PXD004273

PXD004273 is an original dataset announced via ProteomeXchange.

Title	LFQ comparison of total cell lysate, lysosomal and plasma membrane fraction of WT and NPC1 KO cells
Description	Superparamagnetic iron oxide nanoparticles (SPIONs) have so far mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains largely underexploited. We engineered surface functionalized SPIONs (Ø 10 nm) that target very distinct subcellular compartments. Anionic dimercaptosuccinic acid-coated SPIONs are efficiently internalized