bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing airway constriction and inflammation through GABAA receptors in the lung with a novel, orally available drug candidate.
Authors: Nieman Amanda N. , Forkuo Gloria S. , Zahn Nicolas , Kodali Revathi , Li Guanguan , Roni M.S. Rashid , Stephen Michael Rajesh , Harris Ted , Jahan Rajwana , Guthrie Margaret , Yu Olivia , Fisher Janet , Yocum Gene , Emala Charles , Steeber Douglas A. , Stafford Douglas C. , Cook James , Arnold Leggy A. 
Published: January 2023

Abstract
MIDD0301 is a new lead compound designed for the oral treatment of asthma. It was developed from previously described α5β3γ2 selective GABAA receptor (GABAAR) modulators. MIDD0301 showed significant relaxation of Substance P contracted guinea pig tracheal rings ex vivo at low micromolar concentrations. In vivo, MIDD0301 decreased airway hyperresponsiveness in asthmatic ovalbumin-sensitized and challenged mice after five day b.i.d. oral administration. MIDD0301 reduced eosinophil, macrophage, and CD4+T-lymphocyte cell counts in broncoalveolar lavage fluid without stimulating mucus hyperplasia. Pro-inflammatory cytokines (IL-17A, IL-4, TNFα) were decreased in the lung while the anti-inflammatory cytokine IL-10 remained unchanged. Pharmacokinetic studies showed MIDD0301 has a half-life of approximately 14 hours and negligible brain distribution. The lack of adverse CNS side effects was confirmed with rotarod studies. CD4+ T-lymphocytes isolated from ova s/c mice showed a dose dependent change in transmembrane current with GABA and MIDD0301, confirming that MIDD0301 is acting via GABAAR. Overall, MIDD0301 represents a novel, orally available, and safe alternative for the treatment of asthma through airway smooth muscle relaxation and attenuation of airway inflammation.
Unexpected role for androgen and androgen receptor as enhancers of M2 macrophage polarization
Authors: Becerra-Diaz Mireya , Strickland Ashley B. , Keselman Aleksander M. , Heller Nicola M. 
Published: January 2023

Abstract
Allergic asthma is an inappropriate Th2 immune response in the lungs to innocuous inhaled antigens. This results in M2 polarization of alveolar macrophages (AM), which number correlates with asthma severity in humans. Sex differences in asthma suggest that sex hormones modify lung inflammation and macrophage polarization. Since estrogen enhances M2 polarization and androgens have been used as experimental asthma therapy, we hypothesized that androgens [testosterone and dihydrotestosterone (DHT)] and androgen receptor (AR) suppress M2 macrophage polarization.
Here, we demonstrate that although androgen reconstitution in castrated mice reduced inflammation of the bronchoalveolar space in a mouse model of allergic lung inflammation, it enhanced the production of the eosinophil-recruiter and M2 marker YM1 in AM, indicating a cell-specific role for androgens. DHT also enhanced IL-4-induced M2 macrophage polarization in vitro. Using mice lacking the AR in monocytes/macrophages (ARfloxLysMCre), we found that ARfloxLysMCre males had less eosinophil recruitment and lung inflammation in our model of allergic lung inflammation. No differences were found in females. This decreased inflammation was due to impaired M2 polarization and diminished production of eosinophil-recruiting chemokines by AM rather to a regulatory profile of AM lacking AR. Furthermore, macrophages lacking AR did not show an increase in IL-4-induced M2 polarization in vitro with DHT treatment.
These data reveal an unexpected role for androgen/AR in promoting M2 macrophage polarization, and suggest possible mechanisms to counteract diseases that are promoted by M2 macrophages and affect mainly men, such as eosinophilic esophagitis and prostate cancer.
A comparison of IL-5 and IL-10-producing antigen-specific clonal T cell repertoires
Authors: Schulten Véronique MJ. , Westernberg Luise , Peters Bjoern 
Published: January 2023

