scholarly journals A Derived Network-Based Interferon-Related Signature of Human Macrophages Responding toMycobacterium tuberculosis

2014 ◽  
Vol 2014 ◽  
pp. 1-16 ◽  
Author(s):  
Kang Wu ◽  
Hai Fang ◽  
Liang-Dong Lyu ◽  
Douglas B. Lowrie ◽  
Ka-Wing Wong ◽  
...  
Keyword(s):  
Network Analysis ◽  
Binding Sites ◽  
Direct Interaction ◽  
Host Responses ◽  
Human Macrophage ◽  
Human Macrophages ◽  
Transcriptional Signature ◽  
Highly Expressed Genes ◽  
Induced Genes ◽  
Human Infections

Network analysis of transcriptional signature typically relies on direct interaction between two highly expressed genes. However, this approach misses indirect and biological relevant interactions through a third factor (hub). Here we determine whether a hub-based network analysis can select an improved signature subset that correlates with a biological change in a stronger manner than the original signature. We have previously reported an interferon-related transcriptional signature (THP1r2Mtb-induced) fromMycobacterium tuberculosis(M. tb)-infected THP-1 human macrophage. We selected hub-connected THP1r2Mtb-induced genes into the refined network signature TMtb-iNet and grouped the excluded genes into the excluded signature TMtb-iEx. TMtb-iNet retained the enrichment of binding sites of interferon-related transcription factors and contained relatively more interferon-related interacting genes when compared to THP1r2Mtb-induced signature. TMtb-iNet correlated as strongly as THP1r2Mtb-induced signature on a public transcriptional dataset of patients with pulmonary tuberculosis (PTB). TMtb-iNet correlated more strongly in CD4+and CD8+T cells from PTB patients than THP1r2Mtb-induced signature and TMtb-iEx. When TMtb-iNet was applied to data during clinical therapy of tuberculosis, it resulted in the most pronounced response and the weakest correlation. Correlation on dataset from patients with AIDS or malaria was stronger for TMtb-iNet, indicating an involvement of TMtb-iNet in these chronic human infections. Collectively, the significance of this work is twofold: (1) we disseminate a hub-based approach in generating a biologically meaningful and clinically useful signature; (2) using this approach we introduce a new network-based signature and demonstrate its promising applications in understanding host responses to infections.

Genome-Wide Profiling of Epigenetic and Transcription Factor Regulation In Human Macrophage Differentiation

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3875-3875
Author(s):  
Thu-Hang Pham ◽  
Monika Lichtinger ◽  
Chris Benner ◽  
Sabine Pape ◽  
Lucia Schwarzfischer ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Mrna Expression ◽  
Binding Sites ◽  
Cell Types ◽  
Human Macrophage ◽  
Macrophage Differentiation ◽  
Human Macrophages ◽  
Expression Levels

Abstract Abstract 3875 The differentiation of human macrophages is accompanied by distinctive phenotypical changes and generally proceeds in the absence of proliferation. The molecular events governing this process are still poorly understood. Using ChIP-Seq technology we studied epigenetic changes as well as alterations in transcription factor occupancy during human monocyte differentiation and correlated these events with gene expression levels in hematopoietic cell types. We show that putative enhancer regions marked by histone H3 lysine4 monomethylation (H3K4me1) at different developmental stages (human progenitor cells, peripheral blood monocytes and in vitro differentiated macrophages) are enriched in distinct sets of transcription factor motifs corresponding to lineage-determining factors. Cell stage-specific histone methylation at promoter-distal sites corresponds with increased mRNA expression levels of neighboring genes. We generated global DNA-binding maps in monocytes and macrophages for two transcription factors (PU.1 and C/EBPβ) with a well established role in monocyte/macrophage differentiation. Comparison of human binding sites with corresponding mouse data revealed a surprisingly low level of conservation (∼10-15%) of PU.1-or C/EBPβ -bound sites between man and mouse, despite a highly conserved binding preference for both transcription factors. During monocytic differentiation, human macrophages primarily gained additional binding sites for both transcription factors (as well as promoter-distal H3K4me1). Interestingly, only neighboring genes with multiple binding events showed significantly increased, macrophage-specific mRNA expression as compared to monocytic as well as lymphocytic cell types. Human macrophage-specific H3K4me1-marked regions as well as macrophage-specific PU.1- and C/EBP-bound sites were characterized by overlapping sets of novel sequence motifs, suggesting that the combinatorial interaction of corresponding DNA-binding factors with PU.1 and C/EBPβ may be required for the establishment of human macrophage-specific enhancers. These data provide novel insights into PU.1 and C/EBPβ mediated gene regulation during human macrophage differentiation. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Differential Bacterial Survival, Replication, and Apoptosis-Inducing Ability of Salmonella Serovars within Human and Murine Macrophages

