 12 CD8+ T cell phenotypes shared across subjects. Overlaying antigen-specific tetramer-positive cells on this phenotypic landscape revealed that both islet- and virus-reactive cells were enriched for an exhausted-like memory phenotype (p=1.7E-07 and 1.6E-05, respectively) consistent with chronic antigen exposure, while islet-reactive cells were enriched for two transitional memory phenotypes (p=0.01 and 0.03). The characterization of these rare antigen-specific cells using DISCOV-R reveals unique phenotypes associated with their specificity that may indicate different function, and enables comparison over time and between individuals to identify biomarkers and potential pathways to disease development and progression.
Tuning peptide specificity for T cell tolerance in Type 1 diabetes
Authors: Smith Jennifer Anne , Balolong Jared , Jin Nijun , Whitty Caroline , Kappler John W , Anderson Mark S 
Published: August 2023

Abstract
Type 1 Diabetes (T1D) is a classical T-cell mediated autoimmune disease, and fundamental data have implicated insulin as the dominant autoantigen in T1D disease. In the NOD mouse model of T1D, notable studies have found that mice lacking native insulin expression but with an altered insulin sequence to maintain blood glucose levels are protected from insulitis and diabetes. Growing evidence also indicates how the insulin peptide is bound within MHC Class II (peptide register) is essential in determining the strength of interactions and recognition of autoreactive T-cells. We have uncovered a unique peptide binding characterized by the dominant insulin epitope InsB:9–23. The majority of InsB:9–23-specific CD4 T-cells in the periphery recognize insulin bound in the unusual register 3, and knocking in this single amino acid variation into just one copy of the insulin gene in NOD mice, confers protection against T1D. In addition, these mice were protected from T1D, even when treated with checkpoint inhibitor blockade, unlike their wild-type littermates. Introducing this superagonist epitope into the NOD mouse has allowed us to address several key questions surrounding pathways of peptide generation, presentation by MHC molecules, and recognition by auto-reactive pathogenic T cells. In addition, we have been able to model how central and peripheral tolerance mechanisms can be altered when major epitopes in the Insulin gene are mutated, allowing us to explore means of dominant tolerance to understand the potential for translation into treatments for T1D.
Supported by grants from NIH (R01 DK133443-01A)
Single cell characterisation of tissue homing CD4+ and CD8+ T cell clones in immune-mediated refractory arthritis
Authors: Bhattacharya Dipabarna , Theodoropoulos Jason , Kelkka Tiina , Nurmi Katariina , Juutilainen Timo , Eklund Kari , Koivuniemi Riitta , Mustjoki Satu , Lönnberg Tapio 
Published: August 2023

Abstract

Background
Immune-mediated arthritis (IMA) is a group of autoimmune diseases where chronic inflammation primarily targets different joints in the body. Rheumatoid Arthritis (RA) is the most common subtype. In childhood, RA mostly manifests as juvenile idiopathic arthritis (JIA). In this study, we aimed to characterize the tissue homing inflammatory pathogenic T cells in patients with IMA.

Methods
We collected paired synovial tissue (ST) and peripheral blood (PB) samples from three patients with IMA and analyzed CD45+, CD4+ and CD8+ sorted cells with paired single-cell RNA and TCRα/β sequencing and validated the findings with published datasets.

Results
Despite being disparate diseases, CD4+ T cells in IMA represented uniform phenotype across patients with no major patient specific clusters. The ST cells were more cytotoxic (GZMB), highly activated (LAG3, PDCD1) and proliferative (NME1, FABP5, G0S2 and MKI67). A modest clonal expansion within the Treg cluster was found in the ST compartment as compared to PB (p&lt;0.05). Conversely, the CD8+ T cell clusters showed strong patient specific characteristics. All T cell clones enriched to the ST upregulated genes belonging to TNF receptor superfamilies, inflammation markers (LMNA, RGCC, CREM), and transcription factor NR4A2. Pathway enrichment analysis showed enrichment of the TNFA signalling via NFKB and apoptosis pathways.

Conclusions
Our data suggests that in patients with IMA, the synovial tissue is dominated with cytotoxic, highly activated CD4+ T cells with proliferation-associated gene expression signature. Shared CD4+ and CD8+ T cell clones can be found between PB and ST, but they have a more proliferative and activated phenotype when trafficking from PB to ST.

