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1.
Nature ; 588(7839): 664-669, 2020 12.
Article in English | MEDLINE | ID: mdl-33328632

ABSTRACT

Current organoid models are limited by their inability to mimic mature organ architecture and associated tissue microenvironments1,2. Here we create multilayer bladder 'assembloids' by reconstituting tissue stem cells with stromal components to represent an organized architecture with an epithelium surrounding stroma and an outer muscle layer. These assembloids exhibit characteristics of mature adult bladders in cell composition and gene expression at the single-cell transcriptome level, and recapitulate in vivo tissue dynamics of regenerative responses to injury. We also develop malignant counterpart tumour assembloids to recapitulate the in vivo pathophysiological features of urothelial carcinoma. Using the genetically manipulated tumour-assembloid platform, we identify tumoural FOXA1, induced by stromal bone morphogenetic protein (BMP), as a master pioneer factor that drives enhancer reprogramming for the determination of tumour phenotype, suggesting the importance of the FOXA1-BMP-hedgehog signalling feedback axis between tumour and stroma in the control of tumour plasticity.


Subject(s)
Organoids/pathology , Organoids/physiology , Regeneration , Urinary Bladder Neoplasms/pathology , Urinary Bladder Neoplasms/physiopathology , Urinary Bladder/pathology , Urinary Bladder/physiology , Adult , Animals , Bone Morphogenetic Proteins/metabolism , Female , Hedgehogs/metabolism , Hepatocyte Nuclear Factor 3-alpha/metabolism , Humans , Male , Mice , Mice, Inbred C57BL , Organoids/physiopathology , Single-Cell Analysis , Stem Cells/cytology , Stem Cells/pathology , Stem Cells/physiology , Transcriptome , Urinary Bladder/cytology , Urinary Tract Infections/metabolism , Urinary Tract Infections/pathology
2.
Genes Dev ; 32(23-24): 1562-1575, 2018 12 01.
Article in English | MEDLINE | ID: mdl-30478249

ABSTRACT

Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. In Caenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Forkhead Transcription Factors/metabolism , Longevity/genetics , Molecular Chaperones/metabolism , Transcription Factors/metabolism , Animals , Insulin/metabolism , Insulin-Like Growth Factor I/metabolism , Intestines/physiology , Molecular Chaperones/genetics , Protein Binding , Signal Transduction/genetics , Subcutaneous Tissue/physiology , Transcriptional Activation/genetics
3.
Nucleic Acids Res ; 51(12): 6143-6155, 2023 07 07.
Article in English | MEDLINE | ID: mdl-37158258

ABSTRACT

Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.


Subject(s)
Colorectal Neoplasms , Histones , Humans , Chromatin/genetics , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Enhancer Elements, Genetic , Forkhead Transcription Factors/genetics , Forkhead Transcription Factors/metabolism , Histones/genetics , Histones/metabolism
4.
Cell ; 132(5): 887-98, 2008 Mar 07.
Article in English | MEDLINE | ID: mdl-18329373

ABSTRACT

The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites is directly correlated to RNA polymerase II (Pol II) binding. Furthermore, the first nucleosome downstream of a start site exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome.


Subject(s)
Genome, Human , Nucleosomes/metabolism , CD4-Positive T-Lymphocytes/metabolism , Chromosomes , Enhancer Elements, Genetic , Histones/metabolism , Humans , Lymphocyte Activation , Promoter Regions, Genetic , RNA Polymerase II/metabolism , Sequence Analysis, DNA/methods , Transcription Initiation Site
5.
PLoS Genet ; 16(3): e1008617, 2020 03.
Article in English | MEDLINE | ID: mdl-32130226

ABSTRACT

The oligosaccharyl transferase (OST) protein complex mediates the N-linked glycosylation of substrate proteins in the endoplasmic reticulum (ER), which regulates stability, activity, and localization of its substrates. Although many OST substrate proteins have been identified, the physiological role of the OST complex remains incompletely understood. Here we show that the OST complex in C. elegans is crucial for ER protein homeostasis and defense against infection with pathogenic bacteria Pseudomonas aeruginosa (PA14), via immune-regulatory PMK-1/p38 MAP kinase. We found that genetic inhibition of the OST complex impaired protein processing in the ER, which in turn up-regulated ER unfolded protein response (UPRER). We identified vitellogenin VIT-6 as an OST-dependent glycosylated protein, critical for maintaining survival on PA14. We also showed that the OST complex was required for up-regulation of PMK-1 signaling upon infection with PA14. Our study demonstrates that an evolutionarily conserved OST complex, crucial for ER homeostasis, regulates host defense mechanisms against pathogenic bacteria.


