PXD015880

PXD015880 is an original dataset announced via ProteomeXchange.

Title	Exploring the impact of PARK2 mutations on the total and mitochondrial proteome of human skin fibroblasts
Description	Mutations in PARK2 gene are the most frequent cause of familial forms of Parkinson’s disease (PD). This gene encodes Parkin, an E3 ubiquitin ligase involved in several cellular mechanisms, such as the mitophagic process. Mutations in this gene, which cause the loss of function of Parkin, are responsible for the accumulation of damaged mitochondria. This improper disposal may generate increased levels of ROS, lower ATP production and apoptosis activation. Given the importance of mitochondrial dysfunctions and mitophagy impairment in PD pathogenesis, the aim of the present project was to investigate both whole-cell and mitochondrial proteome alterations in human skin fibroblasts of PARK2-mutated patients. To this purpose, total and mitochondrial-enriched protein fractions from fibroblasts of five PARK2-mutated patients and five control subjects were analyzed by quantitative shotgun proteomics, in order to identify proteins specifically altered by Parkin loss. Both the network-based and the GSEA analysis of proteomics results pointed out the importance of pathways in which Rab GTPase proteins are involved. An alteration of their levels also in the mitochondrial fraction may indicate a re-localization of these GTP/GDP molecular switches, master regulators of membrane trafficking. To have a more comprehensive view of the mitochondrial alterations due to PARK2 mutations, we investigated the impact of Parkin loss on mitochondrial function and network morphology. We unveiled that the mitochondrial membrane potential was reduced in PARK2-mutated patients. Nevertheless, PINK1 did not accumulate on depolarized mitochondria. Even after the treatment with CCCP, an ionophore that triggers mitophagy, the accumulation of PINK1 was less efficient in PARK2-mutated patients than in controls derived fibroblasts. The analysis of the mitochondrial network morphology showed a filamentous network with mitochondria distributed all over the cell that was comparable between PARK2-mutated patients and control subjects. Thus, our results suggested that the network morphology was not influenced by the mitochondrial depolarization and by the lack of Parkin, revealing a possible impairment of fission and, more in general, of mitochondrial dynamics. In conclusion, the present work highlighted new molecular factors and pathways altered by PARK2 mutations. Furthermore, we obtained a definition of the mitochondrial landscape and molecular mechanisms underlying the PARK2 form of Parkinson’s disease, which will help to unravel possible biochemical pathways altered also in the sporadic form of the disease. Indeed, it is known that in sporadic cases the genetic/epigenetic background and the environment lead over time to mitochondria impairment and to the accumulation of damaged organelles.
HostingRepository	PRIDE
AnnounceDate	2020-05-11
AnnouncementXML	Submission_2020-07-22_06:47:02.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015880
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Federica Marini
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-18 01:41:22	ID requested
1	2020-05-10 22:50:39	announced
⏵ 2	2020-07-22 06:47:03	announced	2020-07-22: Updated publication reference for PubMed record(s): 32596240.

Zilocchi M, Colugnat I, Lualdi M, Meduri M, Marini F, Corasolla Carregari V, Moutaoufik MT, Phanse S, Pieroni L, Babu M, Garavaglia B, Fasano M, Alberio T, Mutations on the Total and Mitochondrial Proteome of Human Skin Fibroblasts. Front Cell Dev Biol, 8():423(2020) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project, Mitochondria (HPP)

submitter keyword: PARK2 mutation, mitochondria, mass spectrometry, human skin fibroblast, shotgun proteomics, immunoprecipitation, Parkinson’s Disease

Luisa Pieroni
contact affiliation	Proteomic and Metabonomic Laboratory, IRCCS-Fondazione Santa Lucia, Rome, Italy Via del Fosso di Fiorano 64/65, 00143, Rome, Italy +3906/501703215
contact email	l.pieroni@hsantalucia.it
lab head
Federica Marini
contact affiliation	Catholic University of Sacred Heart (Rome)
contact email	federica.marini@unicatt.it
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/2020/05/PXD015880

PRIDE project URI

• PRIDE
  1. PXD015880
     1. Label: PRIDE project
     2. Name: Exploring the impact of PARK2 mutations on the total and mitochondrial proteome of human skin fibroblasts