bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intestinal IL-17R signaling modulates commensal microbiota by regulating expression of Nox1 and Pigr
Authors: Kumar Pawan , Monin Leticia , Castillo Paticia , Elsegeiny Waleed Abdel Wahab , Horne William , Eddens Taylor John , Good Misty , Bibby Kyle , Montelaro Ronald , Metzger Dennis W , Gulati Ajay , Kolls Jay K 
Published: January 2023

Abstract
Despite recent advances in understanding the role of IL-17 in host immunity, its role in regulating enteric immune responses as well as its impact on the commensal microbiome has not been well studied. To further understand this, we have generated intestinal epithelial cell specific IL-17R knockout mice.
Our data shows that global and intestinal epithelial cell specific Il17r−/− mice have overgrowth of segmented filamentous bacteria (SFB), suggesting a critical role of IL-17 signaling in SFB colonization. Higher SFB colonization in Il17rafl/fl x villin cre+ mice resulted in expansion of IL-17A and IL-22 producing Th17 cells. The expansion of SFB was also confirmed by 16S rRNA. Furthermore this analysis also showed higher abundance of S24-7 and the Clostridiales family in Il17rafl/fl x villin cre+ mice. RNA sequencing data from the distal small intestine of SFB-colonized Il17ra−/− and Il17rafl/fl x villin cre+ mice revealed substantial reduction of Nox1 (an apical NADPH oxidase) and Pigr genes. Mouse and human primary intestinal organoid culture further confirmed a direct role of IL-17 in regulating Nox1 and Pigr expression. Reduced Nox1 expression correlated with significant reduction in H202 levels in the terminal ileum of Il17rcfl/fl x villin cre+ mice. Furthermore, Nox1−/− and IgA−/− mice showed a higher degree of SFB colonization in the feces and terminal ileum as compared to cohoused control WT mice. We have evidence that Il17rafl/fl x villin cre+ mice are more susceptible to autoimmune inflammation.
Collectively, our data indicate IL-17R-dependent intestinal signaling controls commensal bacteria by regulating the expression of Nox1 and Pigr which regulates lumenal H202 and sIgA concentrations respectively.
Short chain fatty acids regulation of neutrophil production of IL-10
Authors: Chen Feidi , Wu Wei , Cong Yingzi 
Published: January 2023

Abstract
Despite questions regarding the role of microbiota in regulation of host immune responses within the intestines, evidence suggests that in the context of disease and autoimmunity bacterial metabolites might impact the systemic immune response. Otherwise indigestible carbohydrates are metabolized into short-chain fatty acids (SCFAs) by gut bacteria. SCFAs have been shown to inhibit intestinal inflammation in experimental colitis through regulation of mucosal T cells and macrophages. Recently, neutrophils have been shown to regulate intestinal homeostasis and the pathogenesis of IBD, however, how SCFAs may regulate neutrophil function is unclear. In this study, we demonstrate that SCFA differentially regulate neutrophil cytokine production. Of the three major SCFAs butyrate, acetate, and propionate, only butyrate down-regulated neutrophil IL-10 production. We further showed that butyrate-inhibition of neutrophil IL-10 is independent of GPR43, in that butyrate also inhibited IL-10 production in GPR43 deficient neutrophils. We recently showed that IL-23 induced neutrophil production of IL-17 and IL-22 in a mTOR dependent manner; however, butyrate did not affect IL-23-induced IL-17 and IL-22 production in neutrophils. Taken together, our data indicates that microbiota metabolites differentially regulate neutrophil cytokine production.
Aryl hydrocarbon receptor activation fails to alter Cholera toxin-specific fecal IgA secretion after oral immunization in mice.
Authors: Dekrey Gregory K , Gawronska Elleanour , Metten Madeline 
Published: January 2023