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/metabolism , Endoplasmic Reticulum/metabolism , Proteostasis/physiology , p38 Mitogen-Activated Protein Kinases/metabolism , Animals , Hexosyltransferases/metabolism , Immunity, Innate/physiology , MAP Kinase Signaling System/physiology , Membrane Proteins/metabolism , Pseudomonas aeruginosa/metabolism , Signal Transduction/physiology , Transcription Factors/metabolism , Unfolded Protein Response/physiology , Up-Regulation/physiology , Vitellogenins/metabolism
6.
J Allergy Clin Immunol ; 149(4): 1253-1269.e8, 2022 04.
Article in English | MEDLINE | ID: mdl-34653517

ABSTRACT

BACKGROUND: Diesel exhaust particles (DEPs) are the main component of traffic-related air pollution and have been implicated in the pathogenesis and exacerbation of asthma. However, the mechanism by which DEP exposure aggravates asthma symptoms remains unclear. OBJECTIVE: This study aimed to identify a key cellular player of air pollutant-induced asthma exacerbation and development. METHODS: We examined the distribution of innate immune cells in the murine models of asthma induced by house dust mite and DEP. Changes in immune cell profiles caused by DEP exposure were confirmed by flow cytometry and RNA-Seq analysis. The roles of sialic acid-binding, Ig-like lectin F (SiglecF)-positive neutrophils were further evaluated by adoptive transfer experiment and in vitro functional studies. RESULTS: DEP exposure induced a unique population of lung granulocytes that coexpressed Ly6G and SiglecF. These cells differed phenotypically, morphologically, functionally, and transcriptionally from other SiglecF-expressing cells in the lungs. Our findings with murine models suggest that intratracheal challenge with DEPs induces the local release of adenosine triphosphate, which is a damage-associated molecular pattern signal. Adenosine triphosphate promotes the expression of SiglecF on neutrophils, and these SiglecF+ neutrophils worsen type 2 and 3 airway inflammation by producing high levels of cysteinyl leukotrienes and neutrophil extracellular traps. We also found Siglec8- (which corresponds to murine SiglecF) expressing neutrophils, and we found it in patients with asthma-chronic obstructive pulmonary disease overlap. CONCLUSION: The SiglecF+ neutrophil is a novel and critical player in airway inflammation and targeting this population could reverse or ameliorate asthma.


Subject(s)
Air Pollutants , Asthma , Adenosine Triphosphate/metabolism , Air Pollutants/toxicity , Animals , Humans , Inflammation/metabolism , Lung , Mice , Neutrophils/pathology , Vehicle Emissions/toxicity
7.
Genes Dev ; 29(23): 2490-503, 2015 Dec 01.
Article in English | MEDLINE | ID: mdl-26637528

ABSTRACT

Glucose-rich diets shorten the life spans of various organisms. However, the metabolic processes involved in this phenomenon remain unknown. Here, we show that sterol regulatory element-binding protein (SREBP) and mediator-15 (MDT-15) prevent the life-shortening effects of a glucose-rich diet by regulating fat-converting processes in Caenorhabditis elegans. Up-regulation of the SREBP/MDT-15 transcription factor complex was necessary and sufficient for alleviating the life-shortening effect of a glucose-rich diet. Glucose feeding induced key enzymes that convert saturated fatty acids (SFAs) to unsaturated fatty acids (UFAs), which are regulated by SREBP and MDT-15. Furthermore, SREBP/MDT-15 reduced the levels of SFAs and moderated glucose toxicity on life span. Our study may help to develop strategies against elevated blood glucose and free fatty acids, which cause glucolipotoxicity in diabetic patients.


