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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expresson from human THP-1 stimulated with IFN-g and/or infected with TB

ABSTRACT: Investigation of interacting effects of TB and IFN-g on gene expression regulation within human macrophage-like THP-1 cells To investigate the effect TB infection has on THP-1 macrophageâ??s response to IFN-g post-infection, in multiple experiments, THP-1 cells were exposed to each of the following four conditions: not treated, IFN-Î³ treated, M. tuberculosis infected and M. tuberculosis infected then IFN-Î³ treated. Total cellular RNA was then extracted. Recovered RNAs were pre-qualified for reproducibility by comparing qRT-PCR results of IFIT-2 and IP10 between replicate experiments. Four most reproducible replicate experiments were then selected for genome-wide mRNA abundance assays using Affymetrix microarray-based technology.

ORGANISM(S): Homo sapiens

SUBMITTER: Richard Pine

PROVIDER: E-GEOD-17477 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of interferon-stimulated genes in primary cells and immortalized cell lines

Project description:Analysis of interferon-stimulated genes (ISGs) in various primary cells and immortalized cell lines, following type 1 interferon (IFN) treatment. Some cell types become resistant to HIV-1 infection following type 1 interferon treatment (such as macrophages, THP-1, PMA-THP-1, U87-MG cells and to a lesser extent, primary CD4+ T cells) while others either become only partially resistant (e.g., HT1080, PMA-U937) or remain permissive (e.g., CEM, CEM-SS, Jurkat T cell lines and U937); for more information see (Goujon and Malim, Journal of Virology 2010) and (Goujon and Schaller et al., Retrovirology 2013). We hypothesized that the anti-HIV-1 ISGs are differentially induced and expressed in restrictive cells compared to permissive cells and performed a whole genome analysis following type 1 IFN treatment in cell types exhibiting different HIV-1 resistance phenotypes. 48 samples; design: 9 cell lines, primary CD4+ T cells and primary macrophages, untreated and IFN-treated; 2 replicate experiments per cell line; 3 replicate experiments per primary cell type

2013-09-13 | E-GEOD-46599 | biostudies-arrayexpress

Expresson from human THP-1 stimulated with IFN-g and/or infected with TB

Project description:Investigation of interacting effects of TB and IFN-g on gene expression regulation within human macrophage-like THP-1 cells

2010-02-28 | GSE17477 | GEO

THP-1 cells infected with the clinical isolates of extensively drug-resistant and drug sensitive tuberculosis

Project description:Extensively drug resistant tuberculosis (XDR-TB) showed many different characteristics including the extreme drug resistance versus the drug sensitive clinical isolates (DS-TB), to know better about the reasons we used the tuberculosis host cells named as THP-1 (one kind of the macrophage cells) to be infected by the XDR-TB and DS-TB.DS strain A36 and the XDR strain B42 and was typical and selected by our lab. Then the total RNA of infected or uninfected THP-1 cells was extract and purified for the analysis by the chip (22K Human Genome chip representing the 21522 ORF of human with the oligonucleotide probe of 70 mer from CapitalBio Corp., Beijing, China). The results reflected the different expressed genes involved in apoptosis, secreted cytokines and signal pathway and so on. Those results might indicate the how the XDR-TB cause the pathogenesis. In this study, the well grown THP-1 cells were separated and cultured in three ampoules. Cells in one ampoules were infected with XDR-TB strain of B42. Cells in another ampoules were infected with DS-TB strain of A36, with the cells in the third one were not infected and just treated with PBS as the control. Then the dual channel method was used for detecting the hybridization of B42 vs the control or A36 vs control. This work was repeated for three times.

