bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic regulation of inflammatory genes involving histone methylation is associated with hyperimmune response in COVID-19 patients
Authors: Yang Xiaoming , Yang Xiaoming C , Julian Julian , Schnell Timothy , Albrecht Helmut , Owens William , Yang Xiaoming S 
Published: January 2023

Abstract
One of the leading causes of the severe COVID-19 disease symptoms is the production of massive amounts of pro-inflammatory cytokines. Although the precise mechanisms that trigger such hyperimmune response is unclear, epigenetic mechanisms are known to play important roles in the regulation of cytokine production and inflammation. In this study we examined global gene expression and histone methylation profile in the PBMCs of hospitalized COVID-19 patients. Despite individual variations, the expressions of many inflammation-related genes such as Arginase 1 (ARG1) and IL1 receptor 2 (IL1R2) were significantly upregulated in COVID-19 patients. We also found the expressions of coagulation-related genes, VWF and Protein S, were altered in COVID-19 patients. The expression patterns of some genes such as IL1R2 correlated with their histone methylation marks. Pathway analysis revealed that most of these dysregulated genes were in the TGFb, IL1b, IL6 and IL17 pathway. Interestingly, we found that the majority of those altered genes were in the dexamethasone targeting pathway. We also found that the expression of BMX, a member of TEC family kinases, was significantly increased in the PBMCs of COVID-19 patient at both RNA level and protein level. Interestingly, some TEC kinase inhibitors have been used to treat COVID-19 patients in clinical trials. Overall, this study has identified genes in PBMCs of COVID-19 patients with altered histone mark and gene expression profile, providing important information towards identifying potential biomarkers and therapeutic targets for COVID-19 disease. (Supported by NIH grants P01AT003961, P20GM103641, R01AT006888, R01ES030144, R01AI129788 and R01AI123947 to P.S.N and M.N.)
Supported by NIH grants P01AT003961, P20GM103641, R01AT006888, R01ES030144, R01AI129788 and R01AI123947 to P.S.N and M.N.
12/15-lipoxygenase is required for inflammation resolution in a murine model of Lyme arthritis
Authors: Jackson Christa D , Brown Charles R 
Published: January 2023

Abstract
Lyme arthritis is a major sequela of disseminated Lyme disease that can persist despite antibiotic clearance of the etiological agent Borrelia burgdorferi. In the murine model of Lyme arthritis (mLA), infected mice develop an inflammatory arthritis characterized by robust innate cell infiltrate and synovial hyperplasia in the tibiotarsal joint, followed by spontaneous resolution around 4–5 weeks post-infection. Eicosanoids are bioactive lipid mediators that play a critical role in both the development and resolution of inflammation. As such, temporal regulation of eicosanoid class-switching from proinflammatory to proresolving is vital. In other inflammation models, late-phase cyclooxygenase (COX)-2 metabolite prostaglandin (PG) E2 skews the 5-lipoxygenase (LO) eicosanoid biosynthesis pathway away from leukotriene B4 production and towards proresolving lipoxin (LX) A4 production via 12/15-LO activity. Indeed, we have previously described a defect in mLA resolution in COX-2−/− and 5-LO−/− mice. Therefore, we hypothesize that 12/15-LO production of LXA4 is required to facilitate mLA resolution. To investigate this, we characterized mLA in 12/15-LO−/− mice and observed a pronounced resolution defect, as evidenced by significant ankle swelling and persistent innate immune infiltrate compared to wild-type mice after 4–5 weeks, despite efficient control of Borrelia burdens. We are currently investigating the mLA eicosanoid profile in 12/15LO−/− mice as well as whether exogenous treatment with LXA4 promotes mLA resolution. These experiments will determine how eicosanoids regulate inflammation resolution and may identify therapeutic targets for inflammatory diseases, including human Lyme arthritis.
Supported by a grant from the NIH (R21 AR175160) and the G. Ellsworth Huggins Graduate Fellowship.
Determining chicken immunoglobulin-like receptors (CHIRs) expression and their effect on immune response in a macrophage disease model
Authors: Sparling Brandi Ann Terrance Elize , Drechsler Yvonne 
Published: January 2023

