bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allergy and asthma in inner-city children: possible roles of MAIT cells and variation in the home environment
Authors: Chandra Shilpi , Wingender Gerhard , Greenbaum Jason A , Khurana Archana , Gholami Amin Moghaddas , Rosenbach Michael , Jaffee Katy , Gern James E , Wood Robert , O’Connor George , Sandel Megan , Kattan Meyer , Bacharier Leonard , Togias Alkis Togias , Horner Anthony A. , Kronenberg Mitchell 
Published: January 2023

Abstract
Humans have two populations of innate-like T lymphocytes with an invariant T cell antigen receptor (TCR) a chain: invariant natural killer T (iNKT) cells and mucosal associated invariant T (MAIT) cells. iNKT cell involvement in human asthma has been suggested, but is controversial, while there has been little analysis of MAIT cells. Using peripheral blood cells from the urban environment and childhood asthma (URECA) birth cohort study, we carried out a comprehensive investigation to determine if iNKT cell frequency or MAIT cell frequency early in life is correlated with the cytokine polarization of mainstream CD4+T cells and/or the development of asthma by age seven. We also determined if iNKT cell antigenic activity in house dust samples was associated with environmental endotoxin or clinical outcomes including aeroallergen sensitization and recurrent wheeze at 3 and asthma at age 7. We also analyzed the correlation between cytokines released by activated iNKT and MAIT cells and various clinical outcomes. Our results shows that the frequency of MAIT cells was associated with increased production of IFNg by activated CD4+ T cells from children that did not go on to develop asthma. Moreover, an increased MAIT cell frequency early in life was associated with a decreased risk of asthma by age seven. In contrast, iNKT cell frequency early in life was not correlated with the development of asthma or allergic sensitization. iNKT cell antigen content in house dust varied greatly, and increased antigen was associated not only with endotoxin levels in the surroundings but also with protection from asthma. Together, these data suggest that MAIT cell frequency and iNKT cell antigen content at one year correlates with protection from asthma development.
Epigenetic regulation of proinflammatory chemokines in Cystic Fibrosis lung epithelium
Authors: Chen Kong , Kolls Jay K 
Published: January 2023

Abstract
Functional loss of CFTR in lung epithelial cells leads to pulmonary disease in Cystic Fibrosis (CF) patients. Our preliminary data indicates that proinflammatory chemokines and cytokines are spontaneously released by Human Bronchial Epithelial (HBE) cells established from CF patients and the spontaneous release can be abolished by a bromodomain inhibitor, a small molecule that inhibits epigenetic enhancement of gene transcription. Epigenetics alter gene expression in many other diseases, thus, this mechanism could also be responsible for the dysregulation of inflammatory mediators observed in the CF airway. We hypothesize that the enhanced production of proinflammatory mediators observed in CF airways are in part controlled by an epigenetic regulatory program. RNA-seq analysis revealed a dramatic upregulation of chemokine genes in the airway epithelium from CF patients, which correlated with downregulation of histone deacetylases, suggesting chemokine expression in CF airway can be modified by histone acetylation. In vitro, chemokine productions in polarized HBE cells from CF donors are also enhanced and are sensitive to BET inhibition. ATAC-seq analysis on HBE cells derived from control and CF donors was conducted and more peaks were observed in CF cells at the promoter regions of several chemokine genes suggesting these loci are more accessible compared to control HBE cells. These data strongly implicate that pro-inflammatory environment in CF lungs epigenetically enhances chemokines production through repressing histone deacetylases, suggesting that therapeutic approaches aiming to reverse the consequence of losing histone deacetylases can be beneficial to CF patients through reducing lung inflammation.
CD4+ T cell receptor repertoire in sarcoidosis patients
Authors: Mitchell Angela M , Kaiser Ylva , Falta Michael T , Eklund Anders , Grunewald Johan , Fontenot Andrew P 
Published: January 2023

