bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visual analysis of multidimensional CyTOF data from allergic asthmatics pre and post allergen challenge
Authors: Wang Jing M. , Bhakta Nirav , Ansel Mark , Antalek Bobby , Nguyen Christine P. , Woodruff Prescott G. 
Published: January 2023

Abstract
Allergen-induced airway inflammation is a central feature of asthma. The ability to deeply phenotype cells with mass cytometry (CyTOF) can lead to new insights into the immune response after allergen challenge (AC). We have developed a 33 marker CyTOF-based panel and applied it to human bronchoalveolar lavage (BAL) and whole blood cells from 10 subjects with atopic asthma in a segmental AC study. Because the data generated by CyTOF are high dimensional, traditional bivariate analysis is complicated and limited to traditionally-defined cell types. Therefore, we applied the unbiased visualization method, viSNE. We report data from our initial subject before (baseline) and after diluent (DIL) or AC. Our results show that viSNE captures marker expression differences, cell grouping differences by sample type and rare cell populations. BAL cells showed more macrophages (CD206+) at baseline and more macrophages and neutrophils (CD16++CD15++CD24+) after DIL versus AC. In contrast, AC led to a tremendous influx of eosinophils (CD24++CCR3+) with some basophils (HLA-DR−CD123+FcɛRI+). Interestingly, eosinophils in AC were CD69+ in the BAL but not in the blood, implying that eosinophils were activated after recruitment into the airways. There were no changes in T cell (CD3+CD4+ or CD3+CD8+), B cell (CD19+ or CD20+) or dendritic cell (CD1c+CD123−HLA-DR+ or CD1c−CD123+HLA-DR+) proportions between baseline, DIL and AC BAL cells; additional analyses from this clinical study will focus on subsets of these cells. In conclusion, visual analysis of high-dimensional data in allergic airway inflammation identifies differences and potentially meaningful but as yet undefined inflammatory cell populations.
IRF4 expression by lung dendritic cells promotes allergic Th2 responses by controlling OX40L, IL-10, and IL-33 expression during sensitization
Authors: Camacho Daniel F. , Howard Chanie L. , Darnell Eli P. , Wang Esther , Hrusch Cara L. , Sperling Anne I. 
Published: January 2023

Abstract
The specific mechanisms by which DCs initiate Th2 responses are not completely understood. We previously found that mice lacking the transcription factor IRF4 in DCs do not develop type 2 lung inflammation in response to house dust mite extract (HDM). Further, IRF4-deficient DCs had a reduced capacity for restimulating T cells towards a Th2 phenotype ex vivo. We hypothesized that IRF4 is necessary for DCs to perform one or more of the functions required to successfully initiate Th2 responses in vivo. Here we demonstrate that during in vivo HDM sensitization, IRF4 in DCs is required neither for CD11b+ CD24+ cDCs to take up allergen in the lungs, nor for the lung DCs to process antigens. Instead, IRF4-deficient lung DCs display lower levels of the Th2-associated costimulatory molecule OX40L and express less of the Th2-promoting cytokines IL-33 and IL-10 during sensitization. While HDM-bearing DCs lacking IRF4 arrive in the lung-draining lymph nodes at proportions comparable to WT DCs and are capable of processing antigens, reduced numbers migrate to the lung-draining lymph nodes in the absence of IRF4. Following HDM sensitization, mice with IRF4-deficient DCs display impaired CD4+ effector/memory T cell recruitment to the lung parenchyma and reduced T cell expression of CD69. Thus, IRF4 controls a pro-Th2 program in DCs including expression of OX40L, IL-10, and IL-33 as well as migration to the draining lymph nodes, culminating in Th2 priming in response to HDM.
The crosstalk between developing sympathetic nerves and immune cells contributes to early-life Th2 bias in the lung
Authors: Wang Wei , Cohen Jonathan , Trieu Kenneth , Bai Yan , Ai Xingbin 
Published: January 2023