Abstract
Immunoglobulin-like receptors are large transmembrane glycoproteins who direct the balance of the immune response. However, the full repertoire and effect of putatively activating, inhibiting, or dually working CHicken Immunoglobulin-like Receptors (CHIR-A, -B, and -AB, respectively) on immune responses in chickens, are not well understood. The objective was to characterize CHIRs expression and role in immune responses in the B-type homozygous chicken. B2B2 and B19B19 chicken lines were selected as model for their remarkable differences in disease susceptibility to coronavirus and other viral infections associated with the selectively bred major-histocompatibility complex class I (MHC-I), B locus. We first identified CHIRs from the new GRCg7b genome assembly by amino acids charge and protein motifs of CHIR -A, -B, or -AB. Subsequently, the transcriptomes of IFN-stimulated monocyte-derived macrophages from B2B2 or B19B19 were analyzed for CHIR abundance and ratio of CHIR-A:CHIR-B expression. Also, pooled siRNAs targeting CHIR-AB and or CHIR-B were generated for application in a monocyte-derived macrophage and T cell co-culture model. A higher median expression of CHIR-A in comparison to CHIR-B transcripts was observed in the B2B2 obtained macrophages; and inversely so for the B19B19 genotype 48-hours post-stimulation. Too, preliminary work show that CHIR-Bi enhances macrophage-mediated anti-viral response, endorsing CHIR-Bs suppressive role. These characterizations align with disease susceptibility traits of the B19B19 chicken line such that they link MHC and CHIRs, and highlight CHIRs in active infection and immunity.
Relationships between inflammation, coagulation, and oxidative stress in malaria-induced pregnancy compromise
Authors: Andrew Alicer Keendalyn , Moore Julie M 
Published: January 2023

Abstract
Plasmodium falciparum malaria in pregnancy contributes to poor birth outcomes in association with placental malaria (PM), a syndrome initiated by parasitized erythrocyte binding, precipitating placental oxidative stress, dysregulated inflammation, and coagulation. We have tested the hypothesis that these pathogenic processes are synergistic in PM using C57BL/6J (B6) mice infected with P. chabaudi. Ablation of tumor necrosis factor (Tnf), anticoagulant treatment, and infection in Tnf−/− and tissue factor-deficient (F3flox/flox Tie-2Cre) mice improves pregnancy outcomes. Relative to infected B6 controls, infected Tnf−/− mouse embryos show two to four-fold reduced transcript expression of a key molecular link between coagulation and inflammation, protease activated receptor 2 (F2rl1). Tissue factor (F3) expression is 50% reduced, while endothelial protein C receptor (Procr) transcripts are increased three to five-fold, supporting the bidirectional nature of coagulation and inflammation in PM. Moreover, embryonic transcripts for markers of inflammation (Ifng, Tnf, Il-10, Il-1β, and Ccl2), antioxidants (Sod1, Sod2, and Nfe2l2) and F3 are significantly downregulated in anticoagulant-relative to sham-treated, infected B6 mice, whereas Procr transcripts are elevated, suggesting functionally linkages of the three pathways. Ongoing antioxidant therapeutic studies are expected to confirm perturbations of inflammation and coagulation responses. In sum, this work is contributing to understanding of molecular interactions between the major pathogenic responses to PM, how synergy thereto galvanizes pregnancy compromise, and promises to reveal potential therapeutic options to improve pregnancy outcomes.
Sodium butyrate prevented mortality in Acute Respiratory Distress Syndrome through induction of anti-inflammatory response by regulation of epigenetic pathway
Authors: Sultan Muthanna Ali , Nagarkatti Prakash 
Published: January 2023

Abstract
Acute Respiratory Distress Syndrome (ARDS) is a life-threatening disease that has been identified following pneumonia, inflammation, as well as accompained with COVID19 cases. In this study, we investigated the effect of Sodium Butyrate (BUT) in ARDS induced by Staphylococcus Enterotoxin B (SEB). To that end, C3H/HeJ mice were administered BUT through oral gavage with a dose of 200mg/kg and 30mins later followed by a dual dose of SEB, starting with an intranasal dose of 7ug (i.n.) and 2hrs later with another dose of 2ug intraperitoneally (i.p.). The adminstration of BUT continued as same daily and the sacrifice was 72 hrs after SEB exposure. Our data demonstrated that the mortality rate was 80% in SEB+VEH mice compared to 0% mortality in SEB+BUT mice. Plethysmography data indicated a significant improvement in the clinical pulomonary functions. ELISA results indicated that the cytokine storm parameters including IFNγ were significantly decreased after BUT treatment compared to SEB+VEH. Furthermore, flow cytometry data indicated that CD4+ T cells, Vβ8+ T cells and NK T cells were significantly decreased in SEB+BUT compared to SEB+VEH. Analysis of miRNA from MNCs of lungs indicated that anti-inflammatory genes related to T-regulatory cells (Tregs) and Myeloid Derived Suppressor Cells (MDSCs) were targeted by many downregulated miRNAs which were then validated by qRT-PCR. Furthermore, flowcytometry data indicated a significant increase in T regs and MDSCs. Together, our data indicated that BUT prevented mortality and improved Lungs clinical functions in ARDS through modulation of the miRNAs in MNCs in lungs leading to induction of anti-inflammatory genes and suppression of inflammatory T cell subsets as well as increase in Tregs and MDSCs.
Supported by NIH P01AT003961, P20GM103641, R01AI129788, R01ES030144, R01AI160896 and R01AI123947
Increased mitochondrial metabolism profile is required for immunologic function in age associated B cells
Authors: Kim Sun Jung , De Oleo Ivan Ramirez , Diamond Betty 
Published: January 2023