2000 ◽  
Vol 68 (3) ◽  
pp. 1005-1013 ◽  
Author(s):  
William R. Schwan ◽  
Xiao-Zhe Huang ◽  
Lan Hu ◽  
Dennis J. Kopecko
Keyword(s):  
Typhoid Fever ◽  
Systemic Infection ◽  
Peritoneal Macrophages ◽  
Human Macrophage ◽  
U937 Cells ◽  
Bacterial Survival ◽  
Human Macrophages ◽  
Macrophage Cells ◽  
Serovar Typhimurium ◽  
Murine Peritoneal Macrophages

ABSTRACT Salmonella serovars are associated with human diseases that range from mild gastroenteritis to host-disseminated enteric fever. Human infections by Salmonella enterica serovar Typhi can lead to typhoid fever, but this serovar does not typically cause disease in mice or other animals. In contrast, S. enterica serovar Typhimurium and S. entericaserovar Enteritidis, which are usually linked to localized gastroenteritis in humans and some animal species, elicit a systemic infection in mice. To better understand these observations, multiple strains of each of several chosen serovars of Salmonellawere tested for the ability in the nonopsonized state to enter, survive, and replicate within human macrophage cells (U937 and elutriated primary cells) compared with murine macrophage cells (J774A.1 and primary peritoneal cells); in addition, death of the infected macrophages was monitored. The serovar Typhimurium strains all demonstrated enhanced survival within J774A.1 cells and murine peritoneal macrophages, compared with the significant, almost 100-fold declines in viable counts noted for serovar Typhi strains. Viable counts for serovar Enteritidis either matched the level of serovar Typhi (J774A.1 macrophages) or were comparable to counts for serovar Typhimurium (murine peritoneal macrophages). Apoptosis was significantly higher in J774A.1 cells infected with serovar Typhimurium strain LT2 compared to serovar Typhi strain Ty2. On the other hand, serovar Typhi survived at a level up to 100-fold higher in elutriated human macrophages and 2- to 3-fold higher in U937 cells compared to the serovar Typhimurium and Enteritidis strains tested. Despite the differential multiplication of serovar Typhi during infection of U937 cells, serovar Typhi caused significantly less apoptosis than infections with serovar Typhimurium. These observations indicate variability in intramacrophage survival and host cytotoxicity among the various serovars and are the first to show differences in the apoptotic response of distinctSalmonella serovars residing in human macrophage cells. These studies suggest that nonopsonized serovar Typhimurium enters, multiplies within, and causes considerable, acute death of macrophages, leading to a highly virulent infection in mice (resulting in death within 14 days). In striking contrast, nonopsonized serovar Typhi survives silently and chronically within human macrophages, causing little cell death, which allows for intrahost dissemination and typhoid fever (low host mortality). The type of disease associated with any particular serovar of Salmonellais linked to the ability of that serovar both to persist within and to elicit damage in a specific host's macrophage cells.

Nuclear location of PLA2-I in proliferative cells

1998 ◽  
Vol 111 (7) ◽  
pp. 985-994 ◽  
Author(s):  
J.M. Fayard ◽  
C. Tessier ◽  
J.F. Pageaux ◽  
M. Lagarde ◽  
C. Laugier
Keyword(s):  
Binding Sites ◽  
Culture Medium ◽  
Aristolochic Acid ◽  
Direct Interaction ◽  
Nuclear Level ◽  
Proliferative Effect ◽  
Stromal Cell Line ◽  
Normal Rat ◽  
Nuclear Location ◽  
Insight Into