Subject(s)
Aging/genetics , Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/metabolism , Fatty Acids/metabolism , Sterol Regulatory Element Binding Proteins/metabolism , Transcription Factors/metabolism , Aging/drug effects , Aging/metabolism , Animals , Caenorhabditis elegans/drug effects , Caenorhabditis elegans/enzymology , Caenorhabditis elegans Proteins/genetics , Diet , Dietary Sucrose/pharmacology , Enzyme Induction/drug effects , Fatty Acid Desaturases/genetics , Gene Expression Regulation, Developmental/drug effects , Genome-Wide Association Study , Glucose/metabolism , Glucose/pharmacology , Glucose/toxicity , RNA Interference , Sterol Regulatory Element Binding Proteins/genetics , Transcription Factors/genetics
8.
FASEB J ; 35(4): e21507, 2021 04.
Article in English | MEDLINE | ID: mdl-33724572

ABSTRACT

Retinoic acid-related orphan receptor γ (RORγ) maintains the circadian rhythms of its downstream genes. However, the mechanism behind the transcriptional activation of RORγ itself remains unclear. Here, we demonstrate that transcription of RORγ is activated by heterogeneous nuclear ribonucleoprotein K (hnRNP K) via the poly(C) motif within its proximal promoter. Interestingly, we confirmed the binding of endogenous hnRNP K within RORγ1 and RORγ2 promoter along with the recruitment of RNA polymerase 2 through chromatin immunoprecipitation (ChIP). Furthermore, an assay for transposase accessible chromatin (ATAC)-qPCR showed that hnRNP K induced higher chromatin accessibility within the RORγ1 and RORγ2 promoter. Then we found that the knockdown of hnRNP K lowers RORγ mRNA oscillation amplitude in both RORγ and RORγ-dependent metabolic genes. Moreover, we demonstrated that time-dependent extracellular signal-regulated kinase (ERK) activation controls mRNA oscillation of RORγ and RORγ-dependent metabolic genes through hnRNP K. Taken together, our results provide new insight into the regulation of RORγ by hnRNP K as a transcriptional activator, along with its physiological significance in metabolism.


Subject(s)
Chromatin/metabolism , Circadian Rhythm/physiology , Heterogeneous-Nuclear Ribonucleoprotein K/metabolism , Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism , Animals , Chromatin Immunoprecipitation/methods , Circadian Rhythm/genetics , Heterogeneous-Nuclear Ribonucleoprotein K/genetics , Mice , Transcription Factors/metabolism , Transcriptional Activation/physiology
9.
Circulation ; 142(18): 1736-1751, 2020 11 03.
Article in English | MEDLINE | ID: mdl-32883094

ABSTRACT

BACKGROUND: Macrophages produce many inflammation-associated molecules, released by matrix metalloproteinases, such as adhesion molecules, and cytokines, as well, which play a crucial role in atherosclerosis. In this context, we investigated the relationship between Ninjurin-1 (Ninj1 [nerve injury-induced protein]), a novel matrix metalloproteinase 9 substrate, expression, and atherosclerosis progression. METHODS: Ninj1 expression and atherosclerosis progression were assessed in atherosclerotic aortic tissue and serum samples from patients with coronary artery disease and healthy controls, and atheroprone apolipoprotein e-deficient (Apoe-/-) and wild-type mice, as well. Apoe-/- mice lacking systemic Ninj1 expression (Ninj1-/-Apoe-/-) were generated to assess the functional effects of Ninj1. Bone marrow transplantation was also used to generate low-density lipoprotein receptor-deficient (Ldlr-/-) mice that lack Ninj1 specifically in bone marrow-derived cells. Mice were fed a Western diet for 5 to 23 weeks, and atherosclerotic lesions were investigated. The anti-inflammatory role of Ninj1 was verified by treating macrophages and mice with the peptides Ninj11-56 (ML56) and Ninj126-37 (PN12), which mimic the soluble form of Ninj1 (sNinj1). RESULTS: Our in vivo results conclusively showed a correlation between Ninj1 expression in aortic macrophages and the extent of human and mouse atherosclerotic lesions. Ninj1-deficient macrophages promoted proinflammatory gene expression by activating mitogen-activated protein kinase and inhibiting the phosphoinositide 3-kinase/Akt signaling pathway. Whole-body and bone marrow-specific Ninj1 deficiencies significantly increased monocyte recruitment and macrophage accumulation in atherosclerotic lesions through elevated macrophage-mediated inflammation. Macrophage Ninj1 was directly cleaved by matrix metalloproteinase 9 to generate a soluble form that exhibited antiatherosclerotic effects, as assessed in vitro and in vivo. Treatment with the sNinj1-mimetic peptides, ML56 and PN12, reduced proinflammatory gene expression in human and mouse classically activated macrophages, thereby attenuating monocyte transendothelial migration. Moreover, continuous administration of mPN12 alleviated atherosclerosis by inhibiting the enhanced monocyte recruitment and inflammation characteristics of this disorder in mice, regardless of the presence of Ninj1. CONCLUSIONS: Ninj1 is a novel matrix metalloproteinase 9 substrate in macrophages, and sNinj1 is a secreted atheroprotective protein that regulates macrophage inflammation and monocyte recruitment in atherosclerosis. Moreover, sNinj1-mediated anti-inflammatory effects are conserved in human macrophages and likely contribute to human atherosclerosis.