Abstract
Specific metabolic programs are activated by immune cells to fulfill their functional roles. Age-associated B cells (ABCs) are a subset of B cells that are identified by expression of non-canonical B lineage marker, CD11c. An expansion of ABCs has been identified in various autoimmune diseases, including systemic lupus erythematosus (SLE). They have many distinct properties, such as capacity to stimulate T cells and the ability to secrete autoreactive antibodies when they are stimulated in vitro. The metabolic pathways that support these functions are unknown. Using mouse models of human SLE, we confirmed ABCs induce T cell activation effectively and these activated T cells acquire follicular helper T (Tfh) cell phenotypes, including BCL6 expression, up-regulation of surface expression of CXCR5 and PD-1 and IL-21 production. Metabolically, ABCs are bioenergetically more active than follicular (FO) B cells, with higher rates of glycolysis and oxidative phosphorylation. They have increased mitochondrial activation with an increased production of reactive oxygen species (mtROS). Treatment of ABCs with mitochondrial complex I inhibitor or mtROS scavenger leads to a selective loss of their capacity to induce Tfh differentiation but not T cell activation or proliferation. The aberrant activation of mitochondrial metabolism and mtROS production was also consistently observed in ABCs from SLE patients as well. Therefore, ABCs have evolved a distinct metabolism adapted to their specific functional properties.
Supported by NIH NIAMS R01 AR075565 NIH NIAMS U19 AI144306
Rag GTPase critically contributes to humoral immunity independent of canonical mTORC1 signaling
Authors: Zhu Xingxing , Zhou Xian , Li Chaofan , Li Yanfeng , Sun Jie , Raybuck Ariel , Boothby Mark Robin , Zeng Hu 
Published: January 2023

Abstract
The humoral immune response requires that B cells undergo a rapid metabolic shift and high demand of nutrients, which are vital to sustain the formation of germinal center. Rag GTPase senses amino acid availability to activate mechanistic target of rapamycin complex 1(mTORC1) pathway and modulate the function of transcription factor EB (TFEB), a member of the microphthalmia (MiT/TFE) family of HLH-leucine zipper transcription factors. However, little is known about how Rag GTPase coordinates amino acid sensing, mTORC1 activation and TFEB activity in humoral immune response. Here, we show that B cell intrinsic Rag GTPase is critical to the development and activation of B cells. Disruption of Rag GTPase complex, but not mTORC1 complex, abrogates germinal center formation, antibody production as well as plasma cell generation upon respiratory influenza infection. Mechanistically, the Rag GTPase complex senses specific amino acids to suppress TFEB activity, independent of canonical mTORC1 activation. Collectively, our data support the idea that Rag GTPase critically contributes to humoral immunity partly through suppressing TFEB and it is largely not necessary for canonical mTORC1 signaling.
Supported by Mayo Foundation for Medical Education and Research
Mechanisms of TRAF3 regulation of TLR signaling in B lymphocytes
Authors: Ybarra Tiffany K , Bishop Gail A 
Published: January 2023