We have previously demonstrated that pancreatic PLA2 (PLA2-I) stimulates the proliferation of UIII cells, a stromal cell line derived from normal rat uterus. In order to gain further insight into the mechanism of action of PLA2-I, we have investigated the intracellular processing of PLA2-I. Either highly proliferative or growth arrested UIII cells were analyzed. Growth arrested cells were obtained from a contact inhibited monolayer or from aristolochic acid-treated cultures. Using cellular fractionation, western blotting, immunocytochemistry and confocal microscopy, we demonstrate that endogenous PLA2-I was mainly located in the nucleus in highly proliferative cells whereas its location was cytoplasmic in non proliferative cells. When non confluent UIII cells were incubated with nanomolar amounts of exogenous PLA2-I, the enzyme was internalized and, in the majority of cells, appeared within the nucleus. Both internalization and nuclear location of exogenous PLA2-I were suppressed by the addition of aristolochic acid to the culture medium. Binding experiments performed on purified nuclear preparations showed the presence of specific cooperative binding sites for PLA2-I. Collectively our data suggest that the proliferative effect exerted by pancreatic PLA2 in UIII cells is mediated by a direct interaction of the enzyme at the nuclear level. Putative mechanisms and targets are discussed.

scholarly journals Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response

2018 ◽  
Vol 115 (25) ◽  
pp. 6464-6469 ◽  
Author(s):  
Elias R. Gerrick ◽  
Thibault Barbier ◽  
Michael R. Chase ◽  
Raylin Xu ◽  
Josie François ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Large Scale ◽  
Direct Interaction ◽  
Human Macrophage ◽  
Binding Interaction ◽  
Bacterial Gene ◽  
Rna Profiling ◽  
Iron Deprivation ◽  
Bacterial Gene Expression ◽  
Small Regulatory Rnas

One key to the success of Mycobacterium tuberculosis as a pathogen is its ability to reside in the hostile environment of the human macrophage. Bacteria adapt to stress through a variety of mechanisms, including the use of small regulatory RNAs (sRNAs), which posttranscriptionally regulate bacterial gene expression. However, very little is currently known about mycobacterial sRNA-mediated riboregulation. To date, mycobacterial sRNA discovery has been performed primarily in log-phase growth, and no direct interaction between any mycobacterial sRNA and its targets has been validated. Here, we performed large-scale sRNA discovery and expression profiling in M. tuberculosis during exposure to five pathogenically relevant stresses. From these data, we identified a subset of sRNAs that are highly induced in multiple stress conditions. We focused on one of these sRNAs, ncRv11846, here renamed mycobacterial regulatory sRNA in iron (MrsI). We characterized the regulon of MrsI and showed in mycobacteria that it regulates one of its targets, bfrA, through a direct binding interaction. MrsI mediates an iron-sparing response that is required for optimal survival of M. tuberculosis under iron-limiting conditions. However, MrsI is induced by multiple host-like stressors, which appear to trigger MrsI as part of an anticipatory response to impending iron deprivation in the macrophage environment.

scholarly journals Orchestration of human macrophage NLRP3 inflammasome activation by Staphylococcus aureus extracellular vesicles

2020 ◽  
Vol 117 (6) ◽  
pp. 3174-3184 ◽  
Author(s):  
Xiaogang Wang ◽  
William J. Eagen ◽  
Jean C. Lee
Keyword(s):  
Staphylococcus Aureus ◽  
Extracellular Vesicles ◽  
Biological Effects ◽  
Endocytic Pathway ◽  
Host Cells ◽  
Human Macrophage ◽  
Inflammasome Activation ◽  
Human Macrophages ◽  
Caspase 1 ◽  
Tlr2 Signaling

Release of extracellular vesicles (EVs) is a common feature among eukaryotes, archaea, and bacteria. However, the biogenesis and downstream biological effects of EVs released from gram-positive bacteria remain poorly characterized. Here, we report that EVs purified from a community-associated methicillin-resistant Staphylococcus aureus strain were internalized into human macrophages in vitro and that this process was blocked by inhibition of the dynamin-dependent endocytic pathway. Human macrophages responded to S. aureus EVs by TLR2 signaling and activation of NLRP3 inflammasomes through K+ efflux, leading to the recruitment of ASC and activation of caspase-1. Cleavage of pro–interleukin (IL)-1β, pro-IL-18, and gasdermin-D by activated caspase-1 resulted in the cellular release of the mature cytokines IL-1β and IL-18 and induction of pyroptosis. Consistent with this result, a dose-dependent cytokine response was detected in the extracellular fluids of mice challenged intraperitoneally with S. aureus EVs. Pore-forming toxins associated with S. aureus EVs were critical for NLRP3-dependent caspase-1 activation of human macrophages, but not for TLR2 signaling. In contrast, EV-associated lipoproteins not only mediated TLR2 signaling to initiate the priming step of NLRP3 activation but also modulated EV biogenesis and the toxin content of EVs, resulting in alterations in IL-1β, IL-18, and caspase-1 activity. Collectively, our study describes mechanisms by which S. aureus EVs induce inflammasome activation and reveals an unexpected role of staphylococcal lipoproteins in EV biogenesis. EVs may serve as a novel secretory pathway for S. aureus to transport protected cargo in a concentrated form to host cells during infections to modulate cellular functions.