Subject(s)
Anti-Inflammatory Agents/pharmacology , Atherosclerosis , Cell Adhesion Molecules, Neuronal , Macrophages/metabolism , Nerve Growth Factors , Peptidomimetics/pharmacology , Signal Transduction/drug effects , Animals , Atherosclerosis/drug therapy , Atherosclerosis/genetics , Atherosclerosis/metabolism , Cell Adhesion Molecules, Neuronal/genetics , Cell Adhesion Molecules, Neuronal/metabolism , Cell Adhesion Molecules, Neuronal/pharmacology , Female , Male , Matrix Metalloproteinase 9/genetics , Matrix Metalloproteinase 9/metabolism , Mice , Mice, Knockout, ApoE , Nerve Growth Factors/genetics , Nerve Growth Factors/metabolism , Nerve Growth Factors/pharmacology , Phosphatidylinositol 3-Kinases/genetics , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins c-akt/genetics , Proto-Oncogene Proteins c-akt/metabolism , Signal Transduction/genetics
10.
Nat Immunol ; 9(11): 1288-96, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18820682

ABSTRACT

T helper type 2 (T(H)2) cells are essential for humoral immunity and host defense. Interleukin 4 (IL-4) drives T(H)2 differentiation and IL-2 augments the accessibility of Il4 chromatin. Here we demonstrate that IL-2, by inducing binding of STAT5 to the Il4ra locus, which encodes IL-4 receptor alpha-chain (IL-4Ralpha), was essential for inducing and maintaining IL-4Ralpha expression. Although IL-4 induced IL-4Ralpha expression, T cell receptor-induced IL-4Ralpha expression was normal in Il4(-/-) cells but was much lower in Il2(-/-) cells. Notably, forced IL-4Ralpha expression restored the T(H)2 differentiation of Il2(-/-) cells. Moreover, genome-wide mapping by chromatin immunoprecipitation coupled with sequencing showed broad interaction of the transcription factors STAT5A and STAT5B with genes associated with T(H)2 differentiation. Our results identify a previously unappreciated function for IL-2 in 'priming' T cells for T(H)2 differentiation and in maintaining the expression of Il4ra and other genes in T(H)2-committed cells.


Subject(s)
Gene Expression Regulation , Interleukin-2/metabolism , Interleukin-4 Receptor alpha Subunit/genetics , Th2 Cells/immunology , Animals , Cell Differentiation/genetics , Cell Differentiation/immunology , Interleukin-2/genetics , Mice , Mice, Inbred C57BL , Mice, Transgenic , STAT5 Transcription Factor/metabolism , Up-Regulation
11.
BMC Microbiol ; 20(1): 208, 2020 07 13.
Article in English | MEDLINE | ID: mdl-32660414

ABSTRACT

BACKGROUND: The essential roles of gut microbiome have been emphasized in modulating human health and disease. Fusobacterium nucleatum (F. nucleatum), an obligate Gram-negative microorganism residing in oral cavity, gastrointestinal tract and elsewhere, has been recently considered as a potential oncobacterium associated with human cancers. However, the consequence of its enrichment was not extensively explored in terms of microbial homeostasis and stability at the early stage of disease development. RESULT: Our analysis on longitudinal metagenomic data generated by the Integrative Human Microbiome Project (iHMP) showed that F. nucleatum was frequently found in inflammatory bowel diseases (IBD) subjects with reduced microbial diversity. Using non-parametric logarithmic linear discriminant analysis (LDA) effect size (LEfSe) algorithm, 12 IBD- and 14 non-IBD-specific bacterial species were identified in the fecal metagenome and the IBD-specific ones were over-represented in the F. nucleatum-experienced subjects during long-term surveillance. In addition, F. nucleatum experience severely abrogated intra-personal stability of microbiome in IBD patients and induced highly variable gut microbiome between subjects. From the longitudinal comparison between microbial distributions prior and posterior to F. nucleatum detection, 41 species could be proposed as indicative "classifiers" for dysbiotic gut state. By multiple logistic regression models established on these classifiers, the high probability of experiencing F. nucleatum was significantly correlated with decreased alpha-diversity and increased number of biomarker species for IBD and colorectal cancer (CRC). Finally, microbial clustering confirmed that biomarker species for IBD and non-IBD conditions as well as CRC signature markers were well distinguishable and could be utilized for explaining gut symbiosis and dysbiosis. CONCLUSION: F. nucleatum opportunistically appeared under early dysbiotic condition in gut, and discriminative classifier species associated with F. nucleatum were successfully applied to predict microbial alterations in both IBD and non-IBD conditions. Our prediction model and microbial classifier biomarkers for estimating gut dysbiosis should provide a novel aspect of microbial homeostasis/dynamics and useful information on non-invasive biomarker screening.