Abstract
The adaptive immunity in early life is polarized towards Th2 response, which contributes to increased susceptibility to asthma in children. However, the molecular mechanism of age-related Th2 bias remains poorly understood. Building upon critical roles of nerves in the modulation of immune responses, we investigated the crosstalk between the developing nervous system and the immune cells in postnatal lungs using murine models and human lung tissues/cells. Notably, like human, mice exhibit similar early-life Th2 bias, as allergen exposure elicits more robust inflammation in neonates than in adult mice. In addition, our previous studies revealed a similar profile of neurogenic factors between mouse and human lungs. Therefore, the neonatal mouse model of asthma provides an invaluable tool to identify potential modulatory roles of nerves in early life Th2 immunity bias. In this study, we identified dopamine as a potent inducer of Th2 phenotypes in a screen for the role of neurotransmitters in the differentiation of CD4+ T cells, which is consistent with a previous finding. Dopamine is selectively expressed by the sympathetic nerves in developing lungs. Besides, we discovered that sympathetic nerves transited from dopamine-producing in early life to norepinephrine-producing in adult life. We proved that the dopamine-rich sympathetic nerve played a role in allergic Th2 inflammation in neonatal mice lungs. However, with age, the level of dopamine decreased and therefore, this immune modulation reduced. Taken together, our findings reveal the crosstalk between the developing nerves and Th2 prone immunity in early life. Our study may provide the foundation for potential therapy strategies for kids with asthma.
Role of TNFα Antagonists in Susceptibility to Mycobacterial Infection in Association with Genetic Polymorphisms in Crohn’s Disease
Authors: Qasem Ahmad , Naser Saleh 
Published: January 2023

Abstract
Crohn’s disease (CD) is a relapsing inflammatory bowel disease that has been associated with bacterial triggers such as Mycobacterium avium subspecies paratuberculosis (MAP). Overreactive immune response in CD patients involves a significant elevation in Tumor Necrosis Factor alpha (TNFα), which causes upregulation in multiple cytokine levels, leading to formation and maintenance of granuloma. Standard CD treatment includes immunomodulators and biologics such as Anti-TNFα. We hypothesize that blocking TNFα promotes MAP survival which worsens the disease condition. Therefore, CD treatment plan should include MAP-specific antibiotics and novel cytokine targets based on personalized medicinal approach. RHB-104, a triple antibiotics formulation ((63.3 %) clarithromycin, (6.7 %) clofazimine, and (30 %) rifabutin), recombinant TNFα, adalimumab (Humira®), and certolizumab pegol (Cimzia®) were evaluated in vitro for effect on MAP culture and macrophages infected with MAP. As expected, RHB-104 was detrmintal to MAP (MIC&lt; 2ug/mL), while anti-TNFα therapeutics had no direct bactericidal effects at concentrations as high as 4x Cmax. Recombinant TNFα reduced MAP survival in infected macrophages by 2.63 logs. On the contrary, both anti-TNFα therapeutics promoted MAP survival by 1.54 logs. Additionally, we have identified 2 significant single nucleotide polymorphisms (rs767455 and rs3397) related to TNFR superfamily 1(A/B) in 54 CD patients compared to 50 healthy subjects by using TaqManTM genotyping assay. This study should provide i) data about the safety of Anti-TNFα biologics in CD patients-associated with MAP infection and ii) predictions toward response to treatment plan based on patient’s pharmacogenomics.
Hypoxia boosts Th17-cell responses in inflammatory bowel disease through increased efflux of ligands reactive with the aryl-hydrocarbon-receptor
Authors: Longhi Maria Serena , Xie Anyan , Robles Rene’ J. , Zhang Haohai , Csizmadia Eva , Wu Yan , Moss Alan C. , Robson Simon C. 
Published: January 2023

Abstract
Despite beneficial influence of hypoxia-inducible-factor (HIF) stabilization in animal models of mucosal inflammation and experimental colitis, hypoxia can be deleterious during protracted inflammation by inhibiting T-regulatory-1 and favoring differentiation of T-helper (Th)-17 cells.
We report here that Th17 cells from Crohn’s disease patients display heightened levels of HIF-1α and become refractory to the immunoregulatory effects of unconjugated bilirubin (UCB), an endogenous ligand for aryl hydrocarbon receptor (AhR), when exposed to hypoxia in vitro. Molecular blockade of HIF-1α reconstitutes Th17 cell ability to respond to UCB and upregulates CD39, an ectonucleotidase that catalyzes ATP and ADP into immunosuppressive adenosine. Inability of Th17 cells to respond to AhR derives from induction of ATP transporters multidrug-resistance-protein-1 (MDR1) and multidrug-resistance-associated-protein-4 (MRP4) by HIF-1α; this results in increased efflux of AhR ligands like UCB out of Th17 cells. Ritonavir, a drug with inhibitory effects over HIF-1α, MDR1 and MRP4, restores UCB regulation over Th17 cells in Crohn’s and enhances UCB salutary effects in dextran-sulfate-sodium-induced experimental colitis.
We conclude that inhibitory effects of hypoxia in limiting Th17 cell response to AhR in Crohn’s disease are mediated through upregulation of ATP transporters that decrease AhR substrate availability. Concurrent treatment with HIF-1α inhibitors and AhR ligands provide effective therapeutic options to overcome Th17 functional alterations in inflammatory bowel disease.
Novel UNC13D intronic variant disrupting a NF κB enhancer in a patient with recurrent macrophage activation syndrome and systemic juvenile idiopathic arthritis
Authors: Cron Randy Q. , Schulert Grant S. , Zhang Mingce , Husami Ammar , Fall Ndate , Brunner Hermine , Zhang Kejian , Grom Alexei A. 
Published: January 2023

