bluuebunny/crossref_metadata_2025_split huggingface dataset:
Follicular T cells are clonally and transcriptionally distinct in B cell-driven autoimmune disease
Authors: Akama-Garren Elliot H , van den Broek Theo , Simoni Lea , Castrillon Carlos , van der Poel Cees , Carroll Michael C 
Published: February 2023

Abstract
Pathogenic autoantibodies contribute to tissue damage and clinical decline in autoimmune disease. Follicular T cells are central regulators of germinal centers, although their role in epitope spreading towards autoantigens remains unclear. We performed single cell RNA and T cell receptor (TCR) sequencing of follicular T cells in autoantibody-mediated disease, allowing for analyses of paired transcriptomes and unbiased TCRab repertoires at single cell resolution. A minority of clonotypes were preferentially shared amongst autoimmune follicular T cells, and clonotypic expansion was associated with differential gene signatures in autoimmune disease. Antigen prediction using algorithmic and machine learning approaches revealed convergence towards shared specificities between non-autoimmune and autoimmune follicular T cells. However, differential autoimmune transcriptional signatures were preserved even amongst follicular T cells with shared predicted specificities. These results demonstrate that follicular T cells are phenotypically distinct in B cell-driven autoimmune disease, providing potential therapeutic targets to modulate autoreactive epitope spreading.
Supported by grants from NIH (R01AI130307, R01AR074105, T32GM007753).
Functional SARS-CoV-2-specific immune memory persists after mild COVID-19
Authors: Rodda Lauren Barbara , Netland Jason , Shehata Laila , Pruner Kurt B. , Morwaski Peter A. , Thouvenel Christopher D. , Takehara Kennidy K. , Eggenberger Julie , Hemann Emily A , Waterman Hayley R. , Fahning Mitchell L. , Chen Yu , Hale Malika , Rathe Jennifer , Stokes Caleb , Wrenn Samuel , Fiala Brooke , Carter Lauren , Hamerman Jessica A , King Neil P. , Gale Michael , Jr.  , Campbell Daniel J. , Rawlings David J , Pepper Marion 
Published: February 2023

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is causing a global pandemic, and cases continue to rise. Most infected individuals experience mildly symptomatic coronavirus disease 2019 (COVID-19), but it is unknown whether this can induce persistent immune memory that could contribute to immunity. We performed a longitudinal assessment of individuals recovered from mild COVID-19 to determine whether they develop and sustain multifaceted SARS-CoV-2-specific immunological memory. Recovered individuals developed SARS-CoV-2-specific immunoglobulin (IgG) antibodies, neutralizing plasma, and memory B and memory T cells that persisted for at least 3 months. Our data further reveal that SARS-CoV-2-specific IgG memory B cells increased over time. Additionally, SARS-CoV-2-specific memory lymphocytes exhibited characteristics associated with potent antiviral function: memory T cells secreted cytokines and expanded upon antigen re-encounter, whereas memory B cells expressed receptors capable of neutralizing virus when expressed as monoclonal antibodies. Therefore, mild COVID-19 elicits memory lymphocytes that persist and display functional hallmarks of antiviral immunity.
A distinct non-enzymatic role for Indoleamine-2,3-dioxygenase (IDO)2 vs. IDO1 in autoimmune arthritis
Authors: Peng Weidan , Merlo Lauren MF , DuHadaway James B , Montgomery James D , Murray Peter J. , Yeh Syun-Ru , Prendergast George C , Muller Alexander J , Mandik-Nayak Laura 
Published: February 2023

Abstract
IDO1 and IDO2 are closely related immune modulating enzymes encoded by linked genes. Whereas IDO1 is best known for its immunoregulatory role in tumor immune evasion, IDO2 acts as a proinflammatory effector of B cell-mediated autoimmunity. Given their opposing roles in inflammatory responses, interpretation of results obtained using IDO1 or IDO2 single knockout (ko) mice have been complicated by the expression of the other enzyme. Using single and double knockout (dko) mice and the KRN arthritis model, we distinguished differential roles for IDO1 and IDO2 in autoreactive B vs. T cell responses driving arthritis. Both autoreactive T and B cell responses and severity of arthritis were decreased in IDO2, but not IDO1, ko mice. Despite a similar attenuation of disease, only autoreactive B cell responses were reduced in dko mice, demonstrating that IDO2 directly mediates autoreactive B cell responses, while autoreactive T cell responses are indirectly affected by IDO1. Like IDO1, IDO2 was originally identified as a tryptophan catabolizing enzyme. However, we recently showed that the enzymatic activity of IDO2 is not required to drive arthritis. To define the non-enzymatic mechanism mediating IDO2 function, we identified IDO2-interacting proteins using a yeast two-hybrid screen. Specific interaction between IDO2, but not IDO1, and several candidate proteins was confirmed using overexpressing cell lines and co-IP/Western. Using site-directed mutagenesis and an in vitro IDO2-expression model, we identified potential regions outside of the catalytic site on IDO2 that mediate these interactions, providing the first evidence for the non-enzymatic mechanism by which IDO2 mediates proinflammatory B cell responses.
Mechanisms of TRAF3 Regulation of TLR Signaling in B Lymphocytes
Authors: Ybarra Tiffany K. , Bishop Gail A 
Published: February 2023