Abstract
Secretory IgA plays a critical role in neutralizing enteric toxins and protecting against some intestinal pathogens. In mice, activation of the aryl hydrocarbon receptor (AhR) with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been shown to suppress antigen-specific systemic IgM and IgG responses, whereas the impact of AhR activation on mucosal IgA responses is less clear. The goal of this study was to determine if TCDD exposure could alter fecal levels of antigen-specific IgA after oral immunization. Female C57Bl/6 mice were administered peanut oil (vehicle) or TCDD (10 μg/Kg, po), and, on the following day, each animal was immunized with whole Cholera toxin (CT, 10 μg, po) with two subsequent immunizations being given at 10 day intervals. Antibody levels were measured by ELISA in fecal extracts each week (normalized to protein) and in serum at termination (week 4). We found that total serum IgA levels were significantly decreased (P &lt; 0.05) in TCDD-treated animals, relative to controls. In contrast, no change in total fecal IgA levels was observed in TCDD-treated mice at any time point measured (weeks 1–4). Interestingly, no change in CT-specific serum IgA levels was observed in TCDD-treated mice, whereas TCDD exposure significantly decreased (P &lt; 0.05) CT-specific serum IgG1 and IgM levels. In Feces, as in serum, no change in CT-specific IgA levels was found in TCDD-treated mice at any time point measured (weeks 3–4). These results suggest that intestinal IgA responses are not adversely impacted by TCDD exposure, an observation that markedly contrasts with the suppression of systemic antibody responses widely seen in animals after TCDD treatment.
Human B cell responses to cholera infection
Authors: Wrammert Jens , Kauffman Robert , Bhuiyan Taufiqur , Rashu Rasheduzzaman , Mayo-Smith Leslie , Khan Ashraful Islam , Chowdhury Fahima , Ryan Edward , Qadri Firdausi , Harris Jason 
Published: January 2023

Abstract
Vibrio cholerae causes an acute diarrheal disease estimated to lead to 3 to 5 million cases of cholera and over 100,000 deaths annually. Vaccine-induced immunity rapidly wanes and provides only partial protection. In contrast, natural infection induces 90–100 % protection for up to 10 years. However, it remains unknown why current vaccines are markedly less effective. Understanding mucosal humoral immunity and mechanisms regulating homing of immune cells to mucosal tissues in humans is of key importance, not only for V. cholerae infection, but for many other pathogens with a mucosal route of infection. To better understand the immune response induced by natural infection, we have characterized acute plasmablast responses in infected adults at the ICDDR, b in Dhaka, Bangladesh. To understand these potent responses in more detail we have generated a panel of 150 human monoclonal antibodies from plasmablasts isolated from six patients. These antibodies have provided a unique insight into the dynamics and variability of the functional characteristics of antibody responses to cholera, in terms of toxin neutralization, direct vibriocidal activity, the ability to induce bacterial agglutination or interfere with bacterial propagation. Furthermore, the fine specificity of these antibodies raise interesting questions about the longevity of B cell memory against bacterial polysaccharides. These studies provide unprecedented insight into heterogeneity of the acute plasmablasts responses to cholera, the ability to provide long-lived immunity after infection is resolved and the antigenic specificity of the BCR, at a single cell level. These findings may instruct future vaccine development for this important human pathogen.
Systemic dysregulation of cellular immune responses to H1N1 infection during pregnancy
Authors: Littauer Elizabeth Q , Esser E. Stein , Antao Olivia Q , Williams Dahnide T , Compans Richard W , Skountzou Ioanna 
Published: January 2023