Abstract
Sarcoidosis is a multisystem disorder that most commonly affects the lungs and involves granuloma formation with the accumulation of CD4+ T cells at sites of disease. Considerable evidence indicates that CD4+ T cells are involved in the initiation and perpetuation of sarcoidosis. Particular T cell clones within the bronchoalveolar lavage (BAL) are preferentially expanded in patients with sarcoidosis, and these oligoclonal T cell populations accumulate within the lung and disappear with disease resolution. A link between the expansions of CD4+T cells expressing the T cell receptor (TCR) α-chain variable (V) region Vα2.3 and the presence of the HLA-DRB1*0301 (DR3) allele in sarcoidosis patients has been seen. We hypothesize that sarcoidosis-specific CD4+ T cells accumulate and expand in the lungs of sarcoidosis patients in response to a specific antigen. To determine whether these expanded CD4+T cell clones play a pathogenic role in disease progression, as well as to address their antigen specificity, we analyzed the TCR repertoire of CD4+ T cells isolated from the BAL of sarcoidosis patients utilizing iRepertoire, emulsion PCR, and single cell PCR analyses. We identified TCR Vα2.3/Jα42 CDR3 motifs that were found exclusively in HLA-DR3+ sarcoidosis patients (the motifs were not found in DR3− or DR3+ healthy control patients), suggesting a public TCR repertoire in this subset of patients. Importantly, these α-chains were paired with differing β-chains, suggesting a critical role of the α-chains in recognizing the HLA-DR3-peptide complex.
Blocking the TNF Superfamily member LIGHT to control lung and skin fibrosis
Authors: Herro Rana , Croft Michael 
Published: January 2023

Abstract
Anti-inflammatory drugs have so far failed to reduce fibrosis and tissue remodeling in the clinic. Alternatively, 5 TNF inhibitors have been FDA approved to treat different inflammatory diseases and are safe to administer to patients. In human, LIGHT and its receptors have been linked to numerous autoimmune and inflammatory diseases with fibrotic components. We show that blocking LIGHT signaling in isolation is efficient in reducing fibrosis in the skin and lung of mice induced with bleomycin to mimic human Systemic Sclerosis and Idiopathic pulmonary fibrosis, as well as in 2 severe allergen-driven models of asthma and atopic dermatitis. Neutralizing LIGHT signaling through its receptors by genetic deletion or antibody blocking, dramatically decreased collagen and smooth muscle deposition in the lungs and skins. Moreover the specific deletion of LIGHT-receptor HVEM on keratinocytes or the therapeutic blocking of LIGHT-HVEM interaction post-disease onset, abrogated skin fibrosis induced by house dust mite in a model of atopic dermatitis. LIGHT seems to play a central role in lung and skin fibrosis since it can control the expression of major pro-fibrotic factors such as TSLP, IL-13, TGF-b and Periostin. Also LIGHT alone can induce a fibro-proliferative disorder that mimics human SSc, in the lung and skin when administered alone, by increasing the accumulation of both fibers collagen and smooth muscle actin. Lastly we observed an upregulation of LIGHT and its receptors in lung biopsies of patients suffering from asthma, scleroderma and idiopathic pulmonary fibrosis. The relevance of this work to fibrosis therapies associated with asthma, atopic dermatitis, scleroderma and idiopathic pulmonary fibrosis are tremendous.
An aberrant immune response to an ocular commensal results in disease in a mouse model of Muckle-Wells Syndrome
Authors: Raychaudhuri Kumarkrishna , St Leger Anthony , Almaghrabi Fatimah , Fuss Ivan J. , Strober Warren , Caspi Rachel R 
Published: January 2023

Abstract
Appropriate regulation of host immunity by commensal bacteria at mucosal tissues, including the ocular surface, can prevent infection and limit disease. Our recent data (St. Leger et al, this conference) suggest that Corynebacterium mastitidis (=C. mast), an ocular commensal, elicits production of protective IL-17 from conjunctival gdT cells. What is not known is whether this relationship, when dysregulated, can lead to pathology and disease. In this study, we used a mouse model of Muckle-Wells Syndrome (MWS), which is a human autoinflammatory disease that results in spontaneous inflammation of the conjunctiva, skin and joints. This is caused by a mutation in the NLRP3 gene (cias1) that leads to an overactive NLRP3 inflammasome and results in production of multiple proinflammatory cytokines, including, most prominently, IL-1b. Here, we show that ocular colonization with a commensal bacterium, C. mast, induces ocular inflammation in MWS mice, but not in WT controls. Dendritic cells from MWS mice produced increased amounts of IL-1b upon stimulation with C. mast lysates. In keeping with this, DCs harvested from MWS mice more efficiently activated gdT cells (in particular, Vγ4+ cells) in co-culture experiments, compared to DCs from WT mice. Our results suggest that the commensal C. mast can act as a pathobiont and trigger ocular inflammation in mice with an overactive NLRP3 inflammasome. Thus, an aberrant immune response to commensal microbes in humans with this mutation may be the cause of recurrent conjunctivitis in patients with MWS or similar autoinflammatory diseases.
Impaired AHR Signaling Contributes To Intestinal ILC3/ILC1 Conversion In The Inflamed Terminal Ileum Of Crohn’s Disease Patients
Authors: Li Jian , Doty Andria , Glover Sarah 
Published: January 2023

