bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutrophil maturation and responses to infectious pathogens are regulated by microbiota
Authors: Kugadas Abirami , Geddes-McAlister Jennifer , Gadjeva Mihaela 
Published: January 2023

Abstract
It has long been considered that neutrophils are cells with prepacked anti-microbial granules whose responses to various infectious challenges are innately pre-determined. Here, we provide data that clearly demonstrates definition of neutrophil transcriptomes and proteomes modulated by the microbiota. Using RNAseq and quantitative proteomic approaches we defined mature neutrophil transcriptome and proteome signatures at steady state and during ocular infection with Pseudomonas aeruginosa. Following in-solution digestion and LC-MS/MS analysis, we quantified 3585 proteins from mature neutrophils derived from either non–infected or infected germ free (GF) and specific pathogen free (SPF) mice. We found that the proteomic signatures of mature neutrophils derived from the GF and SPF were significantly different at steady state. Similarly, RNAseq analysis revealed significant differential expression of 327 genes at steady state. During infection with P. aeruginosa, GF-derived neutrophils responded with significant alterations in transcriptional regulation, ncRNA processing, rRNA metabolic processes, mRNA processing, and splicing, while the SPF-derived neutrophils responded with alterations in acetylation. Consistently, GF mice were more susceptible to ocular keratitis compared to SPF controls. Cumulatively, the data support the concept that microbiota drives neutrophil maturation by defining not only the quantity, but also the quality of mature neutrophils. Based on our data, we predict that neutrophil responses can be diverse and specifically tailored to pathogens. In conclusion, neutrophil responses, although innately determined, are constantly adapted and molded by the commensal presence.
The microbiome of NLR knockout animals reveals insights into susceptibility to experimental colitis.
Authors: Ringel-Scaia Veronica Marie , Thomas Cassidy A. , Qin Yufeng , Wade Paul A. , Allen Irving C. 
Published: January 2023

Abstract
Upon sensing particular pathogen associated molecular patterns (PAMPs), inflammasome-forming NOD-like receptors (NLRs) initiate pyroptosis and the cleavage of pro IL-18 and pro IL-1β to their active forms. Consequently, the absence of an NLR or its malfunction in the gut has been shown to result in dysbiosis. There is significant evidence linking dysbiosis with chronic inflammation in the gut and colon cancer. Prior work in our laboratory has revealed that mice lacking NLR inflammasomes, specifically Nlrp1−/− mice, are highly susceptible to experimental colitis and colitis-associated cancer. Here, we extend these findings by evaluating the microbiome of mice lacking either Asc or Nlrp1. 16s rRNA sequencing revealed 6 unique genera prevalent in Nlrp1−/− mice compared to WT and 9 genera in Asc−/− mice compared to WT. Remarkably, the microbiome composition in both knockout animals was more pathogenic, including such genera as Helicobacter, Mucispirillum, and Clostridium. The abundance of volatile free fatty acids was assessed to investigate functional metabolic differences due to the uniqueness of the microbiome in these animals, and interestingly the abundance of acetate, butyrate, and proprionate were distinctly different in Nlrp1−/− and Asc−/− mice compared to WT. Crucially, our analyses were conducted prior to any experimental colitis model. The differences in the microbiomes of these mice have the potential to resolve conflicting data in the field regarding inflammasome deficient mice and subsequent predisposition to or protection from colitis and cancer. Future work will establish which NLR is responsible for sensing the specific bacteria present in the microbiome of the inflammasome-deficient mice at rest.
Identification of CNS-specific biomarkers for monitoring the progression of multiple sclerosis
Authors: Chase Carol Ann , Raphael Itay , Forsthuber Thomas 
Published: January 2023

