bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of commensal microbiota on CD8 T cell response to Listeria monocytogenes infection
Authors: Cho Kyungjin , Surh Charles D 
Published: January 2023

Abstract
Commensal microbiota is composed of trillions of microorganisms including fungi, protozoans, viruses and bacteria, which have co-evolved with the host immune system. In particular, the gut is the largest reservoir of microorganisms that are involved in dynamic interaction with the immune system, including maintaining intestinal homeostasis, induction of several metabolic pathways, and protection from pathogenic microbes. To better understand the mechanisms involved microbiota-mediated protection from the pathogenic bacteria, we have studied oral infection of germ-free (GF) mice with a strain of Listeria monocytogenes (L. monocytogenes) that has been engineered to efficiently infect the intestinal epithelial cells of the mouse. We found that GF mice are more susceptible to orally administrated L. monocytogenes than conventional SPF mice, with an increased Listeria burden in the mLN, small intestine and feces. In addition, in the infected GF mice, L. monocytogenes-specific CD8 T cells were vigorously activated and induced to differentiate into memory precursor effector cells (MPECs) and tissue resident memory (CD69+ CD103+) T cells in the intestinal epithelium at a faster rate than in infected SPF mice. L. monocytogenes-specific CD8 T cells in GF mice also secrete more effector cytokines, such as interferon-γ and tumor necrosis factor-α. The mechanisms by how commensal microbiota confers resistance to infection by L. moncoytogenes in SPF mice is currently under investigation.
The APC capture: rapid identification of target CD8+ T cell epitopes by flow cytometry
Authors: Roesler Alexander S , Krishna Sri , Qiu Ji , LaBaer Joshua , Anderson Karen S. 
Published: January 2023

Abstract
Identifying immunoreactive CTLs by current technologies (cytokine secretion, intracellular cytokine, cytolytic release, ELISPOT, and MHC tetramer assays) is often difficult when probing multiple target antigens. We developed a rapid flow cytometry assay to detect targeted IFN-γ secretion by CD8+ T cells using commonly available reagents. PBMCs were obtained from HLA-A2+ healthy donors, and CD8+ and CD8− fractions were purified. FluMI-specific T cells were confirmed by HLA-A2/M1 tetramer, and pooled CEF peptides (a mixture of CMV-, EBV-, and Flu-specific HLA class I epitopes) immunoreactivity was shown by IFN-γ ELISPOT. The CD8+ fraction was rested for 5 days in IL-2 (20 U/ml) and IL-7 (5 ng/ml). In parallel, autologous APCs were generated from the CD4− CD8− fraction using recombinant CD40L (100 ng/ml), IL-4 (5ng/mL), and cyclosporin A (1 μg/ml). After 5 days, the APC culture was &gt;70% CD19+ CD86+ HLA-DR+ activated B cells. The APCs were pulsed with DMSO control or CEF peptide pool (10ug/mL) overnight, labeled with commercial IFN-γ catch (Miltenyi Biotec), washed, and co-cultured for 6–8 hours with purified CD8+ T cells. APC-surface-bound IFN-γ was detected by flow cytometry. CEF-pulsed APCs showed robust presence of surface-captured IFN-γ (ranging from 14%–56.8%) compared to DMSO-pulsed APCs (ranging from 1.6%–4.5% IFN-γ+). APC IFN-γ capture was sensitive even at low effector-target ratios (as low as 1:1) and was applicable to the artificial APC K562/A2. In conclusion, we have demonstrated epitope-reactive CD8+ T cell detection of target cells by capturing IFN-γ onto APCs. We are evaluating capture of other cytokines and cytolytic effectors on target APCs in response to CD8+ recognition.
BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
Authors: Barski Artem , Kartashov Andrey 
Published: January 2023

