Dataset Information

Contribution of primary human fibroblasts and endothelial cells to the hallmarks of inflammation as determined by proteome profiling - cytoplasmic proteins of inflammatory stimulated fibroblasts

ABSTRACT: While the most important players of inflammation have been well described, a systematic analysis of the proteins fulfilling the effector functionalities during inflammation has not yet been undertaken. Here we present a systematic proteome study of inflammatory activated primary human endothelial cells and fibroblasts. Cells were stimulated with interleukin 1-beta and fractionated in order to obtain secreted, cytoplasmic and nuclear protein fractions. Proteins were submitted to a data-dependent bottom up analytical platform using a QExactive orbitrap and the MaxQuant software for protein identification and label-free quantification. Results were further combined with similarly generated data previously obtained from the analysis of inflammatory activated peripheral blood mononuclear cells. Applying an FDR of less than 0.01 at both peptide and protein level, a total of 8235 protein groups assembled from 163858 peptides was identified. Comparative proteome analysis allowed us to determine proteins regulated in each kind of cells during inflammation. Remarkably, cells were working on similar inflammation-related tasks, however, by regulating different proteins. Thus, we were able to determine cell type-specific inflammatory signatures, apparently resulting from cell type-specific regulatory mechanisms. Hallmarks of inflammation emerged from these findings, representing commonly and cell type-specific responsibilities of cells during inflammation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Skin, Fibroblast

SUBMITTER: Christopher Gerner

LAB HEAD: Christopher Gerner

PROVIDER: PXD003413 | Pride | 2016-04-04

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	NHDF_cyt_stim_1a_1.mgf	Mgf
	NHDF_cyt_stim_1a_1.mzid.gz	Mzid
	NHDF_cyt_stim_1a_1.pride.mgf.gz	Mgf
	NHDF_cyt_stim_1a_1.pride.mztab.gz	Mztab
	NHDF_cyt_stim_1a_1.raw	Raw

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Publications

Contribution of Human Fibroblasts and Endothelial Cells to the Hallmarks of Inflammation as Determined by Proteome Profiling.

Slany Astrid A Bileck Andrea A Kreutz Dominique D Mayer Rupert L RL Muqaku Besnik B Gerner Christopher C

Molecular & cellular proteomics : MCP 20160329 6

In order to systematically analyze proteins fulfilling effector functionalities during inflammation, here we present a comprehensive proteome study of inflammatory activated primary human endothelial cells and fibroblasts. Cells were stimulated with interleukin 1-β and fractionated in order to obtain secreted, cytoplasmic and nuclear protein fractions. Proteins were submitted to a data-dependent bottom up analytical platform using a QExactive orbitrap and the MaxQuant software for protein identi ...[more]

PMID: 27025457

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Project description:Fibroblasts have only recently been identified as important effector cells in inflammation. In this study, human dermal fibroblasts were inflammatory stimulated with interleukin-1beta and comprehensively analysed with respect to proteins, eicosanoids and metabolites. For eicosadomics, we have established a data-dependent shotgun analysis method capable of identifying inflammation-regulated lipids of yet unknown function. Several classical inflammatory agonists were found induced, including PGA2, PGB2, PGE2 and TXB2, but also modulators such as PGA3 and PGE3, while 8-HETE and several HODE family members remained unaffected. Using targeted metabolomics, several acylcarnithins, phosphatitylcholins and sphingomyelins were found significantly downregulated. Proteome profiling with orbitrap-MS demonstrated the strong induction of several chemokines, metalloproteinases and other effector molecules. Treatment of stimulated fibroblasts with dexamethasone almost completely abrogated the formation of all inflammation-induced eicosanoids and restored levels of acylcarnithins back to normal. As expected, the secretion of IL-6, MMP1, MMP3, CXCL2 and CXCL3 was strongly down-regulated. However, instead of counter-regulating, dexamethasone further enhanced consequences of inflammatory stimulation with respect to CXCL1, CXCL6, complement C3 as well as sphingomyelins. Shotgun secretome data were confirmed by targeted analysis with triple-quadrupol-MS. These molecules have been described to be involved in chronic inflammation. In peripheral blood mononuclear cells, actually dexamethasone successfully downregulated the formation of all detectable inflammation mediators. The present data suggest that successful pharmacological abrogation of the formation of lipid inflammatory mediators in fibroblasts may not suffice to suppress the release of several other powerful inflammatory mediators which we thus understand to be capable of establishing chronic inflammation states.