Abstract

Introduction
Crohn’s disease (CD) is one form of inflammatory bowel disease (IBD). Traditionally, adaptive immunity has been presumed to play a major role in the pathogenesis of CD. Recently, increasing evidence indicates that innate immunity also plays an essential role in this process. The phenotype and function of newly discovered innate lymphoid cells (ILCs) are crucial for the maintenance of intestinal homeostasis. Aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor which is important for the regulation of ILC biology in the mouse gut. We wanted to explore the potential involvement of AHR in the regulation of intestinal ILC of CD patients.

Hypothesis
AHR signaling pathway is critical for the regulation of the phenotype and function of human intestinal ILC in the terminal ileum of CD patients.

Methods
Surgical terminal ileum samples were collected from CD patients. Histology, Real-time PCR analysis, flow cytometric analysis and immunohistochemistry staining were performed.

Results
The expression of AHR was correlated with CD117 expression on human intestinal ILC subsets. The IFN-γ-producing-ILC1s accumulated in the inflamed terminal ileum of CD patients at the expense of protective IL-22-producing NKp44+ILC3s. Also, the expression of both AHR and CD117 were downregulated in the ILCs from the inflamed tissue. Additionally, there was a disparity between AHR protein and mRNA expression in the inflamed gut of CD patients which suggested the involvement of a posttranscriptional mechanism.

Conclusions
The AHR signaling was impaired in the inflamed gut of CD patients. This transcriptional modification contributed to the ILC3/ILC1 conversion and promoted the process of intestinal inflammation.
Flow Cytometry Multiplexing and its Use in Detailed Characterization of Cell Health
Authors: Low Quentin , Yan Michelle , Wickett Marcy , O’Grady Michael , Montoya Leticia 
Published: January 2023

Abstract
High throughput screening (HTS) is extremely effective method for allowing researchers to identify putative compounds of interest which play a role in their area of cellular research. Recently, flow cytometry has emerged as a powerful HTS tool with the added benefit of cell-by-cell analysis. Flow cytometry not only allows a researcher to study drug effectiveness towards different cell types but also can be used to analyze protein-protein interactions, metabolic activities, as well as DNA/mRNA content in a single or multiplexed assay format.
In this study, we screened the MicroSource Discovery System Killer Plate compound library and compared HTS using a plate reader with flow cytometer multiplexing. Jurkat and Ramos cells, T and B lymphocyte cell types respectively, were used as cell models and cultured under standard conditions and screened either at hypoxic (1%) or hyperoxic (19%) oxygen levels at varied lengths of time (24, 48, or 72 hrs). To assess compound veracity, post-screening analysis was implemented to establish EC50s of “hits” from the compound library. Membrane integrity and metabolic activity were measured as an initial screening output for evaluating cellular viability. Using the multiplexed capabilities of flow cytometry, we performed secondary and tertiary assays to further characterize the possible mechanism of action by analysis of cell cycle, specific RNA expression levels, oxidative stress, and caspase activation across differing concentrations of the compounds. This method and analysis highlights the complicated nature of assessing toxicity in cellular screening assays and the advantage of Flow Cytometry in particular for characterizing cell health.
Tissue infiltration of plasma cells/plasmablasts in patients with active Systemic Lupus Erthematosus (SLE)
Authors: Blanco Isabella K , Heuer Sarah , Catalina Michelle , Robl Robert , Madamanchi Sushma , Lipsky Peter , Grammer Amrie 
Published: January 2023