Subject(s)
Bacteria/classification , Dysbiosis/diagnosis , Fusobacterium nucleatum/isolation & purification , Inflammatory Bowel Diseases/microbiology , Bacteria/isolation & purification , Discriminant Analysis , Feces/microbiology , Female , Gastrointestinal Microbiome , Humans , Logistic Models , Longitudinal Studies , Male , Phylogeny
12.
Immunity ; 30(1): 155-67, 2009 Jan 16.
Article in English | MEDLINE | ID: mdl-19144320

ABSTRACT

Multipotential naive CD4(+) T cells differentiate into distinct lineages including T helper 1 (Th1), Th2, Th17, and inducible T regulatory (iTreg) cells. The remarkable diversity of CD4(+) T cells begs the question whether the observed changes reflect terminal differentiation with heritable epigenetic modifications or plasticity in T cell responses. We generated genome-wide histone H3 lysine 4 (H3K4) and lysine 27 (H3K27) trimethylation maps in naive, Th1, Th2, Th17, iTreg, and natural Treg (nTreg) cells. We found that although modifications of signature-cytokine genes (Ifng, Il4, and Il17) partially conform to the expectation of lineage commitment, genes encoding transcription factors like Tbx21 exhibit a broad spectrum of epigenetic states, consistent with our demonstration of T-bet and interferon-gamma induction in nTreg cells. Our data suggest an epigenetic mechanism underlying the specificity and plasticity of effector and regulatory T cells and also provide a framework for understanding complexity of CD4(+) T helper cell differentiation.


Subject(s)
CD4 Antigens/metabolism , CD4-Positive T-Lymphocytes/immunology , Chromosome Mapping , Histones/metabolism , Oxidoreductases, N-Demethylating/genetics , T-Lymphocyte Subsets/immunology , Animals , Cell Lineage/genetics , Cell Lineage/immunology , DNA-Binding Proteins , Jumonji Domain-Containing Histone Demethylases , Mice , Mice, Inbred C57BL , Oxidoreductases, N-Demethylating/immunology , Protein Modification, Translational , Retinoblastoma-Binding Protein 2
13.
Immunity ; 30(6): 912-25, 2009 Jun 19.
Article in English | MEDLINE | ID: mdl-19523850

ABSTRACT

Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription is important, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naive and memory CD8(+) T cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed four distinct modes (repressive, active, poised, and bivalent), reflecting different functions of these genes in CD8(+) T cells. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8(+) T cell function.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Cell Differentiation/genetics , Chromatin/metabolism , Histones/metabolism , Immunologic Memory/genetics , CD8-Positive T-Lymphocytes/metabolism , Cell Differentiation/immunology , Chromatin/immunology , Gene Expression Profiling , Genome-Wide Association Study , Histones/immunology , Humans , Methylation
14.
IUBMB Life ; 68(6): 436-44, 2016 06.
Article in English | MEDLINE | ID: mdl-27080371

ABSTRACT

Modulation of chromatin structure has been proposed as a molecular mechanism underlying the spatiotemporal collinear expression of Hox genes during development. CCCTC-binding factor (CTCF)-mediated chromatin organization is now recognized as a crucial epigenetic mechanism for transcriptional regulation. Thus, we examined whether CTCF-mediated chromosomal conformation is involved in Hoxc gene expression by comparing wild-type mouse embryonic fibroblast (MEF) cells expressing anterior Hoxc genes with Akt1 null MEFs expressing anterior as well as posterior Hoxc genes. We found that CTCF binding between Hoxc11 and -c12 is important for CTCF-mediated chromosomal loop formation and concomitant posterior Hoxc gene expression. Hypomethylation at this site increased CTCF binding and recapitulated the chromosomal conformation and posterior Hoxc gene expression patterns observed in Akt1 null MEFs. From this work we found that CTCF at the C12|11 does not function as a barrier/boundary, instead let the posterior Hoxc genes switch their interaction from inactive centromeric to active telomeric genomic niche, and concomitant posterior Hoxc gene expression. Although it is not clear whether CTCF affects Hoxc gene expression solely through its looping activity, CTCF-mediated chromatin structural modulation could be an another tier of Hox gene regulation during development. © 2016 IUBMB Life, 68(6):436-444, 2016.


