PXD040661-1

PXD040661 is an original dataset announced via ProteomeXchange.

Title	PROTEOMIC ANALYSIS OF DYSFUNCTIONAL LIVER SINUSOIDAL ENDOTHELIAL CELLS REVEALS SUBSTANTIAL DIFFERENCES IN MOST COMMON EXPERIMENTAL MODELS OF CHRONIC LIVER DISEASES.
Description	Molecular markers of dedifferentiation of dysfunctional liver sinusoidal endothelial cells (LSEC), have not been fully elucidated. We aimed at deciphering the molecular profile of dysfunctional LSEC in different pathological scenarios. Flow cytometry was used to sort CD11bˉ/CD32b+ and CD11bˉ/CD32bˉLSEC from three rat models of liver disease (bile duct ligation-BDL, inhaled carbon tetrachloride-CCl4 and high fat glucose/fructose diet-HFGFD). Full proteomic profile was performed applying nano-scale liquid chromatography tandem mass spectrometry (nLC-MS) and analyzed with PEAKS software. The percentage of CD32bˉ LSEC varied across groups, suggesting different capillarization processes. Both CD32+ and CD32bˉLSEC from models are different from control LSEC but differently expressed proteins in CD32bˉLSEC are significantly higher. Heatmaps evidenced specific protein expression patterns for each model. Analysis of biological significance comparing dysfunctional CD32bˉLSEC with specialized CD32b+ LSEC from controls showed central similarities represented by 45 common downregulated proteins involved in the suppression of the endocytic machinery and 63 common upregulated proteins associated with the actin-dependent cytoskeleton reorganization. In summary, substantial differences but also similarities in dysfunctional LSEC from the three most common models of liver disease were found, supporting the idea that LSEC may harbor different protein expression profiles according to the etiology or disease stage.
HostingRepository	PRIDE
AnnounceDate	2023-10-24
AnnouncementXML	Submission_2023-10-24_13:05:27.518.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MikelAzkargorta
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-07 09:08:20	ID requested
⏵ 1	2023-10-24 13:05:28	announced
2	2023-11-14 09:10:47	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:10:18	announced	2024-10-22: Updated project metadata.

Gil M, Azkargorta M, Fuster C, Mart, í, nez-G, ó, mez M, Raurell I, Barber, á A, Peric, à, s JM, Hide D, Elortza F, Genesc, à J, Martell M, Proteomic Analysis of Dysfunctional Liver Sinusoidal Endothelial Cells Reveals Substantial Differences in Most Common Experimental Models of Chronic Liver Diseases. Int J Mol Sci, 24(15):(2023) [pubmed]

submitter keyword: Proteomics, Liver sinusoidal endothelial cells,Chronic liver disease, Animal models, Endothelial dysfunction

FelixElortza
contact affiliation	Proteomics Service CIC bioGUNE, Bizakaia Tech. Park Build. 800 48160 Derio Spain
contact email	felortza@cicbiogune.es
lab head
MikelAzkargorta
contact affiliation	Proteomics Platform CIC bioGUNE
contact email	mazkargorta@cicbiogune.es
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD040661

PRIDE project URI

• PRIDE
  1. PXD040661
     1. Label: PRIDE project
     2. Name: PROTEOMIC ANALYSIS OF DYSFUNCTIONAL LIVER SINUSOIDAL ENDOTHELIAL CELLS REVEALS SUBSTANTIAL DIFFERENCES IN MOST COMMON EXPERIMENTAL MODELS OF CHRONIC LIVER DISEASES.