Abstract
Development of next generation sequencing (NGS) has revolutionized molecular biology by enhancing our ability to perform genome-wide studies. However, due to the need for bioinformatics expertise and the sheer size of resulting datasets, use of these technologies is still beyond the capabilities of many laboratories. Here we present BioWardrobe, a platform that allows storing, visualizing and analyzing epigenomics and transcriptomics NGS data using a biologist friendly web-based graphical user interface without the need for programming expertize. BioWardrobe can be installed on consumer class hardware within an institutional local network. Analysis capabilities include predefined pipelines that allow the user to download data from either institutional core facility or public databases, perform quality control, map reads, and visualize data on a built-in mirror of the UCSC genome browser. Reads Per Kilobase per Million mapped (RPKMs) are calculated for RNA-Seq, and islands of enrichment are identified for ChIP-Seq and similar datasets. Advanced analysis capabilities include differential gene expression and binding analysis, and creation of average tag density profiles and heatmaps. BioWardrobe package and documentation is available at http://biowardrobe.com.
Column-free magnetic enrichment of pDCs yields significant contamination with DNA-containing dead cells that affect the activation status of the isolated cells
Authors: Richter Anne , Morrissey-Wettey Frank Ralf , Angerer Caroline , Kurig Stefanie , Dzionek Andrzej 
Published: January 2023

Abstract
Despite their role in the induction of adaptive immune responses, plasmacytoid dendritic cells (pDC) play also a crucial role in innate immune defense by recognizing pathogen derived molecular patterns. Unmethylated CpG motifs of bacterial DNA bind specifically endosomal and lysosomal TLR9 in pDCs, thereby inducing secretion of type I IFN or proinflammatory cytokines and classical DC maturation, respectively. However, TLR9 also recognizes CpG motifs in vertebrate DNA of damaged cells as danger-associated molecular patterns (DAMPs) that activate pDCs.
For in-vitro research pDCs may be isolated by indirect magnetic cell separation using either Miltenyi Biotec’s column-based or a column-free system from other suppliers. Here we describe the influence of the isolation method on the functionality of the purified pDCs. In addition to the significantly better separation performance, our column-based method enriched 10- and 30-fold less DNA-containing dead cells and debris, respectively. Although both methods yielded pDCs with a comparable phenotype instantly after isolation, after 24h of culture without stimulation pDCs isolated with the column-free system appeared pre-activated as demonstrated by elevated expression of CD80, −83, −86 and HLA-DR and by significantly higher basal IFN-α secretion. Moreover, upon stimulation with CpG-B pDCs isolated with the column-free method induced extraordinary high amounts of IFN-α, whereas pDCs isolated with our system exhibited normal responses to CpG-A and CpG-B. These results clearly demonstrate that unspecific enrichment of dead cells and debris may significantly influence the activation status of the isolated pDCs and therefore affect the results of downstream applications.
VDJPipe: a pre-processing pipeline for immune repertoire sequencing data
Authors: Christley Scott , Levin Mikhail , Fonner John , Monson Nancy , Rounds William H , Rubelt Florian , Scarborough Walter , Scheuermann Richard H , Toby Inimary , Cowell Lindsay G 
Published: January 2023

Abstract
Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass of the data. These tasks include base composition statistics, read quality statistics, numerous quality filters, homopolymer filtering, length and nucleotide filtering, barcode demultiplexing, 5′ and 3′ PCR primer matching, and filtering of duplicate reads. VDJPipe utilizes a “pipeline” approach whereby multiple processing steps are described in a sequential workflow, with the output of each step passed as input to the next step. The workflow is flexible enough to handle the complex barcoding schemes used in many immunosequencing experiments. VDJPipe is an integral part of the VDJServer (http://www.vdjserver.org) web resource for performing immune repertoire analysis and can be accessed via the VDJServer Software page.
Measuring frequency and quality of pathogen-specific T cells
Authors: Anikeeva Nadia , Grosso Dolores , Flomenberg Neal , Sykulev Yuri 
Published: January 2023

Abstract
The frequency and functional activity of pathogen-specific T cells reflect the effectiveness of immune responses. We have developed an assay to measure the frequency and efficacy of antigen-specific CD8 T cells. The assay measures changes of intracellular Ca2+ in real time by fluorescent microscopy in individual CD8 T cells, which are immobilized on a glass surface to form a monolayer enabling the cells to present cognate peptides to each other. The T cells were labeled with Ca2+ dependent fluorophore, and intracellular fluorescence in the cells was analyzed before and after stimulation with specific antigenic peptides. Subtraction of the fluorescent intensity measured prior and after the stimulation revealed responding T cells and the kinetics of intracellular Ca2+ accumulation. The proposed assay permits comparison of the same cell before and after stimulation providing a significant increase in the sensitivity and utility of the assay. We found that as little as 3–5 responding T cells among 1×104 CD8 T cells could be reliably detected and that as much as 100 T cells with different specificities could be identified in a single round of analysis. We utilized the assay to characterize the frequency and quality of human cytomegalovirus-specific CD8 T cells from peripheral blood of healthy donors and patients who underwent haploidentical stem cell transplantation. The data revealed potential diagnostic and prognostic values of the proposed assay.
Diagnostic for assessing NKT cell function in cancer patients
Authors: Derakhshandeh Roshanak , Webb Tonya J 
Published: January 2023