Abstract
TRAF3 is an adaptor protein that binds to receptors of the TNFR superfamily and exerts multiple regulatory functions in signaling pathways. However, functions are cell type and context dependent. B cell TRAF3 inhibits homeostatic NFκB2 activation, CD40/BAFFR signaling and other pro-survival signaling pathways; restraint of survival is a B cell unique TRAF3 function. Loss of function mutations of human TRAF3 are detected in B cell lymphoma and multiple myeloma. In addition to homeostatic survival, we found that TRAF3 inhibits B cell TLR signaling, a pathway implicated in B cell lymphomagenesis and autoimmunity. Numerous reports describe TLR function in myeloid cells, but specific TLR signaling pathways in B cells are under-studied. B cell TRAF3 inhibits TLR-mediated cytokine and Ab production, and Ig class switching. Our &lt;underline&gt;working hypothesis&lt;/underline&gt; is that B cell TRAF3 regulates the expression, recruitment and/or post-translational modification of TLR signaling proteins. Preliminary data show that B cell TRAF3 associates with signaling proteins MyD88 and IRAK1, and the kinase Syk following TLR stimulation. We are currently investigating how this association normally restrains the functions of these proteins in promoting TLR signals to B cells. We expect that information gained will provide new insights into the molecular mechanisms contributing to the regulation of B cells by TRAF3 in TLR signaling, potentially informing selection and development of more targeted therapies for B cell malignancies and autoimmunity.
Dysregulation of microRNA expression in chronic periodontitis
Authors: Banks Jonathan Matthew , Naqvi Raza Ali , Valverde Araceli , Bambila Maria F. , Martínez Gloria , Chapa Gabriela , Nares Salvador , Naqvi Afsar R. 
Published: February 2023

Abstract

Objective:
Assess microRNA (miRNA) expression in healthy and diseased gingival tissue of human subjects and identify potential miRNA-target gene interactions and biological pathways relevant to periodontal pathogenesis.

Methods:
Gingival biopsies were obtained from subjects meeting the criteria for “healthy” or “diseased” according to the current AAP guidelines. Total RNA (including miRNA) was isolated using miRNeasy kit (Qiagen). Global human miRNA expression was quantified using microRNA microarray (LC Sciences μParaflo® technology platform). Potential gene targets and biological pathways of differentially expressed miRNAs were predicted using bioinformatics analysis.

Results:
Our results show significantly different expression levels of miRNAs when comparing inflamed and healthy gingival biopsies. Among differentially expressed miRNAs, 35 were upregulated and 29 were downregulated in diseased tissue. Using pathway analysis, these miRNAs were predicted to influence the following pathways: ECM-receptor interaction, cell adhesion molecules (CAMs), MAPK signaling pathway, and cAMP signaling pathway. Genes associated with these pathways were scanned for potential miRNA binding sites. We identified IKBKB as a target gene, an endogenous inhibitor of NF-kappa-B and MAPK signaling, which possesses multiple binding sites for candidate miRNAs including hsa-miR-195-5p.

Conclusion:
Our findings reveal human miRNA expression profiles are significantly different in healthy and diseased gingival tissues. Post-transcriptional regulation of gene expression by miRNAs can modulate inflammatory biological pathways, suggesting their integral role in periodontal pathogenesis.
Long noncoding RNAs RN7SK and GAS5 Regulate Macrophage Innate Immune Function and Polarization
Authors: Naqvi Raza Ali , Ahmad Imran , Valverde Araceli , Naqvi Afsar R 
Published: February 2023

Abstract

Objective:
Macrophages (Mϕ) are polarized in two phenotypes: classically activated M1 phenotype and alternatively activated M2 phenotype to marginalize the pathogenic/non-pathogenic threat. Burgeoning reports are now elucidating the regulatory role of lncRNAs in various immune process. In this study, we aimed to identify the lncRNAs that mediate Mϕ function and polarization.