Supported by grants from University of Helsinki, Finland
Neutrophil peptidylarginine deiminase 4 plays a systemic role in obesity-induced chronic inflammation in mice
Authors: Van Bruggen Stijn , Sheehy Casey E , Kraisin Sirima , Wagner Denisa D , Martinod Kimberly 
Published: August 2023

Abstract
Obesity is an increasing problem in our current society. In morbidly obese patients, the level of circulating neutrophil extracellular traps (NETs) was found to be higher than in lean control subjects. Essential in this process of NET formation is the activation of the enzyme peptidylarginine deiminase 4 (PAD4).
We aimed to understand how NETs contribute to the detrimental effects associated with a prolonged state of (morbid) obesity. Therefore, an animal model was adopted in which wild type (WT) and neutrophil specific PAD4 deficient (Ne-PAD4−/−) mice on a C57BL6/J background were fed a high fat containing diet (HFD – 60kcal% fat) for a period of 10 weeks.
Neutrophil activation status, evaluated through the formation of NETs in response to calcium ionophore ionomycin (4 μM) stimulation, was initially reduced after 3 days of HFD feeding. At later timepoints (5- and 10-weeks), neutrophils isolated from HFD-fed mice showed increased levels of NET formation in response to ionomycin stimulation in comparison to neutrophils from control diet-fed mice. Ne-PAD4−/− mice on the HFD gained less weight than WT mice, which had a constant gain of body weight over the 10-week experimental period. Finally, after 10-weeks of high fat intake, cardiac function was evaluated in WT and Ne-PAD4−/− mice by echocardiography. Interestingly, in WT mice diastolic function (early passive vs late active filling, E/A ratio) decreased as compared to baseline values, while Ne-PAD4−/− mice kept E/A ratios comparable to baseline levels.
Here, we demonstrate the importance of systemic NET release under metabolic challenge, and how this can contribute to cardiac deterioration at a young age due to obesity-induced alteration in the innate immune system.
Potent Anti-inflammatory Effects of the Adiponectin Receptor Agonist, ALY688
Authors: Sater Ali Abdul , Tang Jialing , Lone Abdul Hadee , Pignalosa Anglica , Crawford Kathryn , Sweeney Gary 
Published: August 2023

Abstract
Low circulating levels of adiponectin are associated with increased inflammation in a wide range of disease states. In particular, this applies to obesity-related diseases such as type 2 diabetes, heart failure and non-alcoholic fatty liver disease. Numerous studies have shown that adiponectin exerts anti-inflammatory and beneficial metabolic effects. Hence there has been tremendous interest in developing adiponectin-based therapeutics. Here we examined the effect of ALY688, a small peptide adiponectin receptor agonist, on lipopolysaccharide (LPS)-driven inflammation in vivo and in vitro. We show that ALY688 administration significantly diminished LPS-driven production of pro-inflammatory cytokines and chemokines (i.e., IL-1β, TNF-α, IL-12, IFN-β, MCP-1, KC, RANTES) in mice. Moreover, mice injected with ALY688 exhibited a rapid increase in the anti-inflammatory cytokine, TGF-β. Apart from an increase in total CD3+ T cells, there were no marked changes in the circulating immune cells following ALY688 injection. No alterations in cytokine profile was seen in normal mice given ALY688, suggesting that the effects of ALY688 are context-dependent. Mechanistically, we employed phospho-flow cytometry to demonstrate that circulating immune cells responded rapidly to ALY688 injection by upregulating p-AMPK and p-P38, two well established adiponectin downstream signaling events. These results were confirmed in human peripheral blood mononuclear cells (PBMCs), where ALY688 treatment led to a robust increase in phospho-AMPK and phospho-P38. Altogether, these results show that the adiponectin agonist, ALY688, has strong anti-inflammatory effects by triggering AMPK and P38 activation in vivo and in vitro.
Overexpression of miR-10a-3p mediates TGF-β1/Smad Signaling Pathway to suppress adipogenesis and AT inflammation
Authors: Singh Udai P , Kiran Sonia , Mandal Mousumi , Rakib Ahmed 
Published: August 2023

