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Melanoma cell line-induced MDSC transcriptome analysis reveals a unique gene expression profile that is largely reversed to normal monocyte level by MIF inhibition

ABSTRACT: Affymetrix microaaray analysis of healthy donor monocytes cultured for 64 hours in the absence of (culture monocytes), or presence of A375 cells (A375-MDSC) or treated with MIF inihibitor, 4-IPP (MDSC+4-IPP; 100mM, day 0 and 50mM, day 2).

ORGANISM(S): Homo sapiens

PROVIDER: GSE73333 | GEO | 2015/09/23

SECONDARY ACCESSION(S): PRJNA296690

REPOSITORIES: GEO

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Melanoma cell line-induced MDSC transcriptome analysis reveals a unique gene expression profile that is largely reversed to normal monocyte level by MIF inhibition

Project description:Affymetrix microaaray analysis of healthy donor monocytes cultured for 64 hours in the absence of (culture monocytes), or presence of A375 cells (A375-MDSC) or treated with MIF inihibitor, 4-IPP (MDSC+4-IPP; 100mM, day 0 and 50mM, day 2). Significantly modulated genes were clustered into a hierarchical representation. Each column represents one replicate, whereas each row corresponds to the expression of a particular gene across different replicates/experimental conditions.

2015-09-23 | E-GEOD-73333 | biostudies-arrayexpress

Mechanism of biphasic effects of alcohol on gene expression

Project description:the molecular mechanisms for the biphasic effect of alcohol are not fully understood. The goal of the study is to identify genes that are differentially expressed following alcohol exposure of 50mM and 100mM ethanol for 24 hours.

2010-04-05 | GSE12253 | GEO

Proteomic profiling of extracellular vesicles from cancer-associated fibroblast-induced myeloid-derived suppressor cells and related cell types

Project description:Cancer-associated fibroblast (CAF) promote immune suppression in the tumor microenvironment by polarizing monocytes to myeloid-derived suppressor cells (MDSC) that potently suppress T-cell function. Using a patient-derived coculture system, we found that extracellular vesicles (EV) released by CAF-induced MDSC directly suppress T-cell proliferation. In this study, we profiled the protein cargo of the EVs isolated from CAF-MDSC and compared to related cell types.

2024-01-03 | PXD035248 | Pride

Transcription profiling of yeast subjected to different concentrations of caesium chloride salt

Project description:S. cerevisiae BY4741 (Mata; His3Delta1; leuDelta0; lys2Delta0; ura3Delta0) was grown in YPD at 30 degrees C with aeration to exponential growth phase and was subjected to a different concentrations of Caesium Chloride salt: 0mM, 30mM, 50mM, 100mM, 150mM, 200mM and 250mM 20 minutes at 30 degrees C.

2007-11-01 | E-MEXP-1292 | biostudies-arrayexpress

Single-Cell Trajectories of Melanoma Cell Resistance to Targeted Treatment

Project description:In order to identify mechanisms of melanoma treatment resistance, we applied micorofluidic scRNA-Seq to the transcripomes of a total of about 31,000 single cells obtained form A375 melanoma cell line untreated/sensitive or treated with BRAF inhibitor vemurafenib, either alone or in combination with MEK1 inihibitor cobimetinib or trametinib. Analysis by dimensionality reduction software tSNE and SOM identified a clonal heterogeneity clearly seperating all 4 possible treatment conditions.

2021-01-16 | GSE164897 | GEO

Cell surface proteome profiling of cancer-associated fibroblast-induced myeloid-derived suppressor cells and related cell types

Project description:Cancer-associated fibroblasts (CAF) promote immune suppression in the tumor microenvironment by polarizing monocytes to myeloid-derived suppressor cells (MDSC) that potently suppress T-cell function. Using a patient-derived coculture system, we profiled the cell surface proteome of CAF-induced MDSC to identify potential mechanism through which T-cell function is impaired.