Abstract
Significant efforts have been invested into harnessing the therapeutic potential of the immune system for the treatment of cancer. Natural killer T (NKT) cells play a critical role in anti-tumor immunity. However, NKT cells are approximately 50% lower in cancer patients compared to healthy donors of the same age and gender. Thus, prior to initiating immunotherapy, a specific and highly sensitive assessment of immune cell function should occur; yet, no such assay is currently available. Our lab has developed a novel cell-based molecular diagnostic for quantitation of a patient’s NKT cell activity by monitoring IFN-γ induction utilizing qPCR post activation with CD1d-based artificial antigen presenting cells (aAPCs). In this study we sought to assess NKT cell function in healthy donors and cancer patients in order to investigate the potential of NKT cell-based immunotherapeutic strategies. We assessed NKT cell function in 22 healthy donors (HD), 30 breast cancer patients (BCP), and 50 lymphoma patients (LP). The aAPC-qPCR method was more sensitive than flow cytometry and ELISA. We detected NKT cell function in 81% HD, 66% BCP, and 44% LP. In contrast, total T cell function was observed in 91% HD, 90% BCP, and 74% LP. These data suggest that NKT cell-based immunotherapeutic strategies may be more effective in specific cancer types. Collectively, these data demonstrate the need for assessing baseline immune function prior to the initiation of immunotherapy.
Characterization of a small molecule IRAK4 kinase inhibitor for the treatment of autoimmune and inflammatory diseases
Authors: Lamagna Chrystelle , Chan Meagan , Yi Sothy , Young Chi , Frances Roy , Siu Stacey , Braselmann Sylvia , Payan Donald G , McMurtrie Darren , Kelley Ryan , Heckrodt Thilo , Yen Rose , Chen Yan , Li Hui , Singh Rajinder , Park Gary , Masuda Esteban , Taylor Vanessa 
Published: January 2023

Abstract
IRAK4 is a key protein kinase in immune cells. It is responsible for initiating MyD88-dependent signaling from most Toll-Like Receptors (TLR) and Interleukin-1 Receptors (IL-1R), resulting in downstream production of pro-inflammatory cytokines. Hence, inhibitors of IRAK4 kinase activity represent valuable therapeutic tools to treat cytokine-driven autoimmune and inflammatory diseases. Through cell-based screening, we identified potent small molecule IRAK4 kinase inhibitors that block TLR4- and IL-1R-induced cytokine production with potencies less than 100nM. Our inhibitors exhibit good selectivity against a broad panel of kinases. In vivo, our lead compound decreases serum IL-6 in an acute mouse model of IL-1beta-induced cytokine release, demonstrating excellent pharmacokinetics properties. In addition, our IRAK4 inhibitor blocks monosodium urate crystals-induced peritonitis in mice, reduces paw swelling in the chronic rat model of collagen-induced arthritis, as well as the clinical score and overall inflammatory phenotype of mice in the imiquimod-induced psoriasis model. The in vitro and in vivo characterization of our lead candidate is promising and confirms IRAK4 as an attracting therapeutic target for the management of cytokine-driven diseases.
NALP1 inflammasome activation in adjuvant arthritis rats is a novel therapeutic target of carboxyamidotrizole in the treatment of rheumatoid arthritis
Authors: Zhu Lei , Li Juan , Ye Caiying 
Published: January 2023

Abstract

BACKGROUND AND PURPOSE
Pro-inflammatory cytokines play an important role in rheumatoid arthritis (RA) and their production is mainly regulated by NF-κB and inflammasomes. Carboxyamidotrizole (CAI) has been reported to exhibit potent anti-inflammatory activities by decreasing cytokines. Therefore, we investigated NALP inflammasomes in the synoviums of a rat RA model, and explored the therapeutic effects of CAI on RA model and the involvement of inflammasomes relative pathways in the actions of CAI.