Abstract
Allergic rhinitis affects up to 40% of North Americans, and is associated with potentially debilitating symptoms. Allergen-specific immunotherapy (AIT) is a disease-modifying treatment associated with Treg induction and elevated IL-10 production. To date, it is unknown if IL-10-producing T cells are induced de novo or if AIT modulates allergen-specific Th2 cells to become tolerogenic. To investigate whether IL-5 and IL-10-producing antigen-specific T cells share a common T cell repertoire, we performed a longitudinal TCRβ sequence analysis of Timothy grass (TG)-specific T cells from donors who received AIT for 15 months. As a control, TCRβ sequencing was also performed on TG-specific T cells from an allergic donor. TG-specific cells were expanded by 14-day in vitro culture with a pool of immuno-dominant TG-derived T cells epitopes (TG pool). A pertussis epitope pool was used in parallel as a control. Subsequently, cells were restimulated with the same pool and allergen-specific cells were isolated by cytokine capture with column enrichment, sorting IL-5 and IL-10 -producing cells. The TCRβ repertoire was sequence from DNA isolated from sorted cells. Preliminary results revealed that in the TG pool-specific cells, some clonal overlap was observed between IL-10+ and IL-5+ cells, suggesting that a fraction of IL-10+ cells may originate from IL-5+ cells, but some are generated de novo. Longitudinal analysis of the allergen-specific TCR repertoire is a reliable method to determine if tolerogenic T cells are induced de novo or if they are modulated T cells that originate from the same repertoire as allergen-specific Th2 cells.
GATA3, SATB1, IRF4 complex binds to the Th2 cytokine locus through cis-acting element RHS6, regulating allergic airway inflammation.
Authors: Jang Sung Woong , Lee Gap Ryol 
Published: January 2023

Abstract
Rad50 hypersensitive site 6 (RHS6) is a cis-acting element in the Th2 locus control region which is essential for the expression of Th2 cytokine genes. However, molecular mechanisms how it regulates the genes are poorly understood. We found that RHS6 recruits transcription factors GATA3, SATB1, and IRF4 during Th2 cell differentiation. GATA3, SATB1, and IRF4 have a crucial role in regulating Th2 cytokine genes. Knock-out or knock-down of each of GATA3, SATB1, and IRF4 genes significantly decrease the expression of Th2 cytokine genes. Mechanistically RHS6 mediates the transcription factor-induced regulation of Th2 cytokine genes. GATA3, SATB1, and IRF4 physically associates with each other, and forms a protein complex at RHS6 sequence. They directly bind to the many regulatory elements throughout the Th2 cytokine locus, RHS6 dependent manner. Furthermore, deletion of RHS6 caused a dramatic resistance to airway inflammation in ovalbumin-induced allergic inflammation model. Together, RHS6 recruits GATA3, SATB1, and IRF4 coordinating their regulation of Th2 cytokine genes, so is essential for Th2-mediated allergic airway inflammation.
dsRNA induced intestinal epithelial cell activation of immune dysfunction in type 1 diabetes
Authors: Wallet Shannon , Golas Gavin , Tyler Melissa , Sorenson Heather 
Published: January 2023

Abstract
Environmental factors contribute to the initiation, progression, and maintenance of many autoimmune diseases including type 1 diabetes (T1D). We propose the context in which an environmental signal is received by the intestinal epithelial cell (IEC) may be more important to disease than the specific identity of the environmental factor. Viral infections are proposed to be one such trigger. IEC-specific responses to double-stranded RNA, a common intermediate in many viral life cycles, was evaluated by comparing and contrasting the expression of soluble immune mediators from T1D and non-T1D derived primary (murine and human) IECs. The effect of the soluble mediator milieu on innate and adaptive immune cell phenotype and function was also assessed. While poly I:C induces a robust induction of IFN-I in primary IEC derived from non-T1D sources, a significantly less robust IFN-I response was observed in T1D-derived IECs. Similarly, a significantly less robust induction of IL-18, TSLP, and IL-17C mRNA was observed in T1D-derived IECs cultures whereby this hyporesponsive phenotype became more apparent in T1D-IEC derived at later stages of disease. Supernatants from T1D-derived IECs induced an M1 macrophage phenotype and directly enhanced CD3/CD28 induced T cell proliferation. T cells induced to proliferate were polarized to a more Th(c)1 or Th(c)1/Th(c)7 phenotype at the expense of a Th(c)17 phenotype. Supernatants from T1D-derived IECs also enhanced β-cell killing by transgenic T cells. These data support our hypothesis that IECs are key players in driving innate and adaptive immune dysfunction observed in the gastrointestinal track of individuals with T1D, as well as capable of supporting and expanding an autoreactive T cell repertoire.
Integration of genome-wide transcriptome and DNA methylome uncovered aberrant methylation-regulated genes and pathways in the peripheral blood mononuclear cells of systemic sclerosis
Authors: Li Quanzhen , Zhu Honglin , Zhu Chengsong , Mi Wentao , Zuo Xiaoxia , Luo Hui 
Published: January 2023

Abstract

Objectives
To delineate the interaction network between gene transcription and DNA methylation in PBMC of systemic sclerosis (SSc) patients and to identify methylation-regulated genes which are involved in the pathogenesis of SSc.