Abstract
TRAF3 is an adaptor protein that binds to a variety of receptor types on immune cells and exerts multiple regulatory functions in signaling pathways. TRAF3 functions are cell type and context dependent. B cell-TRAF3 inhibits homeostatic NFκB2 activation and other pro-survival signaling pathways; restraint of survival is a B cell-unique TRAF3 function. Loss of B cell-TRAF3 in vivo contributes to early autoimmunity and later lymphomagenesis. TRAF3 inhibits B cell TLR functions, including cytokine production (IL-6, IL-10, IL-12p40 and TNFα), Ig isotype switching, and antibody production in response to ligands for TLRs 3, 4, 7/8 and 9. A key knowledge gap is identifying the molecular mechanisms by which TRAF3 mediates this regulation. Our working hypothesis is that B cell-TRAF3 regulates the activity, recruitment, and/or post-translational modification of specific TLR signaling proteins. Our recent data show that B cell-TRAF3 forms a heterocomplex with TRAF6, associating with the tyrosine kinase Syk and inhibiting early TLR signals, such as pIRAK1 degradation. In the absence of TRAF3, TRAF6 shows a greater association with several TLR signaling proteins. These results suggest that TRAF3 may inhibit TRAF6 access to the TLR signaling complex, and thus early TLR signaling. Further studies aimed at providing new insights into the molecular mechanisms contributing to the regulation of B cell-TRAF3 in TLR signaling can inform selection and development of more targeted therapies for B cell malignancies and autoimmunity.
Supported by VA Merit Review IO1 BX001702 NIH RO1 AI62656 NIH P50 CA97274 NIH T32 Training Grant AI07485
Follicular B cells from old mice are hyper-responsive and produce non-specific antibodies.
Authors: Ticas Rodas Carlos J , Greer Braxton D , Maul Robert W , Gearhart Patricia J 
Published: January 2023

Abstract
Immunosenescence is the increase in immune defects that occurs during aging. To identify any intrinsic defects in old B lymphocytes, we devised a transfer system to introduce follicular B cells from old mice (FOO, &gt;22 months) or young mice (FOY, 8–12 weeks) into young mMT mice which have no B cells. Using this system, we observed that, compared to FOY cells, FOO cells do not produce antigen-specific antibodies to nitrophenyl (NP)-chicken gamma globulin after immunization. Examination of the germinal center (GC) response shows that FOO cells produced increased numbers of GC B cells which have divided faster than their FOY counterparts, but they have significantly decreased NP+ λ+ antigen-specificity. To understand the differences between FOO and FOY cells, single-cell RNAseq was performed on naïve and day 14 GC B cells. Comparing naïve populations revealed very few differences with only 387 differentially expressed genes between FOO and FOY cells. Interestingly, Ccr6 was upregulated in the FOO cells, suggesting that the cells were pre-activated before transfer into mMT mice. Antibody repertoire analysis also confirmed the lack of antigen-specificity in FOO cells, as the canonical NP-specific IgH V-gene, 1–72, was utilized in fewer cells and had zero instances of the CDR2 W33L mutation known to increase affinity. Taken together, old mice produce B cells which are pre-activated and hyper-responsive upon immunization, causing a lack of proper selection and affinity maturation in the GC.
This research was supported in part by the Intramural Research Program of the NIH, National Institute on Aging.
Memory B cells are a heterogenous population regulated by epigenetic programming
Authors: Wiggins Keenan J , Scharer Christopher , Boss Jeremy M 
Published: January 2023

Abstract
Memory B cells (MBC) are a heterogenous population that consist of immunoglobin class switched and non-class switched MBC, and these populations can arise via germinal center dependent or independent mechanisms. The timing of MBC development influences the fate outcome of MBC populations. These different populations of MBC are regulated by cell signaling, but it is not clearly defined what epigenetic factors influence MBC differentiation. EZH2 is an important histone methyltransferase that catalyzes H3K27me3 resulting in gene repression. EZH2 has been shown to regulate B cell differentiation into germinal centers and plasma cells; however, it is unknown if EZH2 regulates MBC development. To address this, a knockout model has been established where EZH2 is conditionally deleted using the CD19 and AICDA driven CRE expression. Here we used the influenza PR8 model to ascertain the kinetics of MBC differentiation and formation in the spleen, dLN, and lungs following a live infection in wild-type and EZH2-KO cohorts. Using B cell tetramers, antigen-specific MBC will be analyzed to define the kinetics of MBC development and determine the similarities and differences between the different populations of MBC. Overall, these data define the early kinetics of MBC establishment and the developmental timing that EZH2-dependent H3K27me3 remodeling is required for MBC formation.
Supported by NIH/NIAID to CDS (R01 AI148471)
Decreased CD40L through disrupted transcriptional stability affects the autoimmune response in a sex-dependent manner in a GVHD model of SLE
Authors: De Maio Diego Javier Prado , Ganapathi Usha , Covey Lori 
Published: January 2023

