bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of IKKα in STAT1 phosphorylation in antiviral signaling
Authors: Matsumiya Tomoh , Xing Fei , Shiba Yuko , Hayakari Ryo , Yoshida Hidemi , Imaizumi Tadaatsu 
Published: January 2023

Abstract
RIG-I-like receptors (RLRs) sense non-self RNA, inducing type I IFNs. Type I IFN promotes the expression of IFN-stimulated genes (ISGs), which requires the activation of STAT1. We previously reported that dsRNA induced STAT1 phosphorylation via a type I IFN-independent pathway in addition to the well-known type I IFN-dependent pathway. IKKα is involved in antiviral signaling induced by dsRNA in the RLR-mediated antiviral signaling; however, its role remains uncertain. In this study, we investigated the role of IKKα in RLR signaling, which is essential for antiviral innate immune responses in non-professional antigen-presenting cells, such as epithelial cells. Silencing of IKKα markedly decreased the level of IFN-β and STAT1 phosphorylation in response to dsRNA. However, the inhibition of IKKα did not alter the RLR signaling-mediated dimerization of IRF3 or activation of NFκB. These results suggest a non-canonical role of IKKα in RLR signaling. In addition, STAT1 phosphorylation was inhibited by IKKα knockdown in IFNAR-deficient cells. These results suggest that the dual regulation of STAT1 by IKKα in the RLR-mediated antiviral signaling.
Structural characterization of TLRs with novel agonists
Authors: Su Lijing , WANG YING , Morin Matthew D. , Jones Brian T. , Whitby Landon R. , Surakattula Murali M.R.P. , Huang Hua , Shi Hexin , Choi Jin Huk , Wang Kuan-wen , Moresco Eva Marie Y , Berger Michael , Zhan Xiaoming , Beutler Bruce , Boger Dale , Zhang Hong 
Published: January 2023

Abstract
Small molecule TLR4 and TLR2 agonists have been reported, but no structural data reveals their activation mechanism and detailed interactions with the TLRs. We have developed two small molecule agonists, Neoseptin-3 and Diprovocim, that activate TLR4/MD-2 and TLR1/TLR2 complexes, respectively, with exquisitely specific structure activity relationships. These two molecules bear no structural similarity to the natural ligands, lipopolysaccharide (LPS) and tri-acylated lipopeptide (Pam3CSK4). The crystal structures of Neoseptin-3 in complex with mouse TLR4/MD-2 and Diprovocim in complex with human TLR2 provide the first glimpse of how these TLRs bind to unconventional agonists, revealing unique and unexpected binding modes. Neoseptin-3 binds as an asymmetrical dimer within the hydrophobic pocket of MD-2, and induces an active receptor complex (a dimer of TLR4/MD-2) similar to that induced by lipid A. However, Neoseptin-3 and lipid A form different molecular contacts with TLR4/MD-2 to achieve receptor activation. Diprovocim forms a symmetrical dimer and interacts with the same hydrophobic pocket of TLR2 as Pam3CSK4, inducing homodimerization of TLR2 that has a different conformation than the active TLR1/TLR2 heterodimer. Diprovocim binds to TLR2 through an extensive intermolecular hydrogen bonding network that is not observed in the Pam3CSK4/TLR2/TLR1 structure. These two structures are now guiding us in optimization of TLR4/MD-2 and TLR1/TLR2 agonists and antagonists for clinical applications.
PKC driven DC differentiation utilizes the NFκB and ERK signaling pathways
Authors: Chavel Colin A , Lee Kelvin P 
Published: January 2023

Abstract
A key activator of adaptive immune responses is the dendritic cell (DC), which is a professional antigen presenting cell that has multiple roles in immunity from combating infections to recognizing tumor cells in order to activate T-cell mediated immune responses. Our lab has previously shown that the PKC isoform PKCβII is required for DC differentiation and that tumor derived factors can inhibit PKCβII expression, which in turn inhibits DC differentiation. However, how PKCβII induces DC differentiation and the pathways activated downstream of PKCβII remains to be characterized. In order to study this, we used the K562 cell line, which our lab and others have shown to be capable of differentiating into DCs with the addition of PMA, a known chemical activator of PKCβII. We have shown previously that PMA specifically activates PKCβII in K562 cells and not the other conventional PKC kinases. We found that both the ERK and NFκB pathways are activated by PKCβII in K562 cells. Chemical inhibition of either pathway yielded DCs with a reduced capacity to stimulate T-cell proliferation. Both the canonical and non-canonical NFκB pathways are activated by PKCβII and knockdown of PKCβII shows inhibition of both pathways. The canonical NFκB pathway is activated in an atypical fashion that has previously not been shown for PKCβII. PKC signaling also induced the activity of specific components of the ERK signaling cascade, including the modulation of downstream ERK effectors. Active Ras levels increased with PKC signaling, indicating GEF induced activity not previously associated with PKCβII. Taken together, these results show that PKCβII utilizes the NFκB and ERK signaling pathways and initiates these pathways in a novel manner to induce DC differentiation.
Expression pattern of TRIM genes in bovine macrophages stimulated with PAMPs
Authors: Toka Felix N , Dunaway Kiera , Mielcarska Matylda , Smaltz Felicia , Bossowska-Nowicka Magdalena 
Published: January 2023