2024-01-03 | PXD035259 | Pride

Project description:Myeloid-derived suppressor cells (MDSC) is a heterogeneous population of cells that can negatively regulate T-cell function. As opposed to murine MDSC, which are characterized as Gr-1+CD11b+ cells, human MDSC are not so clearly defined due to lack of specific markers. Our lab has previously identified a new subset of MDSC as CD14+HLA-DR-neg/low cells from PBMC. CD14+HLA-DR-neg/low MDSC not only suppress proliferation and IFN-gamma secretion of autologous T cells, but also induce CD25+Foxp3+ regulatory T cells that are suppressive in vitro, whereas the counterpart CD14+HLA-DR-high monocytes don’t have the effect. In this study, we compare the immune-related gene expression between CD14+HLA-DR-neg/low MDSC and CD14+HLA-DR-high monocytes to better characterize the difference between these two populations and to find new potential specific marker for human MDSC. PBMC were isolated from fresh blood healthy donor by density centrifugation. CD14+ cells were isolated by AutoMACS CD14 microbeads using a AutoMACS (Miltenyi), and then stained with CD14 and HLA-DR antibodies. MDSC and monocytes control cells were sorted as CD14+ HLA-DR-neg/low and CD14+HLA-DR-high cells respectively. The sorted two populations were immediately frozen in liquid nitrogen and shipped to the company on dry ice for RNA isolation and further microarray.

2011-09-08 | E-GEOD-32001 | biostudies-arrayexpress

Healthy Myeloid-Derived Suppressor Cells Express the Surface Ectoenzyme Vanin-2 (VNN2)

Project description:Study of human monocytic Myeloid-Derived Suppressor cells Mo-MDSC (CD14+ HLA-DRneg/low) has been hampered by the lack of positive cell-surface markers. In order to identify positive markers for Mo-MDSC, we performed microarray analysis comparing Mo-MDSC cells from healthy subjects versus CD14+ HLA-DRhigh monocytes. We have identified the surface ectoenzyme Vanin-2(VNN2) protein as a novel biomarker highly-enriched in healthy subjects Mo-MDSC. Indeed, healthy subjects Mo-MDSC cells expressed 68% VNN2, whereas only 9% VNN2 expression was observed on CD14+ HLA-DRhigh cells (n=4 p<0.01). The top 10 percent positive VNN2 monocytes expressed CD33 and CD11b while being negative for HLA-DR, CD3, CD15, CD19 and CD56, consistent with a Mo-MDSC phenotype. CD14+VNN2high monocytes were able to inhibit CD8 T cell proliferation comparably to traditional Mo-MDSC at 51% and 48% respectively. However, VNN2 expression on CD14+ monocytes from glioma patients was inversely correlated to their grade. CD14+VNN2high monocytes thus appear to mark a monocytic population similar to Mo-MDSC only in healthy subjects, which may be useful for tumor diagnoses. Myeloid-Derived Suppressor Cells (MDSC) are identified by upregulated expression of the cell surface ectoenzyme Vanin-2 in healthy subjects

2021-12-22 | GSE192350 | GEO

2011-09-09 | GSE32001 | GEO

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli

Project description:Isopentenyl pyrophosphate (IPP) is the universal C5 precursor for isoprenoids, the largest class of natural products and frequent targets for metabolic engineering. In engineered microbial systems, IPP toxicity presents a challenge since its formation is unavoidable in the production of high-value, long-chain terpenes. In this work, we develop an experimental platform to study IPP toxicity in E. coli engineered to produce isoprenol, an IPP-derived C5 alcohol. We first characterize the physiological response to IPP accumulation, demonstrating that elevated levels of IPP are linked to growth inhibition, altered morphology, and reduced cell viability. We show that IPP toxicity selects for pathway “breakage”, using proteomics to identify a reduction in phosphomevalonate kinase (PMK) as a probable recovery mechanism. Next, we demonstrate that endogenous E. coli metabolism is globally impacted by IPP accumulation, which results in inhibited nutrient uptake, reduced ATP levels, and an apparent “pause” in metabolism. Finally, we suggest that IPP toxicity is mediated by the formation of an isoprenyl-ATP analog (ApppI). The complementary data presented here represent the most comprehensive assessment of IPP stress to date and suggest potential strategies for the alleviation of IPP and prenyl diphosphate toxicity.

2018-03-14 | GSE102672 | GEO

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