Abstract
There are currently no reliable methods for assessing the progression of multiple sclerosis (MS) from the relapsing-remitting to the secondary progressive form. This gap in knowledge hinders the ability for therapeutic intervention and results in continued relapses and physiological deterioration. To begin to address the urgent need for biomarkers of progressive MS we investigated proteome changes over the disease course of progressive experimental autoimmune encephalomyelitis (EAE) in NOD mice as a preclinical model of the disease. Our lab has pioneered a high-throughput quantitative proteomic technique, which we have previously used to quantify expression levels of central nervous system (CNS) proteins over the course of monophasic EAE in C57BL/6 mice, producing a predictive protein biomarker fingerprint for clinical relapses. In this study, we utilized this established proteomic technique as well as bioinformatics tools to prioritize key proteins whose expression level in the CNS correlated specifically with the progressive phase of disease in the NOD EAE model. Bioinformatics analysis identified 11 proteins with differential expression in the CNS of mice across the time course of NOD EAE, three of which are CNS specific. We are seeking to detect corollary changes in these three CNS-specific proteins in the serum, pointing to a minimally invasive means of monitoring disease progress and measuring drug efficacy. Our studies will provide a proof-of-concept for identifying homologous human biomarkers to guide treatment in individual patients. Furthermore, our results may provide insights into mechanisms that contribute to disease pathology and offer additional therapeutic targets for slowing the progression of MS.
RGC-32 enhances experimental autoimmune encephalomyelitis by promoting Il-17 and GM-CSF production
Authors: Rus Violeta , Nguyen Vinh , Tatomir Alexandru , Mekala Armugam Prasad , Boodhoo Dallas , Rus Horea G 
Published: January 2023

Abstract
Response Gene to Complement (RGC)-32 is an intracytoplasmatic protein expressed in a variety of cells in response to sublytic complement activation, TGF-β and several growth factors. Upon activation it translocates into the nucleus and plays an important role in cell proliferation, migration, angiogenesis and TGF-β induced epithelial mesenchymal transition and fibrosis. We have recently reported that RGC-32 promotes Th17 but not Treg, Th1 or Th2 differentiation in murine CD4 T cells in vitro. To evaluate the relevance of RGC-32 in an IL-17 dependent inflammatory condition we induced EAE in WT and RGC-32−/− mice by immunization with MOG35–55 peptide emulsified in CFA. The timing of disease onset was similar in both groups of mice. However, at peak disease, RGC-32−/− mice had significantly lower clinical scores. The attenuated EAE phenotype was confirmed by histopathologic examination of the spinal cords that showed fewer inflammatory infiltrates and demyelination foci in RGC-32−/− than in WT EAE mice. The percentage and absolute number of IL-17+ and GM-CSF+CD4+ T cells were significantly lower in the CNS of RGC-32−/− EAE mice. The percentage and number of IFNγ+ and FoxP3+ CD4+ T cells did not differ between WT and RGC-32−/− EAE mice. RGC-32 deficiency did not alter antigen specific expansion of RGC-32−/− spleen cells in response to MOG35-55 peptide. Transfer of WT CD4+ T cells into WT or RGC-32−/− mice before MOG immunization resulted in EAE of similar severity suggesting that the attenuated EAE phenotype in RGC-32−/− mice is T-cell-mediated. These data suggest that RGC-32 exerts a proinflammatory role in EAE by promoting Th17 immune responses and the generation of GM-CSF and that RGC-32 blockade might be a novel therapeutic strategy in MS.
Signaling via TNFR2 mediates CNS remyelination in EAE through regulation of oligodendrocyte progenitor cells
Authors: Gomez-Rivera Francisco , Raphael Itay , Forsthuber Thomas 
Published: January 2023

Abstract
Tumor necrosis factor-alpha (TNF) is a pleiotropic inflammatory cytokine that has been associated with the pathogenesis of several autoimmune diseases, including multiple sclerosis (MS). Consequently, TNF-blocking drugs have been widely used to treat many inflammatory conditions and have proven highly effective. However, treatment of MS patients with anti-TNF drugs leads to disease exacerbation and severe demyelination. This effect has been specifically associated with lack of TNF signaling through its receptor, TNFR2. However, the underlying mechanisms are not fully understood. Experimental autoimmune encephalomyelitis (EAE) is the most common animal model used to study MS. Our lab has recently generated TNFR2−/− DR2b+/+ mice to study the role of TNFR2 signaling in EAE in the context of the HLA-DR2b (DRB1*1501), a haplotype strongly associated with MS. We found that these mice developed progressive EAE characterized by increased demyelinating lesions. Strikingly, this phenotype was not due to lack of TNFR2 expression in T cells, but rather was associated with a decreased numbers of oligodendrocyte progenitor cells (OPCs) in the CNS. Moreover, we demonstrated that TNFR2 signaling is critical for expression of chemokines in the CNS, suggesting its involvement in OPC function and recruitment. Our studies provide key insights into CNS repair and regulatory mechanisms controlled by TNF during inflammation, and this information may help develop novel therapeutic strategies.
The neurokinin 1 receptor and its agonists recruited at the DC-T cell synapse are necessary to promote the survival of activated T cells in vivo
Authors: Larregina Adriana T , Sumpter Tina L , Rojas-Canales Darling M , Tkacheva Olga , Shufesky William J , Falo Louis D , Morelli Adrian E 
Published: January 2023