Abstract
In mammals innate immune mechanisms form the first line of defence against invading pathogens. Detection of viruses early in infection relies on intracellular receptors that sense microbial molecular patterns, subsequently leading to gene transcription that eventually produces IFN type I and II. Type I and II IFNs act to prevent replication of viruses. Tripartite Motif-containing (TRIM) proteins belong to a superfamily of RING-domain E3 ubiquitin ligases. They represent a novel class of antiviral molecules involved in innate immunity. These enzymes function in a wide variety of important cellular processes, particularly in innate antiviral response mechanisms. We studied the expression profile of 46 TRIM genes in a bovine macrophage cell line BoMac using RT2 PCR. PAMPs were used to imitate 2 important groups of pathogens. PolyI:C was used in place of viral dsRNA, LPS was used in place of Gram-negative bacteria, Pam3CSK4 was used in place of Gram-positive and negative bacteria, PolyI:C-LyoVec was used in place of viral sRNA and CpG was used in place of bacterial and viral DNA. Of the 46 TRIM genes, only 8 bovine TRIM genes were upregulated following stimulation of BoMac with individual PAMPs. PolyI:C induce upregulation of TRIM21, TRIM25 and TRIM56. All three TRIMs are known for their antiviral activity in human cell lines and mice. Pam3CSK4 and LPS, both upregulated TRIM10. PolyI:C-LyoVec upregulated TRIM9, TRIM40 and TRIM55. TRIM40 is an anti-inflammatory molecule. CpG upregulated TRIM40 and TRIM29. High expression of TRIM29 is regarded as a poor prognostic in many tumors, but no antimicrobial role has been described yet for TRIM29. Data will be discussed in the context of antiviral role of TRIMs in bovine viral infections.
IL-21 maintains CD62L expression during NKT-cell ex vivo expansion and enhances antitumor activity of NKT cell therapy in vivo
Authors: Ngai Ho , Tian Gengwen , Courtney Amy N , Marinova Ekaterina , Huang Wei , Guo Linjie , Metelitsa Leonid S 
Published: January 2023

Abstract
Vα24-invariant Natural Killer T cells (NKTs) have potent antitumor properties and are being developed for cellular immunotherapy of cancer. Such therapy requires extensive ex vivo expansion of NKTs while preserving their longevity and function. In a recent report from our group, CD62L+ subset of NKTs has been shown to have longer persistence in vivo and stronger antitumor activity than CD62L− counterpart. However, the requirements for the preservation of CD62L+ NKTs during ex vivo expansion remain largely unknown. The gene expression analysis comparing CD62L+ and CD62L− NKTs revealed a significantly higher expression level of IL-21R mRNA in the former. FACS analysis confirmed the finding at the cell surface protein level. These led us to hypothesize that IL-21 preferentially supports CD62L+ NKTs. To test this hypothesis, we expanded primary human peripheral blood NKTs using in vitro stimulation with their cognate antigen, α-galactosylceramide. The culture was supplemented with IL-2, IL-21, or both cytokines. We found that in contrast to IL-2, IL-21 alone failed to support NKT-cell expansion. A combination of IL-2 and IL-21 led to similar absolute numbers of NKTs compared with IL-2 alone. However, the proportion of CD62L+ NKT-cell subset was significantly higher in the culture with IL-2/IL-21 combination compared with IL-2 alone after both primary and secondary expansions. Furthermore, after transfer to NSG mice, IL2/IL-21-expanded NKTs persisted significantly longer and had higher therapeutic efficacy in a lymphoma model compared with IL-2-expanded NKTs. Our results suggest that inclusion of IL-21 in the NKT-cell expansion protocol, which currently uses IL-2 alone, would increase antitumor potential of NKT cell therapy.
Identification of Virulence and Virulence Regulatory Factors in Escherichia coli using Dictyostelium discoideum as a Model Phagocyte
Authors: Snyder Michelle , Weichseldorfer Matthew , Lane Jorden , Kazmierski Rachel , Bains Harpal , White Theresa , Parker Dominique , Aklkharouf Nadim , Hemm Matthew 
Published: January 2023

