Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Bulk RNA-Seq of human neutrophils and monocytes isolated from healthy controls, G-CSF-treated donors, HSCT, PDAC and IPMN patients

ABSTRACT: We aimed to characterize transcriptome plasticity of human myeloid cells in response to stress induced myelopoiesis. We performed bulk RNA sequencing (RNA-Seq) analyses of normal density neutrophils (NDNs), low density neutrophils (LDNs), and monocytes isolated from the peripheral blood (PB) of healthy controls (n=19), of G-CSF-treated donors (n=17) as well as of patients receiving hematopoietic stem cell transplantation (HSC-T; n=8), patients with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC; n=15) or intraductal papillary mucinous neoplasms (IPMN; n=14). We also analyzed neutrophil differentiation intermediates from bone marrow samples of controls (n=3) or HSC-T patients (n=7). We generated a total of 210 RNA-Seq samples from 73 individuals.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Eleonora Lusito

PROVIDER: E-MTAB-11190 | 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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Bulk RNA-Seq of human neutrophils and monocytes isolated from healthy controls, G-CSF-treated donors, HSCT, PDAC and IPMN patients

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