Methods:
CD14+ monocytes isolated from PBMCs and differentiated to M1 and M2Mϕ, using GM-CSF or M-CSF, respectively. Expression of 88 different lncRNAs was examined by RT-qPCR. Cells transfected with siRNAs targeting RN7SK, GAS5, IPW and ZFAS1 were examined for Mϕ polarization markers and innate immune functions (phagocytosis and antigen uptake/processing).

Results:
Our results show differential expression of seventeen lncRNAs in M2Mϕ compared to monocytes including RN7SK, GAS5, IPW and ZFAS1. Knockdown of RN7SK and GAS5 showed downregulation of M2 surface markers (CD163, CD206 or Dectin) and concomitant increase in M1 markers (MHC II or CD23). M1/M2 markers were not impacted by IPW or ZFAS1 knockdown. mRNA levels of polarization markers were not effected by RN7SK or GAS5 RNAi. We observed enhanced antigen uptake and processing both in M1/M2 Mϕ transfected with siRNA targeting GAS5 and RN7SK but not IPW and ZFAS1. In addition, knockdown of RN7SK significantly augmented labelled E.coli uptake by M1/M2 Mϕ, while no significant difference was noticed in GAS5 silenced cells.

Conclusion:
This study clearly deciphered that remarkable changes in lncRNA occur during monocyte to Mϕ differentiation, polarization and regulate integral innate functions of Mϕ. Manipulation of lncRNAs could be tested in therapeutic reversal of pro and anti-inflammatory pathologies.
Glycolysis Inhibition Modulates Unique Metabolic and Immune Pathways Across Multiple Tissue Compartments
Authors: Wells Ann , Wilson John , Roopenian Derry C , Chang Chih-Hao , Carter Gregory W. 
Published: February 2023

Abstract
Inhibition of glycolysis via 2-deoxyglucose (2DG), a competitive inhibitor of glucose-6-phosphate, has recently shown efficacy in attenuating tumor growth and reducing autoimmune pathology; however, the mechanism of this efficacy is somewhat unclear. To elucidate how 2DG longitudinally modulates pathways without the influence of immunity in diseased status, wild-type C57BL/6J mice were treated orally with 2DG for 96-hours or 4-weeks, after which the transcriptional profiles of 9 tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) were analyzed using unsupervised clustering and weighted gene correlation network analysis. Principal component analysis showed mice clustered by tissue. Tissues grouped together according to their summary gene expression for modules correlated to time, treatment and/or tissue, and two pathway groups, immune and metabolic, emerged. However, within each tissue cluster, pathways for each module were uniquely altered by time, treatment and/or tissue, according to ANOVA. Furthermore, while most pathways identified were grouped into either immune or metabolic, there was little overlap of specific pathways identified between tissues. These results show that 2DG has a systemic impact altering immune and metabolic pathways, but in a tissue-specific manner. Ongoing work includes identifying genes that are potentially central to pathway alterations for follow-up analysis.
P2X3 is a Female-Dominant Activator of Mast Cells
Authors: Kee Sydney Ann , Haque Tamara , Dailey Jordan , Ryan John J 
Published: February 2023

Abstract
Asthma is characterized by increased mucus production, airway hyperresponsiveness and airway inflammation, all promoted by mast cell activation. There is a clear bias for greater incidence and acuity of asthma among females, but the reasons for this are not clear. In seeking FDA-approved drugs that might be repurposed to suppress mast cell function, we found that the selective serotonin reuptake inhibitor fluoxetine was able to suppress IgE mediated-mast cell degranulation and cytokine secretion in vitro, and protect against anaphylaxis in vivo. Fluoxetine effects appear to be mediated by an off-target interaction with the ATP receptor P2X3. Interestingly, male mice and mast cells cultured from them showed little fluoxetine responsiveness. These data coincided with little detectable P2X3 expression on male mast cells. Our data support the theory that P2X3 is a female-dominant mast cell activator that can be targeted with fluoxetine to reduce allergic inflammation. Female-biased P2X3 expression may also contribute to sexual dimorphism in allergic disease.
Itaconate deficiency results in prolonged bacterial burdens and enhanced T cell responses during Francisella tularensis infection
Authors: Leighton Ian , Roberts Lydia , Wehrly Tara , Bosio Catharine M 
Published: February 2023