Subject(s)
Chromatin/genetics , Homeodomain Proteins/genetics , Repressor Proteins/metabolism , Animals , CCCTC-Binding Factor , Cells, Cultured , Chromatin/metabolism , DNA/chemistry , DNA/metabolism , DNA Methylation , Female , Fibroblasts/physiology , Gene Expression Regulation, Developmental , Homeodomain Proteins/metabolism , Male , Mice, Inbred C57BL , Multigene Family , Proto-Oncogene Proteins c-akt/genetics , Repressor Proteins/genetics
15.
Biochem Biophys Res Commun ; 463(4): 1237-42, 2015 Aug 07.
Article in English | MEDLINE | ID: mdl-26086100

ABSTRACT

Regarding the T cell function in HIV-1 infection, activation of T cells is enhanced in acutely HIV-1-infected T cells upon stimuli. However, T cell immune responses underlying the activation of T cell receptor (TCR) signaling molecules and interleukin (IL)-2 production in latently HIV-1-infected cells are poorly understood. The expression and activation of TCR components and its downstream molecules in acutely and latently HIV-1-infected T cells were compared using quantitative reverse transcription polymerase chain reaction (RT-PCR) for mRNA expression and enzyme-linked immunosorbent assay (ELISA) for levels of IL-2 in phytohemagglutinin M (PHA-M). The levels of T cell surface molecules and TCR signaling molecules in latently HIV-1-infected cells were greatly decreased without changes in their mRNA levels. In addition, downstream TCR-signaling molecules in latently HIV-1-infected cells were not activated even in the presence of PHA-M. The phosphorylation of mitogen-activated protein kinases (MAPKs) in the presence of PHA-M was weakly induced in latently HIV-1-infected cells but was greater in acutely HIVNL4-3-infected cells. Finally, the production of IL-2 was significantly decreased in latently HIV-1-infected cells compared with uninfected parent cells. Thus, IL-2-related immunological functions in latently HIV-1-infected T cells were markedly impaired even in the presence of stimuli.


Subject(s)
HIV Infections/metabolism , Interleukin-2/metabolism , HIV-1/physiology , Humans , Receptors, Antigen, T-Cell/metabolism , Signal Transduction , Virus Latency
16.
J Immunol ; 190(8): 4092-102, 2013 Apr 15.
Article in English | MEDLINE | ID: mdl-23514742

ABSTRACT

Outer membrane vesicles (OMVs), secreted from Gram-negative bacteria, are spherical nanometer-sized proteolipids enriched with outer membrane proteins. OMVs, also known as extracellular vesicles, have gained interests for use as nonliving complex vaccines and have been examined for immune-stimulating effects. However, the detailed mechanism on how OMVs elicit the vaccination effect has not been studied extensively. In this study, we investigated the immunological mechanism governing the protective immune response of OMV vaccines. Immunization with Escherichia coli-derived OMVs prevented bacteria-induced lethality and OMV-induced systemic inflammatory response syndrome. As verified by adoptive transfer and gene-knockout studies, the protective effect of OMV immunization was found to be primarily by the stimulation of T cell immunity rather than B cell immunity, especially by the OMV-Ag-specific production of IFN-γ and IL-17 from T cells. By testing the bacteria-killing ability of macrophages, we also demonstrated that IFN-γ and IL-17 production is the main factor promoting bacterial clearances. Our findings reveal that E. coli-derived OMV immunization effectively protects bacteria-induced lethality and OMV-induced systemic inflammatory response syndrome primarily via Th1 and Th17 cell responses. This study therefore provides a new perspective on the immunological detail regarding OMV vaccination.


