RNA-seq analysis of macrophages that are proximal or distal to tumor cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE221203 | GEO | 2023/05/31
REPOSITORIES: GEO
Similar Datasets
Project description:The first experiment involved the DU-145 tumor cell samples cultured with or without macrophages. This experiment was planned with an aim to evaluate the gene expression changes that might occur in DU-145 cells when grown in proximity to macrophages as compared to DU145 cells being grown alone. Similarly, the second experiment, involved the macrophage samples cultured with or without the DU-145 cells. This experiment was planned with an aim to evaluate the gene expression changes that might occur in Macrophages when grown in proximity to DU-145 cells . Agilent one-color experiment, Organism: Human, Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2012-03-08 | E-GEOD-36047 | biostudies-arrayexpress
Project description:Human guanylate binding proteins (GBPs) are key players of interferon-gamma (IFNγ)-induced cell intrinsic defense mechanisms targeting intracellular pathogens. In this study, we combine the well-established Toxoplasmagondii infection model with three in vitro macrophage culture systems to delineate the contribution of individual GBP family members to control this apicomplexan parasite. Use of high-throughput imaging assays and genome engineering allowed us to define a role for GBP1, 2 and 5 in parasite infection control. While GBP1 performs a pathogen-proximal, parasiticidal and growth-restricting function through accumulation at the parasitophorous vacuole of intracellular Toxoplasma, GBP2 and GBP5 perform a pathogen-distal, growth-restricting role. We further find that mutants of the GTPase or isoprenylation site of GBP1/2/5 affect their normal function in Toxoplasma control by leading to mis-localization of the proteins.
| S-EPMC8752258 | biostudies-literature
Project description:The first experiment involved the DU-145 tumor cell samples cultured with or without macrophages. This experiment was planned with an aim to evaluate the gene expression changes that might occur in DU-145 cells when grown in proximity to macrophages as compared to DU145 cells being grown alone. Similarly, the second experiment, involved the macrophage samples cultured with or without the DU-145 cells. This experiment was planned with an aim to evaluate the gene expression changes that might occur in Macrophages when grown in proximity to DU-145 cells .
2012-03-08 | GSE36047 | GEO
Project description:Macrophages are key cell types of the innate immune system regulating host defense, inflammation, tissue homeostasis and cancer. Within this functional spectrum diverse and often opposing phenotypes are displayed which are dictated by environmental clues and depend on highly plastic transcriptional programs. Among these the ‘classical’ (M1) and ‘alternative’ (M2) macrophage polarization phenotypes are the best characterized. Understanding macrophage polarization in humans may reveal novel therapeutic intervention possibilities for chronic inflammation, wound healing and cancer. Systematic loss of function screening in human primary macrophages is limited due to lack of robust gene delivery methods and limited sample availability. To overcome these hurdles we developed cell-autonomous assays using the THP-1 cell line allowing genetic screens for human macrophage phenotypes. To confirm the relevance of the THP1-based system we performed microarray studies on THP1 cells and primary human cells subjected to various conditions. THP1 cells were treated with PMA (phorbol 12-myristate 13-acetate) to derive macrophages which were then cultured 1, 3 or 6 days with different stimuli.
2017-08-25 | E-MTAB-5917 | biostudies-arrayexpress
Project description:Primary human macrophages were cultured 1, 3 or 6 days with different stimuli. Macrophages are key cell types of the innate immune system regulating host defense, inflammation, tissue homeostasis and cancer. Within this functional spectrum diverse and often opposing phenotypes are displayed which are dictated by environmental clues and depend on highly plastic transcriptional programs. Among these the ‘classical’ (M1) and ‘alternative’ (M2) macrophage polarization phenotypes are the best characterized. Understanding macrophage polarization in humans may reveal novel therapeutic intervention possibilities for chronic inflammation, wound healing and cancer. Systematic loss of function screening in human primary macrophages is limited due to lack of robust gene delivery methods and limited sample availability. To overcome these hurdles we developed cell-autonomous assays using the THP-1 cell line allowing genetic screens for human macrophage phenotypes. To confirm the relevance of the THP1-based system we performed microarray studies on THP1 cells and primary human cells subjected to various conditions.
2017-08-25 | E-MTAB-5913 | biostudies-arrayexpress
Project description:These data suggest that co-culture with macrophages increases expression of NDRG-1 in epithelial cell lines. The finding is confirmed in 1 mouse epithelial cell line, and in tissue derived from mice genetically and dietetically altered to increase macrophage infiltration of the small and large intestinal epithelium. NDRG1 is identified as a potential mediator of macrophage effects on tumorigenesis in the large and small intestine. Array data is part of a larger study involving the effects of Vitamin D, in concert with macrophages, on intestinal homeostasis and tumorigenesis, entitled Cell autonomous and non-autonomous interactions of a western-style diet and the vitamin D receptor in intestinal homeostasis and tumorigenesis Cells from human colon cancer cell lines were cultured either alone, with Vitamin D3, with THP1 macrophages, or with THP1 macrophages and Vitamin D3, in a system which allowed no physical contact but exchange of soluble factors between the cell types.
2014-03-12 | E-GEOD-55810 | biostudies-arrayexpress
Project description:Backgrounds:Macrophages are one of HIV reservoirs. Vpr is essential for infection of macrophages by HIV-1 and has the potential to promote survival of macrophages, which could be a highly significant factor in the development and/or maintenance of macrophage viral reservoirs. However, the impact of vpr on macrophages resistance to apoptosis is yet to be comprehended. Methods:We determined the expression profiles of lncRNAs in THP1-MAC and THP1-MAC treated with Vpr peptides using microarray analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore their function. We also constructed competing endogenous RNA (ceRNA) networks with bioinformatics methods. Results：We identified 410 lncRNAs that were differentially expressed between THP1-MAC and THP1-MAC after Vpr peptides treatment. Significantly enriched GO terms and pathways were identified, some of which were linked to apoptosis and inflammatory responses. CeRNA analysis showed that lncRNA LINC02249 was paired with the most differentially expressed gene. qRT-PCR results confirmed the reliability of the microarray data. Conclusions：LINC02249 associated ceRNA network may play a role in macrophages resistant to vpr induced apoptosis. This will provide a new avenue for investigating the pathogenesis of macrophages resistant to vpr-induced apoptosis.
2022-08-16 | GSE211274 | GEO
Project description:We performed RNA-Seq to confirm the changes in expression of genes in the relevant pathway in human gastric cancer cells (AGS cells) and AGS cells cocultured with macrophages (RAW264.7 cells). In the gene ontology enrichment analysis of the 160 genes that were increased in AGS cells cocultured with RAW264.7 cells, pathways related to immune response, cell adhesion, and cytokine response were enriched.
2022-12-12 | GSE220531 | GEO
Project description:To clarify the role of DMD in macrophages in response to IMQ, we performed transcriptomic analysis by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) from IMQ-induced THP1 macrophages with or without DMD treatment in vitro.
2021-04-09 | GSE171667 | GEO
Project description:We report the impact of altered CMPK2 expression in THP1 macrophages. CMPK2 silencing THP1 macrophages (CM) were constructed by stably expressing siRNA against CMPK2. Scrambled siRNA expressing THP1 cells were used as control (SC). THP1 macrophages stably expressing CMPK2 fused with mCherry was used as CMPK2 overexpressing macrophages (OE). Control cells were constructed by overexpressing mCherry alone (VC). The RNA sequencing was used to identify genes that are differentially expressed in CMPK2 modified THP1 macrophages.
2022-11-11 | GSE199951 | GEO