Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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). 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Kavitha Yaddanapudi

PROVIDER: E-GEOD-73333 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: Cardiovascular diseases remain the leading cause of morbidity and mortality worldwide, most of which are caused by atherosclerosis. Discerning processes that participate in macrophage-to-foam cell formation are critical for understanding the basic mechanisms underlying atherosclerosis. To explore the molecular mechanisms of foam cell formation, the differentially expressed proteins were identified. Methods: In this paper, human monocytes, macrophage colony-stimulating factor induced macrophages, and oxidized low-density lipoprotein induced foam cells were cultured, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) were performed to find associations between foam cell transformation and proteome profiles. Results: Totally, 5146 quantifiable proteins were identified, among which 1515 and 182 differentially expressed proteins (DEPs) were found in macrophage/monocyte and foam cell/macrophage, respectively, using a cutoff of 1.5-fold change. Subcellular localization analysis revealed that downregulated DEPs of macrophages/monocytes were mostly located in the nucleus and upregulated DEPs of foam cells/macrophages mostly located in the plasma membrane and extracellular. Functional analysis of DEPs demonstrated that cholesterol metabolism related proteins were upregulated in foam cells, whereas the immune response-related proteins were downregulated in foam cells. The protein-interaction network showed that the DEPs with the highest interaction intensity between macrophages and foam cells were mainly concentrated in lysosomes and the endoplasmic reticulum. Conclusions: This study for the first time to perform quantitative proteomic investigation by TMT labeling and LC-MS/MS to identify differentially expressed proteins in human monocyte, macrophage, and foam cell. The results confirmed cholesterol metabolism was upregulated in foam cells, while immune response was suppressed, which suggested that foam cells were not the population that promote inflammation. In addition, KEGG enrichment analysis and protein-protein interaction indicated that the differentially expressed proteins locating in the endoplasmic reticulum and lysosomes may be key targets to regulate foam cell formation. These data provide a basis for identifying the potential proteins associated with the molecular mechanism involved in the transformation of macrophages to foam cells.

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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

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