Methods
Genome-wide transcriptome and DNA methylome were profiled on PBMC from 30 SSc patients and 30 matched normal controls (NC). Differential expressed genes (DEGs) and differential methylated positions (DMPs) were integratively analyzed to identify methylation-regulated genes and associated molecular pathways.

Results
Transcriptome profiling distinguished 453 DEGs in SSc. Global DNA methylation analysis identified 925 DMPs located on 618 genes. Integration of DEGs and DMPs revealed 20 DEGs containing inversely associated DMPs. These 20 potential methylation-regulated DEGs (MeDEGs), including 12 up-regulated genes (ELANE, CTSG, LTBR, C3AR1, CSTA, SPI1, ODF3B, SAMD4A, PLAUR, NFE2, ZYX and CTSZ) and 8 down-regulated genes (RUNX3, PRF1, PRKCH, PAG1, RASSF5, FYN, CXCR6 and F2R), are predominantly involved in the migration, proliferation, activation and inflammation of immune cells. Unsupervised cluster analysis of the top MeDEGs distinguished SSc from NC with 90% sensitivity and 87% specificity. 4 MeDEGs, F2R, FYN, PAG1 and PRKCH, exhibited significantly progressive decrease in SSc with interstitial lung disease (ILD) compared with SSc without ILD.

Conclusion
By integration of genome-wide transcriptome and DNA methylome, we identified differential expressed genes associated with aberrant DNA methylation in the PBMC of SSc. The epigenetically dysregulated genes may lead to the abnormal activation of immune regulatory pathways which may contribute to the pathogenesis of SSc.
Pan-Immunome Initiative: Building an integrated T and B cell receptor repertoire map for immune-related diseases
Authors: Liu Xiao , Zhang Wei , Wu Jinghua , Lin Liya , Nie Jianzheng , Zhao Ming , Lu Qianjin 
Published: January 2023

Abstract
The human adaptive immune system provides protection which is directly triggered by the receptors on the surfaces of T cells (TCRs) and B cells (BCRs). However, up till now, there are still difficulties in precise diagnosis for some immune related diseases. Here, we proposed a pan-immunome initiative, building an integrated T and B cell receptor repertoire map for immune related disease. As the early stage of this project, we have established a pan-immune-repertoire database (PIRD, https://db.cngb.org/pird/). We have collected more than 15,000 samples comprising 15 sorts of diseases. All samples have been amplified TCR b chain repertoire and sequenced using high throughput sequencer. We took systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) as examples for in-depth analysis. Significant differences of V, J and V-J pairing usage between SLE or RA and control groups were found and could be utilized as classification variables to discriminate the three groups (V: AUC&gt;0.99). 228 SLE-associated and 169 RA-associated TCRs were identified using statistical test. A statistical model was generated to diagnose diseases using those disease-associated TCRs, with high specificity and sensitivity. Interestingly, lower overall diversities and massive expanded clones were observed in both SLE and RA samples, and higher TCR heterogeneity in SLE was found than in RA. However, clones related to specific organ damage in SLE were not observed. Besides, we have also been able to classify the TRB repertoire data of multiple diseases using an ensemble decision tree model. Thus, the immune repertoire data could reflect the individual immune status and serve as a powerful biomarker for molecular classification of immune related diseases.
Mast cell accumulation drives allergy-driven chronic pain responses in outbred mice
Authors: Chatterjea Devavani , Arriaga-Gomez Erica , Neamonitaki Nefeli , Kline Jaclyn , Boo Beebie 
Published: January 2023