Abstract
Shifts in cellular metabolism and associated metabolites regulate immune cell function. Recently, it has been shown that the metabolite itaconate plays a critical role in modulating inflammatory responses. Using animals that cannot synthesize itaconate due to an absence of aconitate decarboxylase 1 (AOCD KO), we previously established the lack of itaconate increased susceptibility to high dose challenge with the live vaccine strain (LVS) of Francisella tularensis in terms of both bacterial clearance and survival. However, ACOD KO mice that survived sublethal LVS infection had improved survival against a lethal challenge with virulent F. tularensis (Ftt). Since appropriate coordination of both macrophage and T cell function is essential for surviving Ftt, we next determined if the improved survival of ACOD KO mice was due to alterations in macrophage and/or T cell function. LVS immune ACOD KO mice had increased numbers of lung resident and splenic effector CD4+ and CD8+ T cells compared to WT mice following resolution of infection. Utilizing an in vitro macrophage-T cell co-culture system we did not observe any difference in the ability of WT and ACOD KO T cells to control LVS replication in macrophages when T cells were co-cultured with genetically matched macrophages. However, when macrophage sources were mixed, we observed that regardless of the source of LVS immune T cells, WT macrophages controlled bacterial replication significantly better than ACOD derived macrophages. Together, these findings suggest that the lack of itaconate results in increased and prolonged bacterial burdens in vivo, which leads to greater expansion of effector T cells that confer enhanced protection during Ftt challenge.
Chromatin accessibility differences of human monocyte identify age associated inflammatory heterogeneity.
Authors: Singh Amit K , Kaileh Mary , Mazan-Mamczarz Krystyna , Palagani Ajay , Roy Roshni , Sarantopoulou Dimitra , Ubaida-Mohien Ceereena , Moore Ann Zenobia , Qian Yong , Yin Jinhu , Bektas Arsun , Ding Jun , De Supriyo , Zukley Linda , McKelvey Julia , Weng Nan-Ping , Ferrucci Luigi , Sen Ranjan 
Published: February 2023

Abstract
Human aging is associated with low grade chronic inflammation termed, inflammaging, which is a significant risk factor for morbidity and mortality in elderly. The innate immune system is master regulator of this process via regulating expression of cytokines and other key mediators. We assayed chromatin landscape of the human monocytes during healthy aging with an aim to predict the inflammation associated contemporary and imminent states of monocytes. Our deep sequencing ATAC-seq data from healthy donors of the GESTALT cohort identified, chromatin landscape signatures defining heterogeneity of monocytes. Differentially open chromatin (DOC) clustered old individual monocytes in two distinct groups, while young donors demonstrated ethnicity-based differences. DOC’s heterogeneity of old donors was characterized by presence of intergenic enhancer-like elements dominated by the DNA binding motif of the transcription factor NF-κB. We identified the relationships of age-associated DOC with DNA methylation, gene expression and proteome of monocytes and serum. Finally, the intracellular cytokine staining analysis using multi-parameter flow cytometry demonstrated the DOC’s influence on the monocyte’s response to LPS stimulation. Our data revels the age associated heterogenous functional states of monocytes which can help us understanding decision making mechanisms during an immune response.
Non-Thermal Histotripsy Ablation of Osteosarcoma Causes a Local Acute Immune Response
Authors: Sereno Jacqueline , Hendricks Alissa Danielle , Allen Irving C , Vlaisavljevich Eli , Imran Khan Mohammad , Tuohy Joanne 
Published: February 2023