Abstract
Increased levels of CD40L have been observed on CD4 T cells of patients with systemic lupus erythematosus (SLE) and in several murine models of lupus-like disease. Notably, elevated/prolonged expression of CD40L corresponds to the expansion and survival of autoreactive B cells. However, targeting CD40L as a potential therapeutic has been challenging due to the development of off-target events. We have developed a unique mouse model termed CD40LΔ5 (Δ5) which lacks a stability element in the 3’ UTR of the CD40L message and upon immunization, shows decreased CD40L expression on Tfh cells leading to both reduced GC B cell survival and a critically disproportional loss of pre-memory B cells. Using our Δ5 model, we sought to determine whether reduced CD40L could substantially alter the development of disease in an adoptive transfer model of lupus based upon MHC II incompatibility. B6 WT mice were engrafted with CD4 T cells from bm12-WT or bm12-Δ5 mice and analyzed for splenic lymphocyte subsets. In mice that received Δ5 T cells, total CD4 and CD8 subsets were unchanged compared to mice receiving WT cells, however, there was an increase and decrease of Tfh cells in male and female mice, respectively. This was confirmed by a corresponding change in Tfh proliferation as measured by staining for Ki67. Total CD19 B cells were increased in male mice receiving D5 T cells. Finally, intracellular staining of T cell cytokines was different in male and female mice receiving the Δ5 T cells as was the distribution of GC B cell subsets, including pre-memory B cells. Together our results suggest that limiting CD40L in T cells at an early stage of bm12-induced lupus has a significant effect on the maturation of GC subsets that is closely aligned with the sex of the WT recipient mice.
Supported by AAI Careers in Immunology Fellowship 2019-2020
Tet2-mediated programing balances T follicular helper cell and T helper 1 cell differentiation.
Authors: Hale J Scott , Baessler Andrew , Novis Camille L , Shen Zuolian , Perovanovic Jelena , Wadsworth Mark , Sircy Linda M , Harrison-Chau Malia , Varley Katherine E , Tantin Dean R 
Published: January 2023

Abstract
The differentiation of CD4+ T cell subsets in response to infection has been studied extensively, however the epigenetic programs that regulate these processes remain poorly understood. Active demethylation by tet methylcytosine dioxygenases of CpG dinucleotides within DNA is a key component of epigenetic programing that promotes lineage specific gene expression and contributes to cellular differentiation and function. Here we report that Tet2 acts to restrict the differentiation of T follicular helper (Tfh) cells in CD4+ T cells responding to viral infection. Using an adoptive transfer model of virus-specific CD4+ cells we found that Tet2-deficient CD4+ T cells skew away from the Th1 lineage and instead preferentially differentiate into highly functional germinal center (GC) Tfh cells that provide enhanced help for B cell responses. We found that the impact of Tet2-mediated programing on CD4+ T cell differentiation is cell intrinsic and the shift in lineage differentiation occurs as early as 2 days post infection. Using genome-wide expression, DNA methylation and transcription factor binding analyses, we found that Tet2 coordinates with multiple transcription factors to mediate the demethylation and expression of their target genes following activation. Our findings establish Tet2 as an important regulator of Tfh cell differentiation and reveal pathways that could be targeted to enhance GC responses against infectious disease.
Supported by grants from NIH (R01 AI137238 to J.S.H., T32 AI055434 to L.M.S., and T32 AI138945 to A.B.
Microbiota regulation of development of thymic microbiota-specific T cells
Authors: Ruiz Daniel Fernando Zegarra , Kim Dasom V , Saldana-Morales Fatima B , Chen Amanda , Wu Wan-Jung , Longman Randy S , Bettini Matthew L , Diehl Gretchen E 
Published: January 2023

Abstract
While exposure to microbial antigens in peripheral sites causes expansion of antigen-specific T cells, a role for antigen-specific expansion had not been identified during T cell development in the thymus. We recently found that intestinal colonization induced intestinal dendritic cells migration to the thymus, driving thymic expansion of microbiota-specific T cells early in life. In contrast, colonization in adulthood leads to expansion of peripheral but not thymic microbiota-specific T cells. Thymic microbiota-specific T cells developed early in life were undifferentiated and caused intestinal inflammation in immunocompromised hosts upon antigen reencounter. We sought to understand regulation of this developmental window and define if thymic expansion of microbiota-specific T cells could be restarted in adult mice. We found that microbiota manipulation reestablished expansion of microbiota-specific T cells in the thymus of adult mice. We are in the process of characterizing these T cells in adulthood to assess their impact on intestinal inflammation. Our data suggests that intestinal colonization controls the generation of thymic microbiota-specific T cells which has the potential to modulate inflammatory processes.