Bulk RNA-seq profiling the response of human first-trimester and term Hofbauer cells to Listeria monocytogenes infection in vitro
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ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: Qian Li
PROVIDER: E-MTAB-14086 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To establish an in vitro assay using primary human Hofbauer cells, we needed to understand how the cells change in vitro. We therefore profiled and compared the transcriptomes of freshly isolated first-trimester and term Hofbauer cells to those after 7 days in culture. Cells were isolated by fluorescence-activated cell sorting and the RNA library was prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit (Takara Bio).
2025-08-04 | E-MTAB-14087 | biostudies-arrayexpress
Project description:The cellular proteome is the set of expressed proteins at a given time and defines an organism's phenotype under specific conditions. The proteome is shaped and remodeled by both protein synthesis and degradation. In this study, we combined metabolic and chemical isobaric peptide labeling to simultaneously determine protein decay and de novo synthesis of intracellular Listeria monocytogenes, while focusing on the role of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in the human pathogen L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L.monocytogenes remains elusive. We observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlights the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. Importance Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. It is therefore important to profile the underlying changes on the bacterial proteome level during the infection process to understand pathogenesis and host-dependent adaptation processes. The interplay between protein synthesis and decay governs cellular protein abundance. SILAC pulse labeling enables direct readout of these events during infection. Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. We applied this integrated approach to investigate protein turnover during the temporal progression of bacterial adaptation to the host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.
2021-07-16 | PXD023608 | Pride
Project description:To understand how the human macrophages and monocytes (of both fetal and maternal origin) isolated from first-trimester and term placentas differ, we profiled and compared the transcriptomes of cells freshly isolated by fluorescence-activated cell sorting, including fetal Hofbauer cells, placenta-associated maternal macrophages (PAMM), decidual macrophages, maternal and fetal monocytes using the SMART-Seq® v4 PLUS Kit (Takara Bio).
2025-08-04 | E-MTAB-14088 | biostudies-arrayexpress
Project description:Transcriptional profling of a Listeria monocytogenes under nisin treatment comparing ctsR mutant and wild type one condition (nisin treament 20ug/ml, 24 hours) experiment, ctsR mutant vs. wild type Listeria monocytogenes Scott A, 2 biological replicates, 4 technical replicates
2013-02-14 | E-GEOD-41891 | biostudies-arrayexpress
Project description:Listeria monocytogenes is a foodborne intracellular bacterial model pathogen. Protective immunity against Listeria depends on an effective CD8 T-cell responses, but very few T cell epitopes are known in mice as most common animal infection model for listeriosis. To identify epitopes we screened for Listeria epitopes presented in the spleen of infected mice by mass spectrometry-based immunopeptidomics. In between more than 6,000 mouse self-peptides presented on MHC Class I molecules, we detected 26 Listeria peptides from 25 different bacterial proteins, including previously reported antigens. Bacterial immunopeptides with confirmed fragmentation spectra were further tested for their potential to CD8 T cells, revealing VTYNYINI from the putative cell wall surface anchor family protein LMON_0576 as a novel bona fide peptide epitope. Despite its high biological potency in a prime boost model, this epitope did not protect against challenge infection but can be used as a research tool to probe CD8 T cell responses in mouse models of Listeria infection. Our results demonstrate the power of immunopeptidomics for bacterial antigen identification but highlight the need for in-depth immune characterization for vaccine candidate selection.
2024-08-13 | PXD047750 | Pride
Project description:Expression profiling by microarray was used with a murine listeriosis model to better understand increased susceptibility of preterm neonates to infection. We used DNA microarray to identify genes that were differentially expressed in liver of adult and neonatal Balb/c mice after listeriosis infection. A murine listeriosis model was established. The methods for culturing and counting the Listeria monocytogenes (strain CNL 85/163) had been described in previous publications. The Listeria was injected intraperitoneally using a 1-mL U-100 insulin syringe with a 30 gauge needle. Doses of Listeria monocytogenes used were based on work by our laboratory showing that similar bacterial colony counts were obtained with 4.2 x 10^5 total Listeria per adult mouse and 150 Listeria per gram for 3 to 5 day old neonatal mice. In neonatal mice, great care was taken to void deep intraperitoneal injection towards the viscera, or across the central abdominal vessels. At specified time points, liver was removed upon animal sacrifice and immediately flash frozen in liquid nitrogen and stored at -80 degrees Centigrade. Three adult mice and three neonatal mice were used at each time point.