Abstract
To understand the role of plasma cells/plasmablasts (PC/PB) in organ pathology in SLE, we used GSVA (Gene Set Variation Analysis) to interrogate multiple lupus gene expression datasets. Differentially expressed (DE) genes in active SLE peripheral blood, B cells, mononuclear cells and tissues [skin, synovium, glomerulus, kidney tubulointerstitum (TI)] were queried for the previously reported (Lugar et al, 2012) PC/PB signature. There was considerable overlap between the PC/PB signature (20–44%) with the tissue datasets, with skin overlapping the most and synovium the least. IGM heavy chain and light chains (kappa, IGKC and lambda, IGLJ3 and IGLDE) were upregulated in the blood samples and all four tissue datasets, whereas IGHG1 was upregulated in the blood (B cell, PBMC), synovium & TI and downregulated in the skin. The presence of both IgK and IgL and numerous VL genes implied the polyclonal nature of the PC/PB infiltration. XBP1 governs late events in PC differentiation and was increased in the datasets that also had increased IGHG1 (B cell, TI). PRDM1, required for PC/PB differentiation, was increased in the blood datasets as well as in the synovium and glomerulus. Transcripts of genes in the “ER-mediated translocation to the cytosol” (Tram1, Derl1, and Ssr1) were upregulated in the blood and all four tissue datasets. IPA upstream regulator analysis revealed IL4, IL5 and CD40L for both the reference PC/PB set and all blood and tissue datasets with the exception of TI. IPA also revealed IL-6 as an upstream regulator in the PC/PB signature as well for the blood and four tissues datasets. In summary, interrogation of blood and tissue datasets for a PC/PB signature implicated these Ig secreting cell populations in tissue and organ pathology in SLE.
PD-1 blockade alters fate commitment of myeloid progenitors during tumor-mediated “emergency” myelopoiesis
Authors: Strauss Laura , Weaver Jessica , Freeman Gordon J. , Boussiotis Vassiliki A. 
Published: January 2023

Abstract
PD-1 is an immune inhibitory receptor for which blocking agents have achieved significant success as anti-cancer therapeutics. The mechanism(s) of the how PD-1 compromises anti-tumor function and how such effect is reversed by PD-1 blockade remain poorly understood. The rapid change in hematopoietic output that occurs in response to immunologic stress is known as “emergency” myelopoiesis. This process is co-opted by tumors to enhance the generation of tumor-promoting myeloid cells, mostly undifferentiated myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs). We analyzed the myeloid compartment of tumor-bearing mice and determined that myeloid cells express PD-1 and PD-L1. Using PD-1 KO mice or WT mice treated with PD-1 blocking antibody in cancer-driven myelopoiesis experiments we determined a cell-switch fate from MDSCs to effector myeloid cells. PD-1 deletion or blockade, which impaired tumor growth and metastases, stimulated the differentiation of hematopoietic progenitor cells and resulted in increase of Ly6Chimonocytes and monocyte-derived DC (mo-DC). Abrogation of PD-1 signaling enhanced the maturation of MDSCs by inducing the lineage commitment transcription factors IRF8, IRF4 and RORC1. IRF8 and IRF4 promote monocytes/macrophage and hinder granulocyte differentiation, whereas RORC1 is required for expansion of Ly6Chi monocytes and resolution of inflammation. These results reveal a role of the PD-1:PD-L1 pathway in the differentiation of lineage-committed myeloid progenitors to promote undifferentiated MDSCs and suppress effector monocytes/DCs. Switch of myeloid progenitor fate commitment might be a key mechanism by which PD-1 blockade mediates anti-tumor function.
Investigating the effect of anti-CTLA-4 on tumor-infiltrating effector T cells
Authors: Stone Erica Lyn , O’Brien Erin M 
Published: January 2023

Abstract
Despite the relative success of checkpoint inhibitors, a majority of patients fail to respond to these therapies. Thus it is necessary to understand mechanisms of resistance in order to extend the benefits of immunotherapy to more patients. Checkpoint inhibitors are designed to prevent the interaction of immune checkpoints with their ligands, thereby allowing the body’s anti-tumor immune response to be reactivated. Recently, it has been appreciated that anti-CTLA4 therapies, including Ipilimumab, have a second mode of action. They can mediate antibody-dependent cell-mediated cytotoxicity (ADCC). This leads to death of cells bound by anti-CTLA4. While CTLA4 is largely intracellular, it is expressed on the surface of tumor-infiltrating T regulatory cells (Tregs). Thus anti-CTLA4-mediated ADCC can deplete tumor-infiltrating Tregs. In mice, ADCC of tumor-infiltrating Tregs is required for anti-CTLA4 efficacy. Likewise, Ipilimumab can mediate Fc-receptor dependent depletion of human Tregs. We have found that a portion of effector T cells infiltrating mouse and human tumors express surface CTLA-4 at levels similar to tumor-infiltrating Tregs. We further find that this portion of tumor-infiltrating effector T cells is likely to include tumor-reactive T cells. We will discuss the possibility that anti-CTLA4 can lead to Fc-receptor-dependent depletion of effector T cells and the implications for therapy resistance.
The MLL1-H3K4me3 Axis-Mediated PD-L1 Expression and Pancreatic Cancer Immune Evasion
Authors: Lu Chunwan , Paschall Amy V , Shi Huidong , Savage Natasha , Liu Kebin 
Published: January 2023