Abstract
The 2009 H1N1 flu pandemic demonstrated that pregnant women infected with influenza were at risk for severe respiratory distress and premature-rupture-of-membranes (PROM), leading to high incidence of hospitalization, preterm births and small for gestation age (SGA) neonates. We utilize a syngeneic BALB/c pregnant mouse model which recapitulates clinical phenotypes shown during influenza infection of pregnant women. Pregnant mice sublethally infected (0.5xLD50) with pandemic H1N1 A/California/07/09 showed higher viral titers and delayed viral clearance relative to non-pregnant mice, and increased incidence of stillbirths and SGA offspring. Lymphocytes isolated at days 7 and 14 from lungs and spleens of infected pregnant and non-pregnant female mice were analyzed for H1N1 A/Ca/07/09 specific IL-4 and IFN-γ responses. Pregnancy delayed influenza-specific cytokine secretion at the site of infection, indicating systemic dysregulation of anti-viral responses. Lymphocytes from draining mediastinal lymph nodes, spleens and lungs were used to quantify activation of B cells in germinal centers (GC), maturation into antibody secreting cells and memory B cells, and mucosal homing to lung tissue following infection. Pregnancy decreased maturation of GC+ B cells in the spleen and migration of plasma cells from the spleen to the lungs. Infected pregnant mice generated equivalent serum influenza-specific neutralizing antibody titers and increased IgA antibody secreting cells (ASC) in the lungs 6 weeks post-infection relative to infected non-pregnant mice, indicating a potential role in pregnancy favoring the development of mucosal immunity in response to prolonged viral exposure.
TCR immune profiling reveals intrinsic clonal selection of tissue resident memory T cells in genital mucosa during human HSV-2 infection
Authors: Zhu Jia , Bedford Trevor , Williams Anthony , Laing Kerry , Jing Lichen , Li Alvason , Diem Kurt , Johnston Christine , wald Anna , Koelle David M , Corey Lawrence 
Published: January 2023

Abstract
Tissue resident memory (TRM) T cells persist in human genital mucosa long after healing of herpes simplex virus 2 (HSV-2) infection. These TRM T cells provide effective protection to rapidly contain reactivating viruses before clinical manifestation occurs, making them excellent candidates for developing novel approaches to controlling HSV2 reactivation. To understand the dynamics of TCR repertoire and the kinetics of T cell clones during disease resolution, sequential biopsies were obtained in three individuals at the time of active lesions and 2, 4, 8 weeks post-healing, and were subjected to high-throughput sequencing of the TCRβ chain hypervariable CDR3 region. Oligoclonal immune profiles were evidenced in all biopsy tissues with a few TCR sequences constituting 30–40% of the TCR repertoire. The usage pattern of various TCRVB genes was similar among tissues of active lesion and post healed biopsies of the same subject. However, the TCRVB usage differed dramatically between the TCR repertoire in tissues and those of PBMC derived HSV-2 specific T cells taken at the same time point within each individual. This difference was more extreme when evaluating the TCR sequences that selectively persisted in post-healing biopsies. The top ten predominant TCR sequences persisting in tissues during clinical quiescence 4–8 weeks post healing did not overlap with HSV-2 specific T cells isolated from PBMC. These data suggest a TCR intrinsic property might dictate the TRM repertoire, and that the antigen specificity of TRM might differ considerably from circulating HSV-2 specific T cells.
The establishment of a photoactivatable antigen system and its applications in B cell probing and B cell receptor sorting studies
Authors: Wang Jing , Liu Wanli 
Published: January 2023

Abstract
BCR and antigen recognition triggers a series of responses resulting in B cell activation and proliferation. It has been difficult to study the initiation of B cell activation due to its dynamic and fast nature. Here, we constructed a photo-activatable BCR ligand, caged 4-hydroxy-3-nitrophenyl acetyl (caged-NP) antigen that is biologically inert, and only becomes antigenic upon photo-activation with 405 nm photons. This photo-activatable antigen system provided a precisely controllable trigger point for B cell activation. This system in combination with live cell and single molecule imaging techniques by total internal reflection fluorescence microscopy has enabled us to illuminate the unidentified B cell probing termination behaviors and the precise BCR sorting mechanisms in the initiation of B cell activation. B cells in contact with the caged-NP exhibited probing behaviors as defined by the unceasing extension of membrane pseudopods in random directions, which is likely used by B cells to search for antigens in the proximal microenvironments. Such probing behaviors are cell intrinsic with strict dependences on F-actin remodeling but not tonic BCR signaling. B cell probing behaviors were terminated as quickly as 1–2 sec after photoactivation, suggesting probing termination response is sensitive and specific to BCR engagement. The termination of B cell probing was concomitant with the accumulation response of the BCRs into the BCR microclusters. Lastly, single molecule imaging experiments demonstrated antigen-induced trapping of BCRs into the BCR microclusters as a fundamental mechanism for B cells to acquire antigens. Thus, a novel experimental approach was established for immune cell studies.
High Throughput Flow Screening Assays to Profile Cell-Mediated Killing
Authors: Luu Yen Kim , Liu Zhaoping , Duensing Thomas 
Published: January 2023