Abstract
While surgery, chemotherapy, and radiotherapy are available as treatments for osteosarcoma, there is only a 60% 5 year overall survival rate. To address this need, novel therapies are being developed and investigated. Histotripsy is a non-invasive, non-thermal focused-ultrasound ablation therapy that uses acoustic cavitation to mechanically lyse targeted cells. Recent evidence suggests that it is immunomodulatory, and can shift the tumor microenvironment to being more pro-inflammatory. However, given histotripsy’s mechanical mechanism, it is not established to be able to treat stronger tissues such as osteosarcomas at a dose that will allow for the preservation of immune stimulating molecules. In this study, mice with subcutaneous osteosarcoma DLM8 tumors were treated with histotripsy and acute changes to the local tumor immune response were analyzed 72 hours later. Using partial ablation to avoid off-target damage, a 40% average reduction in tumor size was achieved with targeted tissues being fully ablated. Through rtPCR, the levels of various cytokines associated with wound healing were significantly increased in the treated tumors following histotripsy treatment, with the greatest fold change observed in the concentrations for IL-6 and IL-13 over a given period of time. An increase in fold change for CD274, also known as PD-L1, was also observed, implicating the potential to pair histotripsy with checkpoint inhibitors for osteosarcoma therapy. The overall results of the study suggest that histotripsy is able to shift the tumor microenvironment following partial-ablation treatment. Thus, upon activation of the immune system, wound and tissue repair mechanisms are subsequently activated and responses are regulated.
Effect of the elderly human lung mucosa on Mycobacterium tuberculosis infection of the alveolar epithelium
Authors: Olmo-Fontanez Angelica M. , Scordo Julia M , Garcia-Vilanova Andreu , Maselli-Caceres Diego , Peters Jay , Clemens Daniel , Turner Joanne , Schlesinger Larry S. , Torrelles Jordi B. 
Published: February 2023

Abstract
As we age, there is an increased risk for developing tuberculosis (TB), a disease caused by the infectious agent Mycobacterium tuberculosis (M.tb). M.tb infection results in a bacterial deposition in the lung alveolus, where M.tb is bathed in alveolar lining fluid (ALF). We have published that age-associated changes in human ALF soluble components, such as increased levels of oxidized and dysfunctional innate proteins, accelerate M.tb growth within human alveolar macrophages. We are interested in studying the impact of human ALF on M.tb infection of non-professional phagocytes, such as alveolar epithelial cells (ATs). We hypothesized that M.tb exposure to elderly human ALF (E-ALF) drives increased M.tb replication and growth within ATs due to impairment of E-ALF innate soluble components. We observed that E-ALF exposed M.tb had significantly increased intracellular growth in ATs. Despite changes in intracellular bacterial growth, infected ATs with E-ALF-exposed M.tb did not show altered production of inflammatory mediators or cell activation. Interestingly, M.tb exposure to E-ALF did not alter intracellular trafficking, but it drove bacterial translocation to both endosomal and cytosolic compartments in ATs. Overall, rapid bacterial replication and increased growth within ATs was observed in M.tb exposed to E-ALF, and together with inadequate AT activation, could lead M.tb to potentially exploit the AT cytosol as a favorable intracellular niche for replication. These results emphasize the effects of elderly lung mucosa on M.tb infection of non-professional phagocytes (ATs), which may conceivably explain why the elderly population is more vulnerable to developing active TB disease.
SOCS1 mimetics attenuate autoimmune pathology in a murine model of lupus
Authors: Sharma Jatin , Collins Teresa , Lam Brandon , Cain Antia , Roach Tracoyia Roach , Cornaby Caleb , Polk Timothy B , Morel Laurence , Larkin Joseph 
Published: February 2023

Abstract
Autoimmune diseases are driven, in large part, by the aberrant activation of lymphocytes which mediate a dysregulated cytokine milieu and produce pathogenic, auto-reactive antibodies. Notably, many cytokines, including interferon gamma (IFN-γ), utilize the JAK/STAT pathway for signal propagation. Suppressor of Cytokine Signaling-1 (SOCS-1) is an inducible, intracellular protein known to regulate IFN-γ signaling through dampening of the JAK/STAT signaling cascade. We have previously shown that a peptide mimicking the kinase inhibitory region of SOCS1 (SOCS1-KIR) inhibited IFN-γ signaling and inflammation-driven disease progression. Using Fas deficient MRL/lpr mice, which spontaneously develop a lupus-like disease, we tested the hypothesis that SOCS1-KIR administration would alter lymphocyte phenotype and modulate lupus-associated pathologies. SOCS1-KIR administration reduced severity of skin lesions, autoantibody production, and modestly reduced kidney pathology. On a cellular level, peritoneal SOCS1-KIR administration enhanced Foxp3 expression in total splenic and follicular regulatory T cells, reduced the effector memory/naïve T lymphocyte ratio for both CD4+ and CD8+ cells, and reduced the frequency of germinal center B cells. Together, these data show that SOCS1-KIR treatment altered lymphocyte phenotype and suggest that therapeutic targeting of the SOCS1 pathway through peptide administration may have efficacy in mitigating autoimmune pathologies.