Dataset Information

Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus dense bodies

ABSTRACT: A mass spectrometry-based proteomics analysis was performed to study the proteome changes upon treatment with dense bodies derived from human cytomegalovirus infection.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Fibroblast

SUBMITTER: Jia-Xuan Chen

LAB HEAD: Bodo Plachter

PROVIDER: PXD039032 | Pride | 2023-07-24

REPOSITORIES: Pride

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			Action	DRS
	20180731_QEP1_EXT_CF_0389_hs_PR_DML_120.raw	Raw
	20180731_QEP1_EXT_CF_0390_hs_PR_DML_120.raw	Raw
	20190225_QEP1_EXT_CF_0465_hs_PR_DML_240.raw	Raw
	20190225_QEP1_EXT_CF_0467_hs_PR_DML_240.raw	Raw
	20190225_QEP1_EXT_CF_0471_hs_PR_DML_240.raw	Raw

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Project description:Single cell transcriptomic analyses (scRNAseq) of hepatocytes and liver endothelial cells (L-EC) have revolutionized the understanding of the spatial architecture of liver structure and function. The spatial alignment of L-EC and hepatocytes is pivotal for liver function in health and disease given that L-EC act as instructive gatekeeper of nearby hepatocytes including the maintenance of liver metabolic zonation in a Wnt-dependent manner. Advancing liver biology beyond the ’transcript-centric’ view of scRNAseq analyses is presently restricted by the limited resolution of proteomics and genome-wide techniques to analyse post-translational modifications. Here, by combining spatial cell sorting methodology with transcriptomic and quantitative proteomic/phospho-proteomic analyses, we established the first functionally and spatially-resolved proteome landscape of the liver endothelium, yielding deep mechanistic insight into zonated vascular signalling mechanisms. Phosphorylation of receptor tyrosine kinases (RTK) was detected preferentially in the central vein area resulting in an atypical enrichment of tyrosine phosphorylation. Prototypic biological validation of the identified strong phosphorylation gradient of the vascular RTK Tie1 by blockade resulted in the rapid peri-central dysregulation of the L-EC transcriptome. Notably, the expression of Wnt9b in L-EC was discovered as Tie receptor controlled with reciprocal regulation by FoxO1 and STAT3 transcription factors. Genetic inactivation of Tie1 in L-EC or antibody blockade resulted in reduced liver regeneration following partial hepatectomy with reduced Wnt ligand and Wnt target gene expression, including Axin2, Sox9, Tbx3 and Lgr5. Taken together, the study has yielded unparalleled insight into the spatial organization of L EC signalling and discovered a vascular Tie-Wnt signalling axis as regulator of liver function. The employed spatial sorting technique followed by phospho-proteomic analysis may be employed as a universally adaptable strategy for the spatial phosphoproteomic analysis of scRNAseq data-defined relevant cellular (sub)-populations.

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Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus dense bodies

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