Abstract
Escherichia coli is normally found as part of the human gut microbiota, however there exist a number of diarrheagenic strains. Identification and disruption of the virulence factors that promote infection could lead to a reduction in infection period of these E. coli strains and potentially of other species with similar means of virulence. To identify E. coli strains with altered virulence, we used Dictyostelium discoideum, a social amoeba that phagocytizes bacteria for nutritional purposes. Using random mutagenesis, we created mutant stocks of E. coli, each. These stocks were subjected to several rounds of phagocytosis by D. discoideum, enriching the culture and selecting for mutants resistant to intracellular killing. Resistant mutants were isolated and we found that some of the resistant strains showed increased survival when compared to the wild-type strain. Once isolated, the full genomes of our resistant mutant strains were sequenced using Illumina’s next generation MiSeq technology. While analyzing the sequencing data from these mutant strains, we found several potential genes of interest, including genes related to flagella, oxidoreductases, and acid resistance. We have begun to characterize genes of interest through various qualitative and quantitative assays using individual gene knockout strains. These studies should allow for identification of novel factors associated with regulation of virulence in E. coli. In addition, given that the development of mechanisms to resist D. discoideum predation may have contributed to the selection and maintenance of bacterial virulence factors against mammalian hosts, these studies may provide insight on the evolution of host-pathogen interactions.
Ccr7-dependent amelioration of renal tubular injury protects against infection-induced acute kidney injury
Authors: Break Timothy J. , Green Nathaniel G. , Kojima Hiroshi , Yuen Peter S. T. , Lee Chyi-chia “Richard” , Swamydas Muthulekha , Star Robert A. , Lionakis Michail S. 
Published: January 2023

Abstract
Systemic candidiasis (SC) is a leading cause of nosocomial bloodstream infections, with mortality of &gt;40% despite therapy. In a mouse model of SC, the most highly infected organ is the kidney, and myeloid cells, including dendritic cells (DCs), are integral for host defense. We hypothesized that Ccr7, which mediates DC trafficking and survival, is critical for host defense during SC. Ccr7 and its ligands, Ccl19 and Ccl21, were highly up-regulated in the Candida-infected kidney. All Ccr7−/− mice rapidly succumbed during SC, whereas WT mice had 80% survival at day 14. Infected Ccr7−/− mice had significantly greater kidney fungal burden, with greater tissue damage, and more severe renal failure. Infection in Ccl19−/− mice and in plt/plt mice (that lack Ccl19 and the CCL21a isoform of Ccl21) did not phenocopy the susceptibility of Ccr7−/− mice, indicating that the CCL21b-Ccr7 axis is critical for protection. Surprisingly, bone marrow chimeras revealed that the protective effects of Ccr7 are solely mediated by non-hematopoietic cells. Studies using FACS, IHC, and mRNA from sorted renal cells showed that Ccr7 is expressed by renal tubular cells (RTCs), not other renal stromal cells. Our preliminary data show the Ccr7 is a survival factor for RTCs; indeed, Ccr7 deficiency resulted in significantly greater tubulitis and tubular necrosis during SC. The renal protective effects of Ccr7 were also evident during bacterial sepsis, indicating that Ccr7 is broadly protective against infection-induced acute kidney injury. In summary, our data are the first to implicate Ccr7 in innate control of any pathogen and to uncover the contribution of Ccr7 on non-hematopoietic cells in protection against acute kidney injury and systemic fungal infection.
The contribution of acidic mammalian chitinase to disease severity in experimental fungal asthma
Authors: Mackel Joseph J , Garth Jaleesa M , Reeder Kristen M , Blackburn Jonathan , Steele Chad 
Published: January 2023

Abstract
Chitin is a polysaccharide that provides structure and rigidity to the fungal cell wall. Exposure to A. fumigatus cell wall moieties such as chitin has been linked to fungal sensitization and allergic inflammation. Chitin is not present in mammals, however, mammals possess enzymes that function to degrade chitin known as chitinases. Mammals possess two functional chitinases, acidic mammalian chitinase (AMCase) and chitotriosidase. Although chitinase expression has been linked to Th2 respiratory disorders, their exact role in fungal sensitization and fungal asthma has not been determined. In an allergic asthma model associated with chronic A. fumigatus exposure, mice deficient in AMCase displayed attenuated levels of the proallergic/pro-type 2 factors CCL22, CCL17, and IL-33. Furthermore, a deficiency in AMCase led to improved total lung function. Surprisingly, examination of inflammatory responses revealed attenuated IL-17 and IL-22 responses, but not type 2 responses (IL-4, IL-5, IL-13), in the absence of AMCase. Collectively, these data suggest that expression of AMCase during allergic fungal asthma is associated with increased severity that is putatively associated with IL-17A and IL-22 responses.
We Are What We Eat ___ Bioinformatic Prediction of microRNAs in JPS Water Decoctum of Prescription in Traditional Chinese Medicine and Their Mammalian Target Genes
Authors: Shen Chao-Bin , Yu Lan , Cai Hong 
Published: January 2023