2010-06-20 | E-GEOD-15539 | biostudies-arrayexpress

Transcriptomics of vitamin D treatment effects in Mycobacterium tuberculosis-infected THP-1 cells

Project description:Previous reports have shown low vitamin D serum levels and polymorphisms in the vitamin D receptor (VDR) to be associated with increased risk for TB. Given that 1?,25-dihydroxyvitamin D3 has a role in lipid metabolism control, we tested whether the link between 1?,25-dihydroxyvitamin D3 and tuberculosis involves macrophage lipid metabolism. Since formation of lipid droplets (LD) is a hallmark of lipid dysregulation in M. tuberculosis-infected macrophages, we measured LD content as a readout of altered lipid metabolism in infected THP-1 cells. Induction of LD, which peaked by 24 hours post-infection was prevented by addition of 1?,25-dihydroxyvitamin D3 at the time of infection. To investigate the mechanism of 1?,25-dihydroxyvitamin D3 modulation of LD formation, we analyzed the transcriptome of M. tuberculosis-infected THP-1 cells with and without 1?,25-dihydroxyvitamin D3 treatment. THP-1 cells were cultured in 24-well flat bottom plates, pre-treated with 20ng/ml PMA for 24 h, and incubated with M. tuberculosis H37Rv. After 4 hours of infection, cells were washed to remove extracellular bacteria and treated with 100 nM of 1?,25-dihydroxyvitamin D3. THP-1 cells were collected and analyzed at 24h. 3 biological replicates in each of the 4 groups were prepared: Infected, Infected plus 1?,25-dihydroxyvitamin D3, Non-infected, Non-infected plus 1?,25-dihydroxyvitamin D3.

2014-07-01 | E-GEOD-57028 | biostudies-arrayexpress

Label-free Proteomic Analysis of Exosomes Secreted from THP-1-Derived Macrophages in the Absence or Presence of Interferon-α

Project description:Exosomes are extracellular vesicles that function in intercellular communication. We have previously reported that exosomes play a role in the transmission of antiviral molecules during interferon-α (IFN-α)-mediated immune responses. In this study, the protein contents of THP-1-derived macrophages with or without interferon-α treatment and of the exosomes secreted from these cells were analyzed by the label-free LC-MS/MS quantitation technologies. A total number of 1845 and 1550 protein groups were identified in the THP-1 macrophages and the corresponding exosomes, respectively. Treating the cells with IFN-α resulted in the differential abundance of 110 proteins in cells and 260 proteins in exosomes (greater than 2.0-fold), among which 35 proteins were both up-regulated in the IFN-α treated cells and corresponding exosomes while 139 proteins were specifically up-regulated in exosomes but not in the donor cells. GO and KEGG analysis of the protein function categories suggested that IFN-α promoted the abundance of proteins involved in “defense response to virus” in both exosomes and cells, and proteins related to “RNA processing” only in exosomes. Functional analysis further indicated that exosomes from IFN-α-treated cells exhibited potent antiviral activity that restored the impaired antiviral response of IFN-α in hepatitis B virus-replicating hepatocytes. These results have deepened the understanding of the exosome-mediated transfer of IFN-α-induced antiviral molecules and may provide new basis for therapeutic strategies to control viral infection.

2018-12-17 | PXD009746 | Pride

Changes in the Membrane-Associated Proteins of Exosomes Released from Human Macrophages after Mycobacterium tuberculosis Infection - Biotinylated

Project description:Tuberculosis (TB) is the deadliest infectious disease worldwide. One obstacle hindering the elimination of TB is our lack of understanding of host-pathogen interactions. Exosomes, naturally loaded with microbial molecules, are circulating markers of TB. Changes in the host protein composition of exosomes from Mycobacterium tuberculosis (Mtb)-infected cells have not been described, can contribute to our understanding of the disease process, and serve as a direct source of biomarkers or as capture targets to enrich for exosomes containing microbial molecules. Here, the protein composition of exosomes from Mtb-infected and uninfected THP-1-derived macrophages was evaluated by tandem-mass-spectrometry and differences in protein abundances were assessed. Our results show that infection with Mtb leads to significant changes in the protein composition of exosomes. Specifically, 41 proteins were significantly more abundant in exosomes from Mtb-infected cells; 63% of these were predicted to be membrane associated. Thus, we used a novel biotinylation strategy to verify protein localization, and confirmed the localization of some of these proteins in the exosomal membrane. Our findings reveal another important scenario where Mtb could be influencing changes in host cells that unveil new features of the host-pathogen interaction and may also be exploited as a source of biomarkers for TB.

