Gene expression data from THP-1 cells infected with different Mycobacterium tuberculosis strains
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ABSTRACT:
PROVIDER: PRJNA1034532 | ENA |
REPOSITORIES: ENA
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Project description:Host-pathogen interactions in Mycobacterium tuberculosis infection still remain poorly understood. We investigated the host immune response to different reference Mycobacterium tuberculosis strains in THP-1 cells. Major differences in the gene expression profiles were identified in response to infection with these strains. These findings shed new insights into the dynamic variation in tuberculosis immune response and pathogenesis. We used Affymetrix GeneChip Human Exon 1.0 ST microarrays to investigate host differential gene expression in response to different Mycobacterium tuberculosis strains.
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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.
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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.
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Project description:To compare gene expression changes induced by infection with Mycobacterium tuberculosis (Mtb) with changes induced by purified Mtb products, we infected THP-1 cells with Mtb strain H37Rv or treated with purified Mtb products, then performed RNAseq.
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Project description:Interferon-induced protein with tetratricopeptide repeat 2 (IFIT2) is known for its antiviral activity and has recently been implicated in the defense against Mycobacterium tuberculosis (M. tb). This study employed global transcriptomics to investigate the downstream effects of IFIT2 induction in THP-1 macrophages infected with R179 M. tb, aiming to elucidate its role and downstream contributing factors that aid it in intracellular M. tb killing. Using a vector-based overexpression approach, IFIT2 expression was induced in THP-1 cells infected with R179 M. tb, followed by RNA extraction 12 hours postinfection and AmpliSeq-based targeted transcriptome sequencing. Bioinformatics analysis identified 282 differentially expressed genes (DEGs), of which 189 were upregulated and 90 were downregulated (FDR <0.05). Filtering for highly significant DEGs (|log2(fold change) | > 1.5) yielded 70 genes, predominantly upregulated, with functional enrichment in pathways such as defense response to viruses and cytokine-mediated signaling. Signaling pathway impact analysis highlighted pathway activation and inhibition of the tuberculosis (TB) pathway. RT-qPCR validation confirmed the upregulation of selected DEGs (ISG15, CMPK2, RSAD2, IFI44L, IFI44), corroborating the AmpliSeq data. This study provides comprehensive insights into the transcriptomic profile induced by IFIT2 in TB, revealing critical downstream contributors and pathways that underpin IFIT2’s ability to combat M. tb infection.
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