Abstract

Objective
To provide a good start for understanding the roles of microRNA (miRNAs) in Jade Screen Powder (JSP). JSP has been clinically used in China for over 700 years to treat RRTIs, asthma, and ephidrosis in childhood.

Methods
The miRNA profile of JSP have used the next generation high-through put Illumina RNA-seq technology, the miRNAs and their target genes were predicted using bioinformatic approach . We applied a series of transcriptome analysis method, including miRNA differential expression analysis, de novo identification of miRNAs as well as co-expression target reconstruction, to identify prediction epigenetic molecular mechanisms of JSP in mammalian.

Results
We sequenced ~ 8,566,120 small RNA reads from the of JSP Water Decoctum and conserved miRNAs based on similarity to miRNA known in whole plant species and novel miRNAs based on potential hairpin-forming precusors with in miRBase 21. A general transcriptome database with 21,640 sequences was obtained. Based on the transcriptomic sequences, 53 miRNA, classified into 21 families. A total of 149 genes were predicted to be regulated by these high expression 8 miRNAs. Multiple targets were perturbed and the immunoregulatory was identified as the potential primary target pathway of JSP in mammalian.

Conclusion
Our results provide the first clue to the elucidation of miRNA profiles in prescription of JSP by thermodynamic treated. These miRNAs and the corresponding target genes identified in this study will provide a solid basis for understanding their biological functions in JPS Decoctum. Immunoregulation of herbal microRNAs in mammals are a new concept.
Commitment of mitosis in B cells: “before and after”
Authors: Singh Amit K , Spitzer Matthew , Nolan Garry P , Mattson Mark P , Sollott Steven , Sen Ranjan 
Published: January 2023

Abstract
Naïve B cells proliferate differentially in response to various mitogenic signals. However, regardless of the initiating stimulus, B cells that progressed through one mitotic division gain the ability to divide up to 3–4 times in the absence of renewed stimulation. In contrast, cells that had not progressed through mitosis did not divide except when re-stimulated. These observations go against accepted dogma about cell cycle regulation, which posits that cells need to be re-stimulated after each division to progress through G1. To identify the basis for signal-independent cell division we compared cells that had undergone one division and those that had not by several assays. Our findings indicate that divided cells are already pre-programed to cross restriction (R) point. The characteristics of cells that have divided once include bigger cell size in G1, low levels of p27, hyper-phosphorylated Rb, high c-Myc and phospho-CDK2. High throughput CyTOF analysis at single cell level with 25 parameters suggested that the G1 state of once-divided cells differs significantly from the G1 phase of cells progressing through the first cell division cycle. RNA-seq analysis identified Birc5 (Survivin) which is an E2F target gene as highly expressed in the cells that have underwent signal-independent proliferation. Survivin as exclusively present in G1 phase of divided B cells and blocking it with its inhibitor (LLP3) halted the G1-S progression and therefore blocked signal independent proliferation. This in vitro model may recapitulate aspects of signal independent cell division seen in the dark zone of the germinal center (GC) and resolve mechanisms involved in various GC specific B cell lymphomas.
Zymosan tolerizes primary pig monocytes to lipopolysaccharide stimulation
Authors: Byrne Kristen A , Loving Crystal L 
Published: January 2023