Human macrophage maturation in vitro: Expression of functional transferrin binding sites of high affinity

1988 ◽  
Vol 57 (2) ◽  
pp. 77-83 ◽  
Author(s):  
R. Andreesen ◽  
R. G. Sephton ◽  
S. Gadd ◽  
R. C. Atkins ◽  
S. Abrew
Keyword(s):  
Binding Sites ◽  
Human Macrophage ◽  
In Vitro Expression ◽  
High Affinity ◽  
Maturation In Vitro

scholarly journals M. tuberculosis infection of human iPSC-derived macrophages reveals complex membrane dynamics during xenophagy evasion

2020 ◽  
Vol 134 (5) ◽  
pp. jcs252973
Author(s):  
Elliott M. Bernard ◽  
Antony Fearns ◽  
Claudio Bussi ◽  
Pierre Santucci ◽  
Christopher J. Peddie ◽  
...  
Keyword(s):  
Inflammatory Responses ◽  
Ion Beam ◽  
Induced Pluripotent Stem Cell ◽  
Membrane Dynamics ◽  
Live Cell ◽  
Initiation Factor ◽  
Human Macrophage ◽  
Transcriptional Responses ◽  
Macrophage Response ◽  
Human Macrophages

ABSTRACTXenophagy is an important cellular defence mechanism against cytosol-invading pathogens, such as Mycobacterium tuberculosis (Mtb). Activation of xenophagy in macrophages targets Mtb to autophagosomes; however, how Mtb is targeted to autophagosomes in human macrophages at a high spatial and temporal resolution is unknown. Here, we use human induced pluripotent stem cell-derived macrophages (iPSDMs) to study the human macrophage response to Mtb infection and the role of the ESX-1 type VII secretion system. Using RNA-seq, we identify ESX-1-dependent transcriptional responses in iPSDMs after infection with Mtb. This analysis revealed differential inflammatory responses and dysregulated pathways such as eukaryotic initiation factor 2 (eIF2) signalling and protein ubiquitylation. Moreover, live-cell imaging revealed that Mtb infection in human macrophages induces dynamic ESX-1-dependent, LC3B-positive tubulovesicular autophagosomes (LC3-TVS). Through a correlative live-cell and focused ion beam scanning electron microscopy (FIB SEM) approach, we show that upon phagosomal rupture, Mtb induces the formation of LC3-TVS, from which the bacterium is able to escape to reside in the cytosol. Thus, iPSDMs represent a valuable model for studying spatiotemporal dynamics of human macrophage–Mtb interactions, and Mtb is able to evade capture by autophagic compartments.

scholarly journals Chromatin remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast

2020 ◽  
Vol 48 (15) ◽  
pp. 8408-8430 ◽  
Author(s):  
Hongfang Qiu ◽  
Emily Biernat ◽  
Chhabi K Govind ◽  
Yashpal Rawal ◽  
Răzvan V Chereji ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcriptional Activation ◽  
Histone Variant ◽  
Yeast Genome ◽  
Chromatin Remodeler ◽  
Chromatin Remodelers ◽  
Highly Expressed Genes ◽  
Induced Genes ◽  
Yeast Genes

Abstract The chromatin remodelers SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the −1 and +1 nucleosomes flanking NDRs; however, Ino80C’s function in transcriptional activation in vivo is not well understood. Analyzing the cohort of Gcn4-induced genes in ino80Δ mutants has uncovered a role for Ino80C on par with SWI/SNF in evicting promoter nucleosomes and transcriptional activation. Compared to SWI/SNF, Ino80C generally functions over a wider region, spanning the −1 and +1 nucleosomes, NDR and proximal genic nucleosomes, at genes highly dependent on its function. Defects in nucleosome eviction in ino80Δ cells are frequently accompanied by reduced promoter occupancies of TBP, and diminished transcription; and Ino80 is enriched at genes requiring its remodeler activity. Importantly, nuclear depletion of Ino80 impairs promoter nucleosome eviction even in a mutant lacking H2A.Z. Thus, Ino80C acts widely in the yeast genome together with RSC and SWI/SNF in evicting promoter nucleosomes and enhancing transcription, all in a manner at least partly independent of H2A.Z editing.

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