EXPERIMENTAL APPROACH
The anti-arthritic effects of CAI were assessed in rat adjuvant arthritis (AA) model. NALP1 and NALP3 inflammasomes, nuclear factor (NF)-κB pathway, and pro-inflammatory cytokines levels were determined.

RESULTS
CAI administration significantly decreased arthritis index, improved radiological and histological manifestation, and reduced synovial IL-1β, IL-6, IL-18 and TNF-α levels in AA rats. As compared to the normal rats, the level of 70 kDa NALP1 isoform was significantly up-regulated, NALP3 was down-regulated, and the levels of 165kDa NALP1 isoform and the adaptor protein ASC were unchanged in AA synoviums. CAI reduced 70kDa NALP1 isoform and restored NALP3 level in synoviums of AA rats. And CAI inhibited caspase-1 activation in AA synoviums, although it did not directly inhibit the enzymatic activity in vitro. In addition, CAI reduced p65 NF-κB subunit expression and IκBα phosphorylation and degradation in AA rats.

CONCLUSION
NALP1 inflammasome was activated in arthritic synoviums, which might be a novel therapeutic target for RA. CAI may have therapeutic value in RA by inhibiting the activation of NALP1 inflammasome and NF-κB and by decreasing pro-inflammatory cytokines.
Novel mechanism of action of Anti-malarial drugs in the inhibition of Type I interferon production
Authors: An Jie , Woodward Joshua J , Minie Mark , Peng Yufeng , Sasaki Tomikazu , Elkon Keith B 
Published: January 2023

Abstract
Anti-malarial drugs (AMD) such as Hydroxychloroquine (HCQ) and Quinacrine (QC) are effective in the treatment of skin rash and arthritis in systemic lupus erythematosus (SLE). However which mechanism(s) are responsible for their beneficial action is uncertain. Type I interferon, (IFN-I) is strongly implicated in the pathogenesis of SLE and ‘interferonopathies’ such as Aicardi-Goutieres Syndrome (AGS). A new DNA activated IFN-I pathway, cyclic GMP-AMP (cGAMP) synthase (cGAS), was recently discovered and linked to AGS and mouse models of Lupus.
In silico screening of drug libraries identified several antimalarial drugs (AMD) which could potentially inhibit cGAS activity by interacting with cGAS/DNA dimer complex. Electrophoretic Mobility Shift Assay revealed that AMD disrupted the double stranded DNA-cGAS complex in a dose dependent manner. These AMD also inhibited IFN-I expression in THP1 cells transfected with dsDNA and in 293T cells transfected with cGAS/STING plasmids validating that cGAS is a target of AMD. We synthesized several new AMD. One of these compounds, X6, had excellent water solubility and cell penetration. X6 localized to the cytosol and had a lower toxicity profile compared to QC. Biochemical and cellular assay revealed that X6 was a more potent inhibitor of IFN-I production than HCQ.
Our studies identify new DNA sensor cGAS as a target of AMD activity, which provide a novel mechanism of action of these AMD. We have synthesized new AMD like drugs that are also able to inhibit cGAS as well as Toll pathways. These drugs could be beneficial for the treatment of AGS and/or Lupus.
Interferon-γ signaling inhibition by a suppressor of cytokine signaling-1 (SOCS-1) mimetic peptide ameliorates lupus pathology in a spontaneous mouse model.
Authors: Collins Teresa D. , Lam Brandon K. , Mohamed Zaynab Sidi , Mishra Shiwangi , Larkin Joseph 
Published: January 2023