Abstract
Exposure of monocytes to β-1,3 glucans from yeast cell wall can enhance the immune response to heterologous innate agonists, a phenomenon termed innate training. This is in contrast to tolerance, which is well described in relation to lipopolysaccharide (LPS) responses. Yeast extracts are fed to food animals for production and immune benefits, but the mechanism of immune modulation provided by dietary yeast is not clearly defined. With the recent limitations to antibiotic use in food production animals, alternatives are sought to maintain animal health and production. To elucidate the immunological effect of yeast β-glucans on swine monocytes when re-exposed to a heterologous agonist, we primed primary swine monocytes with varying amounts and sources of β-glucan for 24h in vitro and restimulated the cells 5d later to LPS. Monocytes primed with media only or LPS, and exposed to LPS 5d later, served as controls to delineate trained versus tolerant responses. Swine monocytes primed with LPS produced IL-1β and TNF-α, and transitioned to a tolerant state, with decreased production of IL-1β and TNF-α upon re-stimulation with LPS. Interestingly, monocytes primed with the commercial β-glucan, zymosan (S. cerevisiae), at 10mg/mL or higher and restimulated with LPS exhibited a tolerized state. Specifically, zymosan primed cells did not produce IL-1β or TNF-α in response to LPS restimulation. Monocytes primed with laminarin (L. digitata) and restimulated with LPS did not exhibit a trained or tolerant state. These data indicate that dosage and source of β-glucan play an important role in the priming of monocytes to secondary LPS exposure, and warrants further study to elucidate differential responses as they relate to commercial dietary β-glucans.
Helminth-induced B lymphocytes mediate control of emphysema through production of RELMa
Authors: Chen Fei , Wu Wenhui , Millman Ariel , Palma Mark J , Gause William C 
Published: January 2023

Abstract
The intestinal nematode parasite, Nippostrongylus brasiliensis (Nb), can cause emphysema and the mechanisms remain poorly defined. Here we show that emphysema develops as early as 7 days after Nb inoculation and is associated with increased gene expression of Il17a, neutrophil elastase (Ela2), and macrophage matrix metalloproteinase 12 (Mmp12) in the lung. Transfer of Nb-primed neutrophils or macrophages to naïve recipients results in emphysema. Nb infection of Il17a−/−mice results in a less severe emphysematous pathology, decreased neutrophil influx to the lung, and lower gene expression of Ela2. Surprisingly, Nb infection in B cell deficient Jh−/− mice results in a more severe emphysema when compared to WT mice, and is associated with higher numbers of neutrophils and macrophages, as well as increased expression of Il17a, Ela2 and Mmp12 in the lung. Transfer of B lymphocytes from WT mice or Il10−/− mice, but not from Il4Rα−/− mice, or Relmα−/− mice to recipient Jh−/−mice can restore control of emphysema, decrease influx of neutrophils, macrophages, and downregulate IL-17A. B cells from lung tissue of Nb-primed WT mice, but not Il4Rα−/− mice express high levels of Relmα. Co-culture of Nb-primed WT B cells but not Relmα−/− B cells with Nb-primed neutrophils or Nb-primed macrophages decreased ELA-2 and MMP-12 activity, respectively. Taken together, these data suggest that IL-17A promotes emphysema through recruitment and activation of protease secreting neutrophils and macrophages in the lung. IL4R-dependent B regulatory cells control emphysema through two independent mechanisms, downregulation of IL-17A and suppression of myeloid cell protease production, both of which require secretion of RELMα.
Inositol kinase Itpkb is a novel therapeutic target for chronic graft versus host disease (cGVHD)
Authors: Du Jing , Paz Katelyn , Flynn Ryan , Taylor Patricia , Miller Andrew , Dahlberg Carol , Blazar Bruce 
Published: January 2023

Abstract
Chronic graft versus host disease (cGVHD) is a common and life-threatening complication of allogeneic hematopoietic stem cell transplantation. cGVHD is mediated by donor T cells recognizing and attacking host tissues followed by activation of effector cells such as B cells to product pathogenic autoantibodies and macrophages to mediate fibrotic responses. Safer and more effective therapies are needed for cGVHD treatment. Inositol 1,4,5-trisphosphate 3-kinase B (Itpkb) is a Ca2+ dependent kinase downstream of lymphocyte receptor signaling that regulates T and B cell homeostasis and function by controlling the intracellular Ca2+ level, thus regulating apoptotic responses. Genetic deletion of Itpkb results in apoptosis. GNF362, a LMW Itpkb inhibitor blocks T cell driven autoimmunity. In this study, we explore the role of Itpkb in cGVHD pathogenesis and hypothesize that cGVHD can be prevented by disrupting the Itpkb signaling pathway. We test the hypothesis in two preclinical cGVHD models with distinct clinical manifestations and pathophysiology, including a multi-organ system cGVHD mouse model that is characterized by bronchiolitis obliterans (BO) driven by spontaneous germinal center reactions and antibody deposition, and a scleroderma model that is characterized by macrophage infiltration and skin fibrosis. This study demonstrates that depleting Itpkb in donor T cells, but not in donor bone marrow blocked cGVHD lung disease and germinal center reaction in the BO model. In addition, pharmaceutical inhibition of Itpkb with GNF362 significantly reduced cGVHD manifestations in both models. These data identify Itpkb as an essential mediator of cGVHD pathogenesis and suggest Itpkb inhibition as a novel approach to treat cGVHD.