Abstract
We are building novel outbred mouse models of a poorly understood yet prevalent vulvar pain condition – localized, provoked vulvodynia – that affects a substantial proportion of 18–60 year old women. Epidemiologic studies have shown a surprising and increased risk for developing this condition in women with a history of skin and airway allergies. We show that repeated exposures to low doses of the common contact irritant haptens oxazolone or dinitrofluorobenzene on the genital skin of mice produce sustained painful sensitivity to touch as well as a non-normative accumulation of mast cells and an overgrowth of cutaneous nerves in the affected tissue – changes that are also seen in vulvar biopsies taken from women diagnosed with vulvodynia providing the first evidence of biological plausibility for the immunological underpinnings of this chronic pain condition. In addition to laboratory haptens, we show that the hapten methylisothiazolinone (a common cosmetic preservative found in soaps, shampoos, and feminine hygiene products) can induce these responses suggesting that this ubiquitous environmental exposure might be a possible immunological trigger of hitherto unexplained genital pain conditions that affect many women.
We have further characterized infiltrating T cells at the allergic site to show that FoxP3+ regulatory CD4 T cells and CD103+ resident memory CD8 T accumulate at these sites as well. Our mouse models provide new tools to both dissect allergy driven pain conditions as well as test novel therapies targeting immune cells and mechanisms for the management and treatment of these debilitating disorders.
A gene expression module that identifies low-density granulocytes in the blood of patients with systemic lupus erythematosus is associated with low complement, elevated anti-dsDNA titer and both the interferon and TNF signatures
Authors: Kegerreis Brian , Catalina Michelle , Geraci Nicholas S. , Bachali Prathyusha , Lipsky Peter , Grammer Amrie 
Published: January 2023

Abstract
SLE is an autoimmune disease characterized by the presence of abnormal low-density granulocytes (LDG) with a heightened capacity for spontaneous NETosis. To characterize LDGs in SLE, gene expression profiles derived from isolated LDGs were characterized by Weighted Gene Co-expression Network Analysis, and a 92 gene module was identified. This module contains 30 genes with the Neutrophil Degranulation GO designation and many genes associated with DNA synthesis and proliferation. Comparison with gene expression by bone marrow neutrophil precursors demonstrated that the module of genes was most similar to that expressed by promyelocytes/myelocytes. The LDG gene signature was assessed in gene expression data sets from SLE whole blood (WB), PBMC, kidney, synovium, and skin. The LDG module was enriched consistently in blood but inconsistently in tissues. Lack of granule protein transcripts in tissues suggests that LDGs are not enriched in SLE affected organs. The LDG gene signature was also analyzed in WB and PBMC of 1,417 SLE patients by Gene Set Variation Analysis (GSVA). 35% of inactive patients and 50% of active patients expressed an LDG signature, which showed a significant but modest correlation with disease activity as measured by the SLE Disease Activity Index (r = 0.16, p = 4.1E-9). The LDG signature was also associated with the presence of anti-dsDNA (p &lt; 1E-6), decreased levels of C3 and C4 (p &lt; 1E-6), the type 1 interferon signature (p &lt; 1E-11) and a module of genes induced by TNF (p &lt; 1E-15, all by Fisher’s exact test). These findings suggest that LDGs are a population of immature neutrophils over-represented in the blood of SLE patients in association with cytokine stimulation, the presence of autoantibodies, and complement consumption.
Periodontal pathogen exposure facilitates disease activity in Systemic Lupus Erythematosus
Authors: Bagavant Harini , Dunkleberger Micah L. , Wolska Nina , Rybakowska Paulina , Sroka Magdalena , Rasmussen Astrid , Adrianto Indra , Montogomery Courtney , Sivils Kathy , Guthridge Joel M. , James Judith A. , Merrill Joan T. , Deshmukh Umesh S. 
Published: January 2023

Abstract
This study was undertaken to evaluate whether exposure to subgingival plaque bacteria and periodontal dysbiosis influences disease parameters in systemic lupus erythematosus (SLE).
Circulating antibodies to periodontal bacteria are surrogate markers to determine an ongoing bacterial burden, or are indicators of past exposure. SLE patient sera in the Oklahoma Lupus Cohort (n=303) were used to measure antibody titers against periodontal pathogens (A. actinomycetemcomitans, P. gingivalis, and T. denticola) and commensals (C. ochracea and S. gordonii) by ELISA. Correlations between anti-bacterial antibodies and clinical parameters of SLE including autoantibodies, complement, and disease activity (SLEDAI and BILAG) were studied. The effect of oral infection with A. actinomycetemcomitans on SLE in NZM2328 lupus mice was evaluated.
SLE patients had varying amounts of antibodies to different oral bacteria. The antibody titers against A. actinomycetemcomitans, P. gingivalis, T. denticola, and C. ochracea were higher in patients positive for anti-dsDNA, and in patients with low complement. Only antibodies to A. actinomycetemcomitans and P. gingivalis, but not T. denticola, were associated with higher disease activity. A. actinomycetemcomitans infected NZM2328 mice developed an increase in histone reactive T cells and an accelerated onset of proteinuria, and lupus nephritis.
Our results indicate that exposure to only specific pathogenic periodontal bacteria influences disease activity in SLE patients. The results from lupus mice suggest that this may be due to the amplification of local autoimmunity in response to infection. These findings provide a rationale for assessing and improving periodontal health in SLE patients.
2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD)-induced myeloid derived suppressor cells (MDSC) have heightened metabolic activity which correlates with microRNA and gene expression involved in immunosuppression
Authors: Neamah Wurood Hantoosh , Nagarkatti Prakash , Nagarkatti Mitzi 
Published: January 2023

