PXD042379

PXD042379 is an original dataset announced via ProteomeXchange.

Title	Proteomics of plasma and plasma-treated podocytes: application to focal and segmental glomerulosclerosis
Description	Focal and segmental glomerulosclerosis (FSGS) is a severe form of idiopathic nephrotic syn-drome (INS), a glomerulopathy of presumable immune origin and attributed to extrarenal path-ogenic circulating factors. FSGS recurrence (rFSGS) after transplant occurs in 30 to 50% of cases. Direct analysis of patient plasma proteome has been scarcely addressed to date, mainly due to methodological difficulties associated with plasma complexity and dynamic range. In this study, firstly we compared different methods of plasma preparation, secondly we compared the plasma proteome of rFSGS and controls using two preparation methods, and thirdly we analyzed the early proximal signaling events in podocytes subjected to patient plasma, by a combination of phosphoproteomics and lipid raft proteomics (raftomics). By combining immunodepletion and high pH fractionation, we performed a differential proteomic analysis of soluble plasma pro-teins and of extracellular vesicles (EV) obtained from healthy controls, non-INS patient controls, and rFSGS patients (n=4). In both soluble and EV protein sets from rFSGS patients we found a statistically significant increase in a cluster of proteins involved in neutrophil degranulation. A group of lipid binding proteins, generally associated with lipoproteins, was found decreased in the soluble set from rFSGS patients. In addition, three aminoacid transporters involved in mTORC1 activation were found significantly increased in EV from rFSGS. Next, we incubated human podocytes for 30min with 10% plasma from both groups of patients. Phosphoproteomics and raftomics of podocytes revealed profound differences in proteins involved in the mTOR pathway, in autophagy, and in cytoskeleton organization. We analyzed the correlation between the abundance of plasma and plasma-regulated podocyte proteins. The observed changes high-light some of the mechanisms involved in FSGS recurrence and could be used as specific early markers of circulating factor activity on podocytes.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:12:33.739.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cerina Chhuon
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-21 21:44:13	ID requested
1	2023-10-24 15:29:37	announced
⏵ 2	2023-11-14 09:12:41	announced	2023-11-14: Updated project metadata.

Chhuon C, Herrera-Marcos LV, Zhang SY, Charri, è, re-Bertrand C, Jung V, Lipecka J, Savas B, Nasser N, Pawlak A, Boulmerka H, Audard V, Sahali D, Guerrera IC, Ollero M, Proteomics of Plasma and Plasma-Treated Podocytes: Application to Focal and Segmental Glomerulosclerosis. Int J Mol Sci, 24(15):(2023) [pubmed]

submitter keyword: Plasma, immunodepletion, extracellular vesicles, raftomics, phosphoproteomics

Mario Ollero
contact affiliation	Institut Mondor de Recherche Biomédicale, INSERM, U955, 94010 Créteil, France Université Paris Est Créteil, 94010, Créteil, France
contact email	mario.ollero@inserm.fr
lab head
Cerina Chhuon
contact affiliation	Proteomics Platform Necker, PPN-3P5, Structure Fédérative de Recherche SFR Necker, Université Paris Descartes, Paris, France
contact email	cerina.chhuon@inserm.fr
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/PXD042379

PRIDE project URI

• PRIDE
  1. PXD042379
     1. Label: PRIDE project
     2. Name: Proteomics of plasma and plasma-treated podocytes: application to focal and segmental glomerulosclerosis