Abstract
While enhancing T-cell mediated killing of tumor cells is emerging as a successful therapeutic approach for a variety of cancers, improvements to these therapies are actively being sought. Traditional assays for monitoring cell-mediated killing are only capable of homogenous live/dead readouts for an entire sample. As an alternative platform for cell-mediated killing studies, IntelliCyt’s iQue Screener can identify multiple cell types in suspension and report multiple cell killing readouts in streamlined no wash assay formats. We demonstrate two example high throughput assays for cell-mediated killing using NK cells and chimeric antigen receptor (CAR) T-cells. Using the NK92 cell line as an effector cell and fluorescently encoded Jurkat cells as target cells, viability and Caspase 3 activation was determined for both Jurkat and NK92 cells in the same sample, and compounds that were generally cytotoxic to both cells could be identified. Specificity of the cell-mediated killing response was demonstrated using known signal transduction inhibitors including sunitinib, U73122, pp2, and wortmannin that would attenuate the NK cell killing activity, at a fixed target to effector cell ratio. In the CAR T-cell assay, efficacy of different CARs at targeting and killing a B-cell line (NALM-6) was profiled using multiplex readouts for cell health and secreted cytokines. Multiple cytokines including inflammatory markers and Granzyme B were quantified using bead-based ELISA on the same analysis platform. These application examples highlight the robustness and flexibility of the iQue Screener for performing multiplexed screening assays with cells and beads.
BIGG DATA: An accessible web portal for the analysis of immunologic repertoires.
Authors: Durrett Russell Eldon 
Published: January 2023

Abstract
The immune repertoire is an important resource for immunology research and for various clinical purposes. Technological advances over the past several years have led to an explosion of new techniques to capture the wealth of information contained in individuals’ Immunoglobulin and T-Cell Receptor repertoires, and large public datasets using these sequencing techniques have been made available in the last few years. However, a major challenge to understanding immune repertoire data is the high-level knowledge of computational infrastructure required to analyze these datasets, often requiring computationally-focused individuals to be recruited ad-hoc rather than simply being performed by the immunologists gathering the data. Herein, we have developed a simple, accessible web portal to aid in the analysis of these datasets. Our system allows users to bring their own raw datasets (in the form of FASTQ data), and utilize various popular, well-developed tools to derive VDJ-recombination annotations as well as to summarize statistical profiles of the full repertoire. This system provides an important, utilized resource that is employed by our lab for immunorepertoire analysis and is also available to the public in order to facilitate research in this area.
Computational analysis of epitope-specific T-cell repertoires.
Authors: Bradley Philip H , Fiore-Gartland Andrew , Hertz Tomer , Dash Pradyot , Thomas Paul 
Published: January 2023

Abstract
Experimental advances in flow cytometry, single-cell analysis, and high-throughput sequencing are leading to ever-increasing volumes of data on epitope-specific alpha/beta T-cell responses. Paired sequence data, in which the link between the alpha and beta chain sequences is retained, permit a more complete analysis than can be achieved with unpaired data: they allow reconstruction of molecular models for complete receptors, for example, and they enable a more precise assessment of TCR sharing across individuals. We are developing new algorithms for analyzing paired, epitope-specific TCR sequence data with the goal of investigating the mapping between TCR sequence and peptide-MHC recognition, using large, epitope-specific sequence datasets for model viral infections in mice. Our tools facilitate a variety of common repertoire analyses including landscape visualization (by multidimensional scaling or hierarchical clustering), CDR3 pattern detection, convergent evolution analysis, and detection of gene segment enrichment and alpha/beta pairing preferences. A null model for the rearrangement process allows us to assign significance scores to sequence motifs and patterns of TCR sharing across individuals. 3D structural data on TCR:pMHC complexes inform our clustering algorithms, and we use molecular modeling to aid in interpreting recurring TCR motifs. We are also pursuing machine learning approaches for selecting features predictive of binding. We believe these analysis and visualization tools represent an important first step toward developing predictive computational models of epitope recognition. We also expect that they may be useful to other researchers faced with large TCR repertoire datasets.
A scalable multiplex assay enabling assessment of T cell receptor specificity to hundreds of self- and pathogen-derived antigens
Authors: Klinger Mark , Taniguchi Ruth , Hu Joyce , Hayes Tim , Wittkop Tobias , Asbury Thomas , Moorhead Martin , Emerson Ryan , Sherwood Anna , Robins Harlan , Faham Malek 
Published: January 2023