Abstract
Myeloid-derived suppressor cells (MDSCs) are bone marrow (BM)-derived cells consisting of monocytic (M-MDSC) or granulocytic (G-MDSC) subtypes with immunosuppressive activity. In the current study, we examined the metabolism and functions of MDSCs induced by TCDD a highly toxic environmental pollutant. Inasmuch, we injected mice with either vehicle or 10μg/kg TCDD interpersonally and found that TCDD increased both M-MDSCs and G-MDSCs in the peritoneal exudate when compared to controls. We determined the cell bioenergetics in TCDD-induced MDSCs when compared to naïve BM-MDSCs. For this purpose, we examined the mitochondrial oxygen consumption rate (OCR) and found that TCDD-induced MDSCs had heightened basal respiration, ATP-linked respiration, proton (H+) leak, maximal respiration, spare respiratory capacity as well as total proton efflux rate (PER) which means more suppressive function when compared to BM-MDSCs. We next examined whether the heightened metabolic potential in TCDD-induced MDSCs correlated with the microRNA and gene expression. MiRNA array analysis demonstrated that in TCDD-induced MDSCs, certain miRNAs (e.g. mir-543-3p, mir-150-5p) were downregulated which target immunosuppressive genes involved in MDSC functions, such as ARG2, IL-10, STAT-3, and PIM1. Next, we investigated the role of miRNA-150-5p in IL-10, PIM1, and STAT3 expression as well as miRNA-543-3p effects on ARG2 using transfection experiments. We found that MDSCs transfected with mature miRNA-150-5p and miRNA-543-3p were downregulated whereas inhibitors upregulated the expression of respective targets. In summary, our data revealed that TCDD modulates miRNA expression which can impact gene expression and metabolism in MDSC.
Use of fluorescent Fab/Ab complexes and IncuCyte live-cell analysis to dynamically track cell surface markers and cell populations in mixed cultures
Authors: Lovell Gillian F. , Bevan Nicola , Campwala Hinnah , Blancheteau Vincent , Dale Tim , Dana Nicholas , Holtz Nevine , Endlsey Eric , Trezise D. J. 
Published: January 2023

Abstract
Fluorescently-labeled antibodies are widely used for visualising cellular protein expression/distribution (e.g. immunocytochemistry) and immuno-phenotyping (e.g. flow cytometry). However, their applications are largely confined to end-point or short term (min-h) detection, and the cell processing and labeling steps that are required often perturb the biology of interest. To enable longer-term, fully kinetic applications of cell surface protein markers in living cells, we have developed a novel strategy based on fluorescently-labeled antibody fragments (Fabs) and IncuCyte live-cell analysis. An Fc-targeted anti-mouse Fab fragment conjugated to a green-emitting fluoroprobe (IncuCyte FabFluor-488) was used to tag Abs to surface markers (e.g. CD4, CD20, Her2) via a simple one-step, no-wash protocol. Addition of the corresponding FabFluor-488-Ab complex to living cells (e.g. Jurkats, RAMOS, SKOV-3) produced long lasting (up to 5d), specific and stable cellular fluorescence at relatively low Ab concentrations (1mg ml−1) that did not perturb cell morphology or growth (IncuCyte S3). To illustrate the application of this approach the method was used to (a) quantify upregulation of the checkpoint protein PDL-1 over 48h in IFN-gamma-treated MDA-MB231 and SKOV-3 and tumor cells, (b) identify cellular subsets in PBMCs, and (c) observe proximity and engagement of A549 target cells by CD-8 positive PBMCs in immune-cell killing experimentsThis FabFluor-488/IncuCyte method enables long-term tracking and quantification of cell surface protein expression and the ability to identify cell subsets in living cultures over time. This method should prove powerful in analyses on complex and advanced heterogeneous cell models.