Abstract
Cytokine-mediated dysregulation of the Jak/STAT pathway is closely associated with systemic lupus erythematosus (SLE) onset and progression. In the MRLlpr/lprmouse model of spontaneous SLE, aberrant IFN-γ signaling is critical for onset and progression. Notably, Suppressor of Cytokine Signaling-1 (SOCS-1) is known to regulate proinflammatory cytokine production. We have previously shown that a peptide mimicking SOCS1 signaling (SOCS1-KIR) inhibited IFN-γ signaling and auto-inflammatory disease progression. SOCS1-KIR mimics the ability of native SOCS1 to inactivate signal cascade propagation by Jak2 and Tyk2. In this study we test the hypothesis that SOCS1-KIR administration will inhibit lupus pathology in MRLlpr/lpr mice. A 3x/week administration of SOCS1-KIR mediated a statistically significant reduction in lupus associated lymphadenopathy. Mechanistically, SOCS1-KIR inhibited the generation of IFN-γ+ CD8+ and IFN-γ+ CD4+ memory T lymphocytes in vivo and in vitro. Additionally, the mechanistic specificity of SOCS1-KIR was delineated through in vitro culturing experiments with a Jak/STAT agonist, which restored the generation of IFN-γ+ memory T lymphocytes. These data show that administration of a SOCS1-KIR peptide has the ability to limit lupus-associated pathology, in part through regulation of IFN-γ signaling. In addition, these data suggest that strategies targeting regulation of excessive Jak/STAT signaling such as, the use of SOCS1-KIR, should be considered as a therapeutic, due to its ability to dampen excessive cytokine help often observed in disease onset and progression.
Therapeutic blockade of immune complex-mediated glomerulonephritis by highly selective inhibition of Bruton’s tyrosine kinase.
Authors: Chalmers Samantha A. , Doerner Jessica L , Bosanac Todd , Khalil Sara , Smith Dustin , Harcken Christian , Dimock Janice , Der Evan B , Herlitz Leal , Webb Deborah , Seccareccia Elise , Feng Di , Fine Jay S , Ramanujam Meera , Klein Elliott , Putterman Chaim 
Published: January 2023

Abstract
Lupus nephritis (LN) is a potentially dangerous end organ pathology that affects upwards of 60% of SLE patients. Bruton’s tyrosine kinase (BTK) is important for B cell development, Fc receptor signaling, and macrophage polarization. In this study, we investigated the effects of a novel, highly selective and potent BTK inhibitor, BI-BTK-1, in an inducible model of LN in which mice receive nephrotoxic serum (NTS) containing anti-glomerular antibodies. Mice were treated once daily with vehicle alone or BI-BTK-1 (0.3–10 mg/kg, n=16/group), either prophylactically or therapeutically.
When compared with control treated mice, NTS-challenged mice treated prophylactically with BI-BTK-1 exhibited significantly attenuated disease which was dose dependent, as measured by proteinuria, serum creatinine, and serum BUN. Histological assessment confirmed marked renal protection in the BI-BTK-1 treatment groups. BI-BTK-1 treatment resulted in decreased recruitment of inflammatory monocytes from the splenic reservoir, and a decrease in infiltrating IBA-1+ cells, as well as C3 deposition, within the kidney. RT-PCR on whole kidney RNA and serum profiling indicated that BTK inhibition significantly decreased levels of LN-relevant inflammatory cytokines and chemokines. Renal RNA expression profiling by RNA-seq revealed that BI-BTK-1 dramatically modulated pathways related to inflammation and glomerular injury. Importantly, when administered therapeutically, BI-BTK-1 reversed established proteinuria and improved renal histopathology.
Our results highlight the important role for BTK in the pathogenesis of immune complex-mediated nephritis, and BTK inhibition as a promising therapeutic target for LN.
Tumor antigen specific Treg from the bone marrow migrate towards increased S1P and CCL2 gradients established in the blood of breast cancer patients
Authors: Rathinasamy Anchana , Böhm Hans-Henning , Ge Yingzi , Dettling Steffen , Umansky Ludmila , Domschke Christoph , Herold-Mende Christel , Schütz Florian , Beckhove Philipp 
Published: January 2023

Abstract
High regulatory T cell (Treg) infiltration in breast tumors is associated with reduced survival. However, the source of tumor infiltrating Treg and signals underlying their migration from lymphoid organs to the tumor tissue remain elusive. We here demonstrate that pronounced Treg infiltration in human breast tumors correlates with a selective reduction of tumor antigen specifc Treg from the bone marrow. Furthermore using MHC-II tumor peptide tetramers we show that tumor antigen specific bone marrow Treg selectively express the egress receptor Sphingosine-1-phosphate receptor 1 (S1P1) and CCR2. S1P1 and CCR2 were upregulated in Treg upon TCR stimulation and triggered selective Treg but not Tcon cell migration in response to S1P and CCL2 gradients between bone marrow and blood which we found to be significantly increased in breast cancer patients. Taken together, our data suggest that tumor antigen specific Treg population in the bone marrow are mobilized into the blood after TCR stimulation through elevated S1P and CCL2 gradients in breast cancer patients.