Abstract
Initiation of cellular immunity relies on T cell activation by Ag-presenting dendritic cells (DCs). By signaling via the neurokinin-1 receptor (NK1R), the neuropeptides hemokinin-1 (HK-1) and substance P (SP) potentiate cellular immunity by mechanisms not fully elucidated. Although SP is mainly secreted by sensory nerves, it is also synthesized and released by T cells. Here, we investigated the role of NK1R and autocrine SP and HK-1 on T cell activation. Using Imagestream flow cytometry (Amnis) to visualize couplets of OVA loaded WT or SP/HK1double KO DCs and responder OT-II CD4 T cells, we observed that the NK1R, SP and HK-1 colocalize with phalloidin at the site of DC-T cell contact. Following CD3/CD28 activation in vitro, we demonstrate that T cells express the full-length NK1R, and that NK1R signaling induces Ca2 flux, activation of calcineurin, NFAT1/2 and NFκB, which results in IL-2 secretion and survival of CD4 and CD8 T cells. These effects were abrogated in NK1RKO orSP/HK1double KO T cells, or by soluble NK1R antagonists. Addition of exogenous SP or HK-1 to CD3/CD28 activated WT T cells did not increase IL-2 secretion indicating that autocrine SP and HK1 released at the DC-T cell synapse suffice to promote T cell survival. In a model of skin DTH in NK1RKO or HK-1/SPdouble KOT cell chimeras, 73 ± 5% of activated (CD44high) CD4 and CD8 T cells die in the draining lymph nodes after priming, and 79%± 7% of the remaining T cells recruited to the skin die in situ following elicitation. In summary, NK1R signaling by autocrine SP and HK1 at the DC-T cell synapse is necessary for the survival of activated T cells and the development of potent cellular immunity.
Leukocyte immunoglobulin-like receptor A3 (LILRA3) displays anti-inflammatory and neuro-regenerative functions through interaction with multiple ligands
Authors: Tedla Nicodemus , An Hongyan , Fath Thomas , Lord Megan , Bryant Katherine 
Published: January 2023

Abstract
LILRA3 belongs to a family of highly homologous surface activating and inhibitory receptors that are emerging as critical regulators of immune cell activation by transducing opposing signals. Uniquely, LILRA3 is soluble and so cannot transduce intracellular signals, hence its functions are unknown, despite its ubiquitous presence in sera and its strong clinical association with various inflammatory diseases. This is primarily due lack of knowledge of its ligands, absence of a LILRA3 homolog in rodents and difficulties in producing functional protein. We produced full-length rLILRA3 protein typical of the native protein and used it in a proteomic approach to concurrently identify two novel ligands; LAMR1 and Nogo 66, and one known MHC I ligand, HLA-B2705 that were validated by expression cloning. Importantly, LAMR1 and Nogo 66 independently interacted with LILRA3 with high affinities of 9.1 pmol and 22 pmol respectively. LAMR1 is a multifunctional protein involved in LPS-induced inflammation and HLA-B2705 is strongly associated with seronegative arthritis (SpA). Nogo 66 is potent inhibitors of neurite outgrowth in the central nervous system. We discovered that LILRA3 promoted neurite outgrowth and synapse formation in central nervous system by blocking Nogo 66; strongly suppressed LPS-mediated inflammation in vivo via interaction with LAMR1, and inhibited activation of peripheral blood T cell by competitively blocking interaction of HLA-B2705 with a closely related activating receptor (LILRA1) which is highly expressed on a subset of T cells in HLA-B27 +ve patients with SpA. These results led to a new concept that LILRA3 may bind multiple ligands with varying affinities and display clinically relevant tissue-specific functions.
Suppression of foreign body giant cell formation by phospholipase Cγ1 via RUNX1/PU.1/ DC-STAMP axis in macrophages
Authors: Kim Ye Seon , Ok Chang Youp , Park Joon Seong , Lee Ha Young , Bae Yoe-Sik 
Published: January 2023