Subject(s)
Escherichia coli Infections/immunology , Escherichia coli Infections/mortality , Escherichia coli Vaccines/administration & dosage , Escherichia coli Vaccines/immunology , Exosomes/immunology , Th1 Cells/immunology , Th17 Cells/immunology , Adaptive Immunity , Animals , Cell Membrane/immunology , Cell Membrane/microbiology , Cells, Cultured , Escherichia coli Infections/pathology , Male , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Knockout , Sepsis/immunology , Sepsis/microbiology , Sepsis/prevention & control , Systemic Inflammatory Response Syndrome/immunology , Systemic Inflammatory Response Syndrome/microbiology , Systemic Inflammatory Response Syndrome/pathology , Th1 Cells/microbiology , Th1 Cells/pathology , Th17 Cells/microbiology , Th17 Cells/pathology
17.
Retrovirology ; 11: 67, 2014 Aug 13.
Article in English | MEDLINE | ID: mdl-25116364

ABSTRACT

BACKGROUND: Human immunodeficiency virus-1 (HIV-1) Tat protein plays an essential role in HIV gene transcription from the HIV-1 long terminal repeat (LTR) and replication. Transcriptional activity of Tat is modulated by several host factors, but the mechanism responsible for Tat regulation by host factors is not understood fully. RESULTS: Using a yeast two-hybrid screening system, we identified Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 (NUCKS1) as a novel Tat-interacting partner. Here, we report its function as a positive regulator of Tat. In a coimmunoprecipitation assay, HIV-1 Tat interacted sufficiently with both endogenous and ectopically expressed NUCKS1. In a reporter assay, ectopic expression of NUCKS1 significantly increased Tat-mediated transcription of the HIV-1 LTR, whereas knockdown of NUCKS1 by small interfering RNA diminished Tat-mediated transcription of the HIV-1 LTR. We also investigated which mechanism contributes to NUCKS1-mediated Tat activation. In a chromatin immunoprecipitation assay (ChIP), knockdown of NUCKS1 interrupted the accumulation of Tat in the transactivation-responsive (TAR) region on the LTR, which then led to suppression of viral replication. However, NUCKS1 expression did not increase Tat nuclear localization and interaction with Cyclin T1. Interestingly, the NUCKS1 expression level was lower in latently HIV-1-infected cells than in uninfected parent cells. Besides, expression level of NUCKS1 was markedly induced, which then facilitated HIV-1 reactivation in latently infected cells. CONCLUSION: Taken together, our data demonstrate clearly that NUCKS1 is a novel Tat coactivator that is required for Tat-mediated HIV-1 transcription and replication, and that it may contribute to HIV-1 reactivation in latently HIV-1 infected cells.


Subject(s)
HIV Long Terminal Repeat , HIV-1/physiology , Nuclear Proteins/genetics , Phosphoproteins/genetics , Virus Replication/genetics , tat Gene Products, Human Immunodeficiency Virus/genetics , Cell Line , Cell Line, Tumor , Cyclin T/genetics , Gene Expression Regulation, Viral , HEK293 Cells , HIV-1/genetics , HeLa Cells , Humans , Jurkat Cells , Promoter Regions, Genetic , Transcription, Genetic , Transcriptional Activation
18.
Inflamm Res ; 63(5): 389-97, 2014 May.
Article in English | MEDLINE | ID: mdl-24468891

ABSTRACT

OBJECTIVE AND DESIGN: Microglia and macrophages play an important role in the innate and adaptive immune systems. Although the resident location of these cells is different, their functions during the polarization response due to various stimuli are very similar. The present study aimed to analyze differences in microglial and macrophage gene expression during inflammation. METHODS: Mouse microglial BV-2 cells were exposed to LPS (10 ng/ml). The levels of gene expression were measured using real-time RT-PCR and whole transcriptome shotgun sequencing. RESULTS: The level of Jmjd3 gene expression in activated microglia showed a similar pattern to that of macrophages. In both cell types, genes associated with the inflammation response were generally increased whereas genes associated with metabolic and biosynthetic processes were decreased. However, the expression of transcription-related elements other than genes encoding histone modification enzymes showed a significantly different pattern between microglia and macrophages. CONCLUSION: Although the function and the gene expression levels of histone modification enzymes showed a similar pattern in microglia and macrophages during inflammation, the expression of transcription-related elements in both cell types showed a completely different pattern.