Abstract

Background
Pancreatic cancer is one of the cancers where anti-PD-L1/PD-1 immunotherapy has been unsuccessful. The aim of this study is to elucidate the underlying mechanism of PD-L1 expression regulation in the context of pancreatic cancer immune evasion.

Methods
Pancreatic cancer mouse models and human specimens were used to determine PD-L1 and PD-1 expression and cancer immune evasion. Histone methyltransferase inhibitors, RNAi and overexpression were used to elucidate underlying molecular mechanism of PD-L1 expression regulation. All statistical tests were two-sided.

Results
PD-L1 is expressed in 60–90% of tumor cells in human pancreatic carcinomas and in 9 of 10 human pancreatic cancer cell lines. PD-1 is expressed in 51.2–52.1% of pancreatic tumor-infiltrating cytotoxic T lymphocytes (CTLs). Tumors grow statistically significantly faster in FasL-deficient mice than in wild type mice and when CTLs are neutralized. H3K4 trimethylation (H3K4me3) is enriched in the cd274 promoter in pancreatic tumor cells. MLL1 directly binds to the cd274 promoter to catalyze H3K4me3 to activate PD-L1 transcription in tumor cells. Inhibition or silencing of MLL1 decreases H3K4me3 level in the cd274 promoter and PD-L1 expression in tumor cells. Accordingly, inhibition of MLL1 in combination with anti-PD-L1 or anti-PD-1 antibody immunotherapy effectively suppresses pancreatic tumor growth in a FasL- and CTL-dependent manner.

Conclusions
The Fas-FasL/CTLs and the MLL1-H3K4me3-PD-L1 axis play contrasting roles in pancreatic cancer immune surveillance and evasion. Targeting the MLL1-H3K4me3 axis is an effective approach to enhance the efficacy of checkpoint immunotherapy against pancreatic cancer.
PD-1 blockade induces phosphorylated STAT3 and results in an increase of Tregs with reduced suppressive function
Authors: Woods David M , Ramakrishnan Ruap , Sodré Andressa L , Berglund Anders , Weber Jeffrey 
Published: January 2023

Abstract
PD-1 blockade has remarkable response rates in the treatment of melanoma; however, many patients fail to respond, and biomarkers and mechanisms of response remain unknown. We investigated the roles of Tregs, a population of immunosuppressive T-cells, in patient response to nivolumab. Tregs had a decrease in suppressive function in patients with positive outcomes (p=0.03), but not in patients with negative outcomes. Patients with no evidence of disease (NED) displayed increased percentages of Tregs post-nivolumab (p=0.04), but relapsing patients did not. RNA-seq analysis revealed genes significantly changed after treatment were distinct between Tcons and Tregs (~13% overlap) and between NED and relapsing patient Tregs (~2% overlap). Pathway analysis showed an increase in proliferation associated pathways in NED patient Tregs, but not relapsing patients. We found increased phosphoSTAT3 (pSTAT3) expression in Tregs from patients with positive outcomes (p=0.01), but not in patients with negative outcomes. Mechanistically, in vitro culturing of T-cells with αPD-1 resulted in increases in pSTAT3 expression (p=0.03) and increased percentages of Tregs (p=0.001). Culturing with αPD-1 also enhanced production of IL-10 (p=0.02), and the addition of a STAT3 inhibitor reduced the increases in IL-10 levels (p=0.01) and Treg percentages (p=0.01). The addition of an IL-10 neutralizing antibody also reduced the increased Tregs resulting from αPD-1 (p=0.01). These results support a model in which PD-1 blockade increases pSTAT3 expression leading to enhanced IL-10 production and Treg percentages, suggesting that pSTAT3 induction and reduced suppressive function are biomarkers of melanoma patient response to nivolumab.