2013-06-01 | E-GEOD-45051 | biostudies-arrayexpress
Project description:DNA damage response kinase ATM regulates the genetic program of lymphocytes with phsiologically induced DNA DSBs. In bone marrow-derived macrophages, related kinase DNAPKcs is also responsible for activating DNA damage responses after infection with Listeria monocytogenes. Here we show that both ATM and DNA-PKcs regulate the genetic program of Listeria monocytogenes-infected macrophages. Two independent bone marrow-derived macrophage cultures for each genotype (LysMcre/+ and Scid: Atmc/c: LysMcre/+) were infected with Listeria monocytogenes for 24 hrs at an MOI of 5. RNA was isolated using RNeasy (Qiagen). Gene expression profiling was performed using Illumina MouseRef-8 expression microarrays.
2015-07-03 | E-GEOD-70467 | biostudies-arrayexpress
Project description:Listeria monocytogenes causes severe foodborne illness in pregnant women and immunocompromised individuals. After the intestinal phase of infection, the liver plays a central role in the clearance of this pathogen through its important functions in immunity. However, recent evidence suggests that subpopulations of L. monocytogenes may escape eradication after prolonged infection of hepatocytes, by entering a persistence phase in vacuoles. Here, we examine whether this long-term infection alters hepatocyte defense pathways, which may be instrumental for bacterial persistence. We first established models of Listeria infection in human hepatocyte cell lines HepG2 and Huh7 and in primary mouse hepatocytes (PMH). In these cells, Listeria efficiently enters the persistence stage after a 3-day infection, while inducing a type I (PMH) or type I/III (HepG2) or no (Huh7) interferon response. RNA-seq analysis identified a common signature of long-term Listeria infection on the hepatocyte transcriptome, characterized by overexpression of a set of genes involved in antiviral immunity and under-expression of many acute phase protein (APP) genes, particularly involved in the complement and coagulation systems. The decrease in APP transcript amounts correlated with lower protein abundance in the secretome of infected cells, as shown by proteomics, and also occurred in the presence of APP inducers (IL-6 or IL-1b). The results also suggest that long-term Listeria infection affects lipid metabolism pathways. Collectively, these results reveal that long-term infection with L. monocytogenes profoundly deregulates the innate immune functions of hepatocytes, which could generate an environment favorable to the establishment of persistent infection.
2021-11-02 | PXD027154 | Pride
Project description:RNASeq of the human epithelial cell line LoVo following Listeria monocytogenes infection
2015-09-15 | E-MTAB-3649 | biostudies-arrayexpress
Project description:The foodborne pathogen Listeria monocytogenes has the ability to develop biofilm in food-processing environment, which becomes a major concern for the food safety. PrfA, a key transcriptional activator that regulates most of the known listerial virulence gene expression, has been shown to promote L. monocytogenes biofilm formation. In this study, the whole genome microarray was used to identify differentially expressed genes associated with the putative interaction between biofilm formation and PrfA in L. monocytogenes. Comparative transcriptome analyses indicated over 21.9% of the L. monocytogenes EGDe genes (627 out of 2857 predicted) were altered in their expression in biofilm cells relative to planktonic cell populations. These genes were classed into different functional categories which cover most of the biochemical functions encountered in bacterial cells, especially involved in ion transport, DNA repair, and cell wall biosynthesis based on significant enrichment of GO terms. Among them, 185 genes were identified to be associated with PrfA and biofilm formation by comparison of the whole gene expression profiles of L. monocytogenes EGDe and its M-NM-^TprfA mutant. The expression tendency of these PrfA-associated and biofilm-specific genes were mainly opposite in M-NM-^TprfA biofilm, and most of them are involved in phage-related function, membrane bioenergetics, and cell wall. Our results indicated that L. monocytogenes biofilm formation is probably controlled by the complex regulation network involved variable genes required for the different biological pathways. This regulatory network is modified in the prfA deletion mutant in order to maintain its stable biofilm lifestyle. Gene expression of planktonic cells and biofilm cells in Listeria monocytogenes EGDe and prfA isogenic deletion strain EGDeM-NM-^TprfA with cultivated in MEM and BHI for 48 hours, were mesasued using Agilent Listeria monocytogenes customized whole-genome microarray 8x15 array. Three replicates.
2013-05-01 | E-GEOD-43052 | biostudies-arrayexpress