Abstract
Macrophage activation syndrome (MAS) is a life-threatening complication of systemic juvenile idiopathic arthritis (SJIA), and has pathologic similarity to hemophagocytic lymphohistiocytosis (HLH). Intronic variants in UNC13D are found in patients with familial HLH-3 (FHL3), but the role of non-coding variants in MAS is unknown. The objective of this study was to identify deep intronic UNC13D variants in patients with MAS. A custom enrichment library was constructed to sequence approximately 1 MB flanking UNC13D in 24 patients with SJIA, recurrent MAS, and negative prior genetic (exon/coding) testing. Functional consequences of intronic variants were assessed using quantitative PCR on patient derived peripheral blood mononuclear cells (PBMC), electrophoretic mobility shift assay (EMSA), in vitro transcriptional enhancer assays, and in vitro NK cell degranulation assays. We report a patient with SJIA and recurrent episodes of MAS, found to have a novel functional intronic variant in UNC13D, c.117+143A&gt;G. This variant occurs in a proposed regulatory region that drives an alternative, lymphocyte specific UNC13D transcript, and is associated with reduced transcript levels in patient PBMC. In support of this, the patient’s variant disrupts NFκB binding to a functional transcriptional enhancer, leading to reduced enhancer activity and NK cell degranulation in vitro. Another patient was identified with a previously described UNC13D intronic variant, for a total non-coding variant hit rate of 8.3% (2/24). These findings highlight that intronic variants in key regulatory regions may be associated with MAS in patients with SJIA, and support deep sequencing approaches when causative coding variants are not identified.
Blood-based untargeted metabolomics in Relapsing-Remitting Multiple Sclerosis revealed testable therapeutic target
Authors: Giri Shailendra , poisson Laila , Singh Jaspreet , Datta Indrani , Suhail Hamid , Mangalam Ashutosh K. , Cerghet Mirela , Elias stanton B. , Rattan Ramandeep 
Published: January 2023

Abstract
Relapsing-remitting (RRMS), a most common form of MS, is characterized by acute attacks alternated by partial or complete recovery periods. The major focus of our research is to identify the therapeutic target using metabolomics. Metabolomics is a fast emerging field which can provide a direct “functional readout of the physiological state” of an organism. Identification of blood-based metabolic pathway(s) in relapsing-remitting form of MS (RRMS) which could be used for therapy. Using untargeted ultra-performance liquid and gas mass spectrometry, we measured serum metabolites from 33 RRMS patients, and 14 healthy subjects (HS). A total of 621 known metabolites were detected and 60 metabolites were significantly altered in the serum of RRMS compared to HS. Bioinformatics analysis revealed four metabolic pathways altered in RRMS including glycerophospholipid, citrate cycle, sphingolipids, and pyruvate metabolism. PBMCs isolated from RRMS patients exhibited higher glycolysis suggesting altered metabolic state of immune cells. EAE mice treated with glycolytic inhibitor 2-deoxyglucose (2-DG; once daily), resulted in a significantly delayed (P&lt;0.001) the disease progression. 2DG inhibited (P&lt;0.01) interleukin 17 production by reducing glycolysis (P&lt;0.01) in monocytes of treated EAE group. Using untargeted metabolomic and Seahorse bioanalyzer approaches, we document that RRMS patients showed altered metabolic state “metabotype”. Targeting glycolysis, upstream of metabolic pathways altered in RRMS, using pharmacological inhibitor ameliorated the disease progression and pathology in a preclinical model of MS.
Single-cell RNA sequencing of skin and kidney cells in lupus nephritis provides insights into pathogenesis and indicates novel potential biomarkers
Authors: Der Evan B. , Suryawanshi Hemant , Ranabothu Saritha , Goilav Beatrice , Belmont H. Michael , Izmirly Peter , Bornkamp Nicole , Jordan Nicole , Wang Tao , Wu Ming , James Judith A. , Guthridge Joel M. , Raychaudhuri Soumya , Buyon Jill , Tuschl Thomas , Putterman Chaim 
Published: January 2023