Subject(s)
Gene Expression Profiling , Inflammation/immunology , Macrophages/metabolism , Microglia/metabolism , Animals , Cells, Cultured , Gene Expression Regulation , Jumonji Domain-Containing Histone Demethylases/genetics , Lipopolysaccharides/pharmacology , Mice , NF-kappa B/genetics
19.
J Immunol ; 188(4): 1799-808, 2012 Feb 15.
Article in English | MEDLINE | ID: mdl-22262660

ABSTRACT

Formyl peptide receptors (FPRs) are chemoattractant receptors that mediate inflammatory cell responses to infection. Recent evidence indicates that noneosinophilic asthma phenotypes can be developed by both Th1 and Th17 cell responses when exposed to LPS-containing allergens. In this study, we evaluated the effects of airway activation of FPRs by their synthetic agonist, Trp-Lys-Tyr-Met-Val-D-Met (W-peptide), on the development of Th1 and Th17 cell responses in a noneosinophilic asthma mouse model. A noneosinophilic asthma mouse model was generated by intranasal sensitization with 10 µg of LPS plus 75 µg of OVA on days 0, 1, 2, and 7. Mice were then challenged with 50 µg of OVA alone on days 14, 15, 21, and 22. W-peptide was administered during the sensitization period, and immune and inflammatory responses were evaluated after OVA challenge. Lung inflammation after OVA challenge was partly abolished by airway activation of FPRs during sensitization. Maturation of dendritic cells (DCs) and migration of DCs from the lung to lung-draining lymph nodes were inhibited by FPR activation. In addition, airway activation of FPRs inhibited allergen-specific T cell proliferation in the lymph nodes. Production of IL-12 and IL-6 (Th1- and Th17-polarizing cytokines) from lung DCs was decreased by airway activation of FPRs. This effect resulted in the inhibition of allergen-specific Th1 and Th17 cell responses. Airway activation of FPRs during sensitization effectively prevents the development of Th1 and Th17 cell responses induced by LPS-containing allergens via multiple mechanisms, such as inhibition of DC maturation and migration and the production of Th1- and Th7-polarizing cytokines.


Subject(s)
Asthma/immunology , Dendritic Cells/immunology , Lung/immunology , Receptors, Formyl Peptide/metabolism , Th1 Cells/immunology , Th17 Cells/immunology , Animals , Asthma/metabolism , Asthma/pathology , Cell Differentiation/drug effects , Cell Movement/drug effects , Cell Proliferation/drug effects , Dendritic Cells/drug effects , Disease Models, Animal , Interleukin-12/biosynthesis , Interleukin-6/biosynthesis , Lung/metabolism , Lung/pathology , Lymph Nodes/immunology , Lymphocyte Activation , Mice , Mice, Inbred BALB C , Oligopeptides/administration & dosage , Oligopeptides/pharmacology , Ovalbumin/immunology , Receptors, Formyl Peptide/biosynthesis , Th1 Cells/drug effects , Th17 Cells/drug effects
20.
Antimicrob Agents Chemother ; 57(6): 2589-95, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23529736

ABSTRACT

Gram-positive bacteria naturally produce extracellular vesicles. However, little is known regarding the functions of Gram-positive bacterial extracellular vesicles, especially in the bacterial community. Here, we investigated the role of Staphylococcus aureus extracellular vesicles in interbacterial communication to cope with antibiotic stress. We found that S. aureus liberated BlaZ, a ß-lactamase protein, via extracellular vesicles. These extracellular vesicles enabled other ampicillin-susceptible Gram-negative and Gram-positive bacteria to survive in the presence of ampicillin. However, S. aureus extracellular vesicles did not mediate the survival of tetracycline-, chloramphenicol-, or kanamycin-susceptible bacteria. Moreover, S. aureus extracellular vesicles did not contain the blaZ gene. In addition, the heat-treated S. aureus extracellular vesicles did not mediate the survival of ampicillin-susceptible bacteria. The ß-lactamase activities of S. aureus soluble and extracellular vesicle-associated BlaZ were similar, but only the extracellular vesicle-associated BlaZ was resistant to protease digestion, which suggests that the enzymatic activity of BlaZ in extracellular vesicles is largely protected by the vesicle structure. Our observations provide evidence of the important role of S. aureus extracellular vesicles in antibiotic resistance, which allows the polymicrobial community to continue to evolve and prosper against antibiotics.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial , Escherichia coli/drug effects , Extracellular Space/enzymology , Proteolipids/metabolism , Staphylococcus aureus/drug effects , Staphylococcus aureus/metabolism , beta-Lactamases/metabolism , Ampicillin/pharmacology , Escherichia coli/metabolism , Humans , Microbial Sensitivity Tests , Staphylococcus aureus/genetics , Staphylococcus aureus/ultrastructure , beta-Lactamases/genetics , beta-Lactamases/isolation & purification
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