Abstract
Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We previously developed and validated a novel multiplex assay (MIRA, or Multiplexed Identification of T cell Receptor Antigen specificity) that combines conventional immune monitoring techniques and TCR repertoire sequencing to assess T cell specificity to large numbers of query antigens. MIRA is a sensitive assay enabling detection of antigen-specific TCR clonotypes well below the limit of detection of conventional immune monitoring assays including flow cytometry and ELISPOT. Here we report the results from a scaled-up version of the assay using 270 different query peptide antigens (159 self- and 111 pathogen-derived). We identified &gt;500 TCR clonotypes at frequencies as low as 1 per million T cells that were specific to 41 query antigens from 6 healthy HLA-A*02-positive individuals. Most of the antigen-specific TCRs identified recognized one of 27 different peptides derived from a variety of pathogens including CMV, EBV, Flu, Rotavirus, HSV, mTB, WNV and HIV. A subset of antigen-specific TCRs recognized one of 14 different peptides derived from self including MART1, RCC, BCL-2, MAGE, STEAP1, KLK4, CAMEL and MOG. These data support the notion that escape and survival of self antigen-specific T cells occurs without causing overt autoimmunity in healthy individuals. We show here that MIRA can be used to assess TCR specificities to hundreds of query antigens simultaneously. The assay is highly scalable and can be easily modified to accommodate thousands of additional query antigens. This technology may be used to monitor T cell specificity to antigens relevant to infection, autoimmunity and cancer.
Profiling autoreactive IgA antibodies against 124 autoantigens in Systemic lupus erythematosus, systemic scleroderma and idiopathic inflammatory myositis
Authors: Li Quanzhen , Zhao Hongjun , Yan Mei , Zuo Xiaoxia 
Published: January 2023

Abstract
Systemic lupus erythematosus (SLE), systemic scleroderma (SSc) and idiopathic inflammatory myositis (IIM) are systemic autoimmune diseases characterized by existing of circulating autoantibodies (AutoAbs) to a broad range of self-antigens. In this study, we measured the serum levels of IgA AutoAbs against 124 self-antigens in a cohort of 128 SLE, 73 SSc, 75 IIM and 140 healthy controls (HC) using autoantigen microarrays. Our result indicated that IgA AutoAbs were highly prevalent in SLE and SSc compared with IIM and NC. 58.4% SLE and 41.7% SSc have 5 or more IgA AutoAbs compared with 16% in IIM and 14.1% in NC. 9 DNA specific IgA AutoAbs were significantly elevated in SLE including anti-dsDNA (54.7%), anti-ssDNA (51.1%), and anti-genomic DNA (46%). SSc showed significant increase of 32 IgA AutoAbs with the highest reactivity to Scl-70 (55.6%). 3 IgA AutoAbs significantly increased in IIM are Jo-1 (20%), Muscarinic receptor (8%) and B2-microglubulin (6.7%). Significant correlation was observed between IgA and IgG isotypes on most AutoAbs. 3 IgA autoAbs (anit-gDNA, anti-C1q and anti-dsDNA) positively correlated with SLEDAI Score, but only anti-C1q was significantly elevated in lupus nephritis. 14 anti-nuclear IgA AutoAbs negatively correlated with serum complement C3 and/or C4 levels.
This is the first study of large scale profiling of IgA AutoAbs in 3 systemic autoimmune diseases. Our study indicated that autoreactive IgA antibodies against different nuclear components are highly prevalent in SLE and SSC patients. IgA AutoAbs could be used as biomarkers for diagnosis and prognosis of systemic autoimmune diseases, and the molecular mechanisms underlining IgA AutoAbs production in systemic autoimmune diseases warrant further study