PXD028321-1

PXD028321 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS proteomics analysis of neuronal cells and secretomes with timsTOF Pro
Description	LRRK2 mutations are a major cause of both familial and sporadic Parkinson’s disease (PD). LRRK2 has been suggested to be a key regulator of endolysosomal membrane trafficking, a process which relies particularly on membrane fusion mediated by VAMPs. VAMP7 interacts with LRRK1, a paralogue of LRRK2 and VAMP4 is present in protein complexes with LRRK2. Here we investigated the biochemical links between LRRK2 and VAMPs and their potential cellular functions. We found that LRRK2 interacted with several VAMPs with the following hierarchy: VAMP4>VAMP7>VAMP8. R1441C mutant of LRRK2 was the most efficient VAMP4 interactor and formed cytoplasmic filaments to which VAMP4 was recruited in HEK293 cells. Yeast-2-Hybrid assay failed to detect a direct high affinity interaction between LRRK2 fragments and VAMP4 or VAMP7 but identified an interacting domain within the C-terminal of Ras-of-complex domain of LRRK2 with Snapin. Snapin interacted with both VAMP4 and VAMP7, and a tripartite LRRK2/Snapin/VAMP4 was identified suggesting that Snapin could be an intermediate partner between LRRK2, VAMP4 and VAMP7. RUSH assay experiments in HEK293 cells showed that LRRK2 delayed exit of TNFa. VAMP4- and VAMP7-KO neuronal cells’ secreted less pro-VGF and showed impaired VGF localization. R1441C mutant of LRRK2 further affected the subcellular localization of VGF. Altogether, these results suggest that LRRK2 might regulate a subset of v-SNAREs involved in secretion and that mutations in PD patients, particularly R1441C, might lead to alterations in the secretome.
HostingRepository	PRIDE
AnnounceDate	2023-01-31
AnnouncementXML	Submission_2023-01-31_12:59:43.070.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chiaraguerrera
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 08:25:23	ID requested
⏵ 1	2023-01-31 12:59:43	announced
2	2023-04-03 03:27:08	announced	2023-04-03: Updated project metadata.

Dataset with its publication pending

submitter keyword: VAMPs, parkinson’s disease,Secretome, neuronal cells, timsTOF Pro, LC-MS/MS

ChiaraGuerrera
contact affiliation	Chiara Guerrera, IR1, HDR Head of the Proteomics Platform SFR Necker INSERM US24 Faculty of Medecine, University of Paris 160 rue de Vaugirard 75015 Paris Tél. : 01 40 61 54 67
contact email	chiara.guerrera@inserm.fr
lab head
Chiaraguerrera
contact affiliation	Necker proteomics, INSERM
contact email	chiara.guerrera@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/2023/01/PXD028321

PRIDE project URI

• PRIDE
  1. PXD028321
     1. Label: PRIDE project
     2. Name: LC-MS/MS proteomics analysis of neuronal cells and secretomes with timsTOF Pro