Abstract
Foreign body giant cell (FBGC), a fused macrophage, formation is associated with the inflammatory response following material implantation. However, the intracellular signaling events that regulate the process remain unclear. Here, we investigated the potential role of phospholipase C (PLC)γ1, a crucial enzyme required for growth factor-induced signaling, on FBGC formation. Depletion of PLCγ1 using shRNA induced FBGC formation accompanied by increased expression of fusogenic genes such as cathepsin K, DC-STAMP and CD36. Re-addition of PLCγ1 decreased FBGC formation. PLCγ1-deficiency caused a reduce in RUNX1 and subsequent increased expression of PU.1 while subsequent rescue of RUNX1 in sh-PLCγ1-transfected cells strongly inhibited FBGC formation. FBGC generated by knock-down of PLCγ1 using shRNA resulted in strongly increased TNF-α production, with augmented activation of ERK, p38 MAPK and JNK, and subsequently NF-kB. Collectively, we suggest that an important cell signaling molecule PLCγ1 plays a role in the foreign body response by regulating the RUNX1/PU.1/ DC-STAMP axis in macrophages.
Dynamic programming and memory of monocytes by varying signal strengths of innate stimulants
Authors: Geng Shuo , Yuan Ruoxi , Li Liwu 
Published: January 2023

Abstract
In response to changing external signal strength, innate monocytes may be dynamically programmed into distinct functional states, which may bear significance relevance in host pathophysiology. However, molecular mechanisms that control innate memory dynamics are not well understood nor extensively studied. Using lipopolysaccharide (LPS), the model stimulant of Toll-Like-Receptor 4 (TLR4), we observed that the expressions of pro-inflammatory mediators are preferentially sustained in monocytes adapted by subclinical super-lower dose LPS, and suppressed/tolerized in monocytes programmed by higher dosages of LPS. These phenomena are well conserved in both mice and human monocytes. At the molecular level, we observed that monocytes programmed by super-low dose LPS maintain higher levels of transcription factor IRF5. We also observed that the inflammatory monocyte programming is dependent upon TRAM/TRIF but not MyD88. Similar to LPS, we also observed biphasic inflammatory adaptation and tolerance in monocytes challenged with varying dosages of TLR7 agonist. In sharp contrast, rising doses of TLR3 agonist preferentially caused inflammatory adaptation without inducing tolerance. At the functional level, we observed that in vivo programming of monocytes by subclinical dose LPS exacerbates the progression of atherosclerosis. Taken together, our study provides novel mechanisms for the dynamic programming/memory of innate monocytes and their pathological implications in atherosclerosis.
The role of neutrophils in organ tissue damage in SLE
Authors: Deng Guo-Min , Guo Xuanxuan , Fang Xiang , Qiao Wei , Fei Xibing 
Published: January 2023

Abstract
Neutrophils are the most abundant leukocytes in Human blood, but it is not clear whether neutrophils exert an important role in the pathogenesis of organ tissue damage in systemic lupus erythematosus (SLE). We used lupus-prone mouse model and model of lupus serum-induced tissue inflammation in mouse to investigate the role of neutrophils in the organ damage of SLE. We found that there was a little neutrophil infiltration in the inflammatory sites of skin, liver, brain and joint in lupus-prone mice. We also found that there was also little neutrophil infiltration in the site of skin inflammation induced by lupus serum in normal mouse. The severity of skin inflammation induced by lupus serum was not significantly decreased in mice with neutrophil depletion compared to ones without neutrophil depletion. But we found that neutrophils were actually involved in tissue injury induced by lupus IgG. Further studies showed that lupus IgG stimulated and activated neutrophils, and cause the death of neutrophils. Studies also confirmed that Fas plays an important role in neutrophils apoptosis. Our study indicates that neutrophils participate in the early stage of lupus organ damage, and then they died through activation-mediated apoptosis. These findings promote the understanding of the role of neutrophils in the tissue injury with SLE.
The human lung mucosa determines Mycobacterium tuberculosis infection outcome in the alveolar epithelium
Authors: Torrelles Jordi B , Scordo Julia M , Sidiki Sabeen , Moliva Juan I. , Arcos Jesus 
Published: January 2023