Abstract
Obesity, an epidemic of our time is a multifactorial disease characterized by an enhanced amount of fat and energy storage in adipose tissue (AT). Growing evidence suggests that obesity promotes activation in resident T cells and macrophages to maintain low-grade inflammation. MicroRNAs (miRs) are shown to maintain immune response in the AT and are associated with adipocyte differentiation, and function during obesity. Microarray analysis shows differential expression of miRs in the AT immune cells in mice fed with a high-fat diet (HFD) for 12 weeks. Pathways analysis demonstrated that miR-10a-3p (miR-10a) expression is downregulated in AT and its expression has been correlated with obesity progression. Thus, we aimed to evaluate miR-10a overexpression effects on AT inflammation, metabolic markers, and signaling pathways during obesity. Our ex vivo analysis shows that mimicking miR-10a reduces the expression of inflammatory M1 macrophage, TGF-b1, KLF4, IL-17F, and inflammatory cytokine while inducing FoxP3 expression in immune cells derived from AT of HFD-fed mice as compared to ND. Correspondingly, we noticed that mimicking miR-10a in NIH3T3-L1 adipocytes reduces proinflammatory genes, adipocyte size, cytokines, and lipids accumulation as compared to the control. Further, overexpression of miR-10a also reduces TGF-b1, Smad3, CHOP10, and C/EBPa expression in NIH3T3-L1 as compared to the control. Thus, our findings suggest that miR-10a mimics mediate the TGF-β1/Smad3 signaling pathway, which suppresses cytokine, and metabolic markers, to reduce adipogenesis and AT inflammation. Our studies strongly suggest miR-10a as a new target to therapeutically cope with obesity and its associated metabolic disorders.
Supported by NIH grant R01 AI140405).
VEGFR-3 Stimulation on LECs Boosts Type 2 Immunity After Vaccination
Authors: Kurtanich Trevin Robert , Medellin Jorge Emiliano Gomez , Swartz Melody A 
Published: August 2023

Abstract
Lymphatic vessels are the main transport routes for fluid, antigens, exosomes, and immune cells from peripheral tissues to the lymph nodes (LNs). In addition to being pervasive through tissue, lymphatic vessels are also abundant within the LN, where they route lymph and cells around the B cell follicles and throughout the paracortical zone; thus, lymphatic endothelial cells (LECs) have unique access to lymph-borne molecules and interactions with immune cells. Upon acute inflammation or vaccination, LN LECs undergo expansion along with lymphocyte proliferation, a process dependent on the VEGF-C/VEGFR-3 signaling axis; however, it is not well understood how LN lymphatics and their expansion contribute to acute adaptive immune responses. Here, we asked how altering VEGFR-3 signaling LN LECs alters the adaptive immune response, using OVA + CpG (a TLR9 agonist) as a model for vaccination. We found that delivering VEGF-C156S, a VEGFR-3 specific agonist, multiple times prior to and concurrent with the inflammatory stimulus led to increased Th2 responses in terms of higher plasma levels of OVA-specific IgG1, more IgG1+ germinal center B cells, and increased production of Th2 cytokines (IL-4, IL-5, and IL-13) by CD4+ T cells upon restimulation. In loss-of-function experiments using a tamoxifen-inducible LEC-specific deletion of VEGFR-3, vaccination led to reduced plasma levels of OVA-specific IgG1 compared to tamoxifen-treated control littermates. Together, these findings suggest that in response to vaccination, VEGFR-3 signaling in LN LECs bias adaptive immune responses towards type 2 immunity. This highlights the role of lymphatics not just as passive conduits for fluid transport, but as having direct immunomodulatory function.
CD99’s highly conserved region III facilitates the homodimerization and function in cell-cell adhesion
Authors: Chang Hanna , Nam Giri , Choi Eun Young 
Published: August 2023

Abstract
CD99 is a type I transmembrane protein and its function has been known to be implicated in various cellular processes including cell-cell adhesion and leukocyte diapedesis. These functions were all related to actin polymerization and/or reorganization. Nonetheless, the molecular mechanism has remained unclear. In previous studies, we showed that CD99 is capable of forming a homodimer and the homodimerization requires the extracellular domain. This trait was confirmed to be conserved in mouse CD99. In this study, we investigated the molecular basis and functional role of homodimer formation. In sequence comparison analysis, CD99 amino acid sequences from different species have three conserved subdomains in the extracellular domain, named highly conserved region (HCR) I, II, and III. Based on this information, we generated various subdomain-deleted mutants. In the bimolecular fluorescence complementation assay, the HCRIII-deleted mutant (named HCRIIIΔ ext-mut), significantly reduced the ability to form a homodimer, compared with other mutants. Additionally, HCRI and II-deleted mutant, that is, a mutant expressing only HCRIII-subdomain on the cell surface (named HCR3ext-mut), was enough to form the homodimer. Overexpression of HCRIIIΔext-mut in T cells prevented T cells from forming stable interaction with the antigen-presenting cells (APCs), and polarization of polymerized actin to the T-APC interface. However, overexpressing HCRIIIext-mut enhanced the T-APC stable interaction. These results identify the HCRIII of CD99 as the key subdomain required for dimer formation and indicate that the homodimer would contribute to the formation of stable interaction with APCs of T cells via actin cytoskeleton reorganization.