2018-08-06 | PXD010659 | Pride

Dual RNA-seq of M. tuberculosis H37Rv infecting macrophage-like THP-1 cells during 48h

Project description:Transcriptional changes during early infection of macrophage-like THP-1 cell line with pathogenic bacterium Mycobacterium tuberculosis. RNAseq samples were taken at 0h (THP-1 cells growing in the RPMI medium), and after 4h, 24h and 48h post infection. Bacterial enrichment was performed to increase the amount of bacterial mRNA in the samples. Non-enriched samples were used to map THP-1 cells transcripts; enriched samples were used to map M. tuberculosis transcripts the corresponding genomes.

2017-08-01 | E-MTAB-5287 | biostudies-arrayexpress

The association and difference of normal THP-1 cell and H37Rv infected THP-1 cell.

Project description:①Background:Tuberculosis is mainly a respiratory tract infection caused by mycobacterium tuberculosis and one of the leading causes of death worldwide. According to the Global Tuberculosis Report in 2021, About a quarter of the world's population is infected with Mycobacterium tuberculosis and China is the second highest burden of TB. Although TB diagnosis and prevention techniques have become more mature, the number of TB cases is still increasing, mainly due to: the prevalence of drug-resistant tuberculosis bacteria, tuberculosis and HIV co-infection, long incubation time of mycobacterium tuberculosis difficult to early diagnosis and so on. Therefore, it is of great significance to study the pathogenesis of mycobacterium tuberculosis infection.②Method: THP-1 cells were treated with 50ng/ml PMA for 24 hours, so that THP-1 cell can be induced into macrophages. After that THP-1 macrophages were infected with mycobacterium tuberculosis H37Rv(MOI=1), which were collected and applied to RNA-sequencing. The constructed sequencing library was sequenced using an Illumina Novaseq 6000 system.

2022-08-31 | GSE203261 | GEO

Nitric oxide exposure induces production of Rpf-dependent differentially culturable mycobacteria

Project description:Rationale: Tuberculosis has a devastating impact on global health by claiming nearly 1.4 million lives each year. During infection Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, produces heterogenous populations some of which don’t produce colonies on agar but grow in liquid media and often require supplementation with culture supernatants or recombinant Resuscitation-promoting factor, thus defined as differentially culturable bacilli. Objectives: to evaluate whether exposure to nitric oxide (NO), a well-known host defence molecule, alters mycobacterial growth phenotypes and drives generation of Rpf-dependent differentially culturable bacilli. Methods: a novel NO donor was synthesised and tested against Mtb and Mycobacterium bovis BCG in vitro, followed by growth assays, flow cytometry analysis and assessment of transcriptomic responses. Resuscitation-promoting factor (Rpf) inhibitors were used to characterise the role of Rpf proteins in the reactivation of NO-treated mycobacteria. Mycobacterial phenotypes were also investigated during infection of THP-1 macrophages activated with retinoic acid and vitamin D3. Measurements and Main Results: differentially culturable mycobacteria were generated after exposure to the novel NO donor or during infection of activated THP-1 cells. Resuscitation of these differentially culturable bacilli was largely abolished by specific Rpf inhibitors. Transcriptomic analysis revealed redox-associated stress signatures mediated by SigH and SigF, with significant down-regulation of ribosome and cell wall architecture genes, including rpfA, rpfB and rpfE, and induction of genes involved in response to thiol stress, sulphur metabolism and iron acquisition. Conclusion: Our study provides mechanistic insights into the generation of Rpf-dependent Mtb during tuberculosis and outlines a critical role of NO in this process.

2023-09-01 | E-MTAB-10776 | biostudies-arrayexpress

mRNA microarray analysis of gene changes in Huh7 cells treated with IFN-Î»4, IFN-Î»1 and IFN-Î±

Project description:The change of gene expression in Huh7 cells treated with IFN-Î»4, IFN-Î»1 and IFN-Î± was analyzed at 0h, 6h and 16h after different interferon treatments. Huh7 cells that had been treated with IFN-Î± (10 IU/ml), IFN-Î»1 (20 ng/ml) and IFN-Î»4 (20 ng/ml). Time points of 6 h and 16 h after stimulation were selected.

2016-08-08 | E-GEOD-83085 | biostudies-arrayexpress

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