Abstract
Mycobacterium tuberculosis (M.tb) deposited into the alveolar space encounters the human lung mucosa, i.e. alveolar lining fluid, or ALF. We have shown that M.tb exposure to ALF alters the M.tb cell wall surface and subsequently its interactions with human phagocytes, allowing these cells to control better the infection. Understudied host cells in M.tb pathogenesis are alveolar epithelial cells (ATs), nonprofessional phagocytes which are thought to participate in the initial phase and subsequent outcome of M.tb infection. Based on our previous results with phagocytes, we hypothesized that exposure of M.tb to human ALF will allow ATs to control better the infection. However, our results show that exposure of M.tb to ALF drives highly variable rates of bacterial uptake by ATs. Furthermore, independently of this uptake variability, M.tb exposure to ALF resulted in significant differences in M.tb intracellular growth in ATs. Based on these results, we defined two different types of human ALFs: Low-ALF (L-ALF, upon exposure allows better control of the M.tb infection) and High-ALF (H-ALF, upon exposure exacerbates M.tb infection). We further show that H-ALF exposed M.tb reduces the ATs release of pro-inflammatory cytokines and chemoattractants, as well as reduces ATs cytotoxicity. Moreover, H-ALF exposed M.tb affects the crosstalk between infected ATs and phagocytes by downregulating their inflammatory response. These results suggest a novel role for human ALF, where exposure of M.tb to ALF during infection defines ATs as potential M.tb stable reservoirs promoting intracellular bacterial replication and growth, while limiting local inflammation, and phagocyte infiltration and activation.
Autoantibody cross-reactivity with a microbial protein from a prevalent human gut commensal in antiphospholipid syndrome
Authors: ruff william , Roth Alexander S , Dehner Carina Anja , Vieira Silvio Manfredo , Goodman Andrew , Kriegel Martin A 
Published: January 2023

Abstract
Given the vast antigenic source of the gut microbiota, we hypothesized that human gut commensal bacteria induce and sustain autoreactivity via cross-reactivity. As a paradigm, we studied the antiphospholipid syndrome (APS), which is a serious autoimmune clotting disorder of unknown etiology but with a well-defined major autoantigen, b2-glycoprotein I (b2GPI). Infectious triggers are implicated in transient autoantibody production, but the persistent stimuli for anti-b2GPI antibodies remain unknown. To this end, we characterized b2GPI-specific monoclonal autoantibody reactivity to an in silico identified candidate commensal, Roseburia intestinalis (R.int), that is abundant in human stool from APS patients as detected by a species-specific PCR. Using an APS-derived monoclonal antibody, P1-117, that binds to the major B cell epitope in domain I of b2GPI (RGGMR), we tested for cross-reactivity to anaerobically cultured R.int and its candidate cross-reactive R.int protein (WP_006857340.1). P1-117 bound significantly to R.int lysates whereas a control antibody specific for another epitope within b2GPI did not. Further, P1-117 displayed significant binding to the recombinantly expressed R.int cross-reactive candidate protein. BALB/cJ mice immunized with whole heat-killed R.int displayed significant cross-reactive splenocytes and low titers of cross-reactive IgG autoantibodies. In conclusion, we present here in vitro and in vivo studies supporting cross-reactivity of pathogenic b2GPI-specific autoantibody with a common gut commensal. This study provides a concept for persistently colonizing gut commensals as chronic cross-reactive triggers in genetically susceptible autoimmune hosts such as APS patients.
Mapping the chromatin and RNA expression landscapes of human macrophages to interrogate the function of disease-associated genetic polymorphisms
Authors: Martins Andrew J , Narayanan Manikandan , Fixsen Bethany , Tsang John S 
Published: January 2023

Abstract
Macrophages are known to show highly dynamic responses to diverse stimuli, and have been implicated in metabolic syndrome and related diseases. Genome-wide association studies have identified many single-nucleotide polymorphisms (SNPs) associated with these common conditions, largely in non-coding regions; how these SNPs influence disease processes remains largely unknown. We hypothesized that examining RNA expression and chromatin state in macrophages across diverse activation conditions would elucidate the roles of macrophages in mediating the effects of disease-linked SNPs on the development of disease. We measured gene expression via RNAseq and histone 3 lysine 27 acetylation via ChIPseq as an indicator of promoter/enhancer activity in human blood monocyte-derived macrophages stimulated in vitro with a range of inflammatory and disease-relevant stimuli. Over 11,000 genes and 43,000 regulatory elements show condition-dependent activity in this dataset. Functional enrichment in modules of co-expressed transcripts confirmed expected stimuli-specific biology and reveal potentially novel relationships between distinct stimulation states. Correlation of regulatory element activity with module gene expression shows broad inflammatory/anti-inflammatory separation, and metabolic-trait associated SNPs tend to be embedded within regulatory elements whose activity is associated with both non-inflammatory and, surprisingly, some anti-viral macrophage gene modules. Ongoing work includes using these data to infer the transcriptional networks underlying these states. This study was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, NIH.