Abstract
Classification and treatment decisions in lupus nephritis (LN) are largely based on renal histology. Single-cell RNAseq (scRNAseq) analysis may accurately differentiate types of renal involvement at the transcriptomic level, and better inform treatment decisions and prognosis. scRNAseq was performed on kidney and non-lesional skin tissue collected from clinically indicated renal biopsies, and skin biopsies obtained at the time of renal biopsies, in 20 systemic lupus erythematosus (SLE) patients. Cell-types were determined using principal component analysis and tSNE plotting, resulting in the definitive identification of keratinocytes, tubular cells, mesangial cells, fibroblasts, endothelial cells, and leukocytes. Tubular cells in patients with proliferative nephritis demonstrated upregulated TNF signaling compared with membranous nephritis. Interestingly, keratinocytes of patients with proliferative nephritis also demonstrated upregulated TNF signaling. Furthermore, tubular cells of patients who did not respond to standard immunosuppressive treatment showed upregulation of extracellular matrix proteins and fibrotic markers at the time of biopsy. Using logistic regression analysis, a 4-gene tubular fibrosis score was created which predicted response to treatment, with an area under curve of 0.9. We conclude that scRNAseq using small amounts of renal biopsy tissue in SLE can differentiate between the different classes of LN, and provide important insights into potential pathogenic mechanisms. Further, changes in the skin of LN patients can provide a useful source of biomarkers and may reflect important information concerning concurrent kidney pathological events.
Formation of an Argonaut-independent miRNA-mRNA Complex with DDX6 Orchestrates MTOR- dependent Regulation of T-cell differentiation.
Authors: Zhang Nannan , Hu Guowu , Pena Hanna , Qiu Jin , Park Yoon-Dong , Uzel Gulbu , Datta Sandip K. , Steiner Joseph P. , Kelsall Brian L. , Williamson Peter R. 
Published: January 2023

Abstract
The mechanistic target of rapamycin(MTOR) is an important global regulator of growth, metabolism and immunity; however, how MTOR integrates global and sequence-specific signals remains poorly understood. Herein we utilize the MTOR signaling pathway involved CD4+FOXP3+ regulatory T cells (Tregs) and identify sixty-three genes regulated during differentiation including a key transcription factor, Forkhead box 3 (FOXP3). MTOR-dependent DCP2 phosphorylation potentiated decapping/degradation and was facilitated by MIR1246 miRNA binding to the 3′-UTR of FOXP3 mRNA. The physiological relevance of DDX6-dependent FOXP3 mRNA degradation was established in experimental autoimmune encephalitis and fungal mening oencephalitis using Ddx6flox/floxX CD4cre mice, as well as in patient cells having mutations incytotoxic T-lymphocyte associated protein 4 (CTLA4) associated with autoimmunity. These data provide a novel mechanism of miRNA-dependent mRNA regulation of MTOR-dependent targets highlighted by regulation during T cell polarization and suggests new targets for immunotherapy.
Understanding protective plasma levels of penicillin and monitoring antibody responses for the prevention of GAS infection in a paediatric population in New Zealand
Authors: Sika-Paotonu Dianne , Tiatia Ramona , Thornley Craig , Betty Bryan , Wineera-Parai Ranei , Eddie Barbara , Baker Michael , Salman Sam , Marsh Julie , Manning Laurens , Joseph John , Hand Rob , Carapetis Jonathan 
Published: January 2023

Abstract
Acute Rheumatic Fever (ARF) is an autoimmune condition resulting from untreated Group A Streptococcal (GAS) infection of the upper respiratory tract and possibly skin. Repeated untreated and severe episodes of ARF can cause permanent cardiac damage known as Rheumatic Heart Disease (RHD). Rates of ARF in New Zealand and Australia are among the highest in the world, particularly amongst Māori and Pacific and Indigenous Aboriginal children. Monthly injections of Benzathine Penicillin G (BPG) are given intramuscularly to prevent GAS infections that can lead to ARF and cause RHD. Early studies exploring the Pharmacokinetics (PK) properties of BPG were conducted in healthy, fit, young military recruits without ARF/RHD. BPG bioavailability, metabolism may differ in paediatric populations groups with ARF who have comorbidities and vary in Body Mass Index. This project seeks to determine the PK characteristics in a paediatric population currently receiving monthly injections of BPG while at the same time monitoring antibody immune responses to possible GAS infections. This is a prospective cohort study in a paediatric population of Wellington based children and teens (aged 5–21 years of predominantly Pasifika and Māori heritage) with a previous diagnosis of ARF and are receiving monthly BPG injections via community services. Participants will contribute finger prick blood samples over time for Dried Blood Spot assays designed to quantify penicillin G levels in the blood and measure streptococcal serology. Routine throat swab samples will also be collected with ASOT antibody levels monitored for GAS breakthrough infections. This is the first population PK study exploring use of BPG in Māori and Pacific children previously diagnosed with ARF.
A Novel Mendelian Disease of Autoimmunity caused by Mutations in a small GTPase
Authors: Leney-Greene Michael Alexander , Park Ann , Chao Brittany , Vilarinho Silvia , Su Helen , Ozen Ahmet , Lenardo Michael J. 
Published: January 2023

Abstract
In this study, we harness Whole Exome Sequencing (WES) to interrogate the underlying genetic cause in a patient cohort suffering from a Mendelian disease of immune dysregulation characterized by severe lymphopenia, splenomegaly, anemia, thrombocytopenia and liver failure. Bioinformatic analysis revealed novel mutations in a small GTPase that led to a near complete loss of mature protein in patient cells. Animal models lacking these genes develop a disease remarkably similar to that observed in the human patients, however, the molecular role of this GTPase in the immune system remains a fundamental gap in our knowledge. Due to a remarkable similarity in phenotypes between mice deficient for this small GTPase and T cell specific deletions of regulators of mTORC1, we hypothesized that this gene may be involved in the mTORC1 signaling pathway. We observe a robust association between this GTPase and members of the ragulator complex which is required for recruitment of mTORC1 to the lysosome and subsequent signalling. Furthermore, treatment with inhibitors of mTORC1 led to remarkable clinical improvements in our mouse model and also one of our human patients. Overall, we have described a novel, T cell specific member of the ragulator complex and it’s role in maintaining immune homeostasis in humans.
This research was supported by the Intramural Research Program of NIAID, NIH.
Hypomethylation of STAT1 and HLA-DRB1 in CD8+ T cells is associated with type-I interferon dependent activation of CD4+ T cells in systemic lupus erythematosus
Authors: Sawalha Amr , Miller Shaylynn , Coit Patrick , Gensterblum-Miller Elizabeth , Renauer Paul , Kilian Nathan , Schonfeld Mark 
Published: January 2023

Abstract

Background
Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease characterized by autoantibody and type I interferon (IFN) production. The goal of this study was to explore possible pathogenic roles of CD8+ T cells in lupus through characterizing DNA methylation changes.

Methods
Genome-wide DNA methylation of SLE and matched healthy control CD8+ T cells was measured using Infinium Human Methylation 450k arrays. Cell surface expression of HLA-DRB1 on CD8+ T cells with and without IFNα was measured by flow cytometry. Co-incubation of IFNα-treated CD8+ T cells with autologous naïve CD4+ T cells was performed.

Results
SLE CD8+ T cells had 188 hypomethylated CpG sites compared to healthy controls. Among the most demethylated were sites associated with HLA-DRB1 (Δβ = −0.33) and STAT1 (Δβ = −0.15). The proportion of CD8+ T cells expressing HLA-DRB1 was significantly higher in SLE compared to controls. Treatment with IFNα upregulated cell surface expression of HLA-DRB1 on CD8+ T cells of SLE patients but not healthy controls, as measured by median fluorescence intensity. Co-incubation of naïve CD4+ T cells with IFNα-treated CD8+ T cells led to increased expression of the stimulation marker CD69 on CD4+ T cells in SLE patients, but not in healthy controls. There was a significant increase in STAT1 mRNA levels in both SLE patients and controls with IFNα treatment.

Conclusion
HLA-DRB1 and STAT1 loci are hypomethylated and epigenetically poised for overexpression in SLE CD8+ T cells in the presence of type-I interferon. IFNα-treated lupus CD8+ T cells stimulate autologous CD4+ T cells in vitro. These data suggest a possible pathogenic role for CD8+ T cells that is dependent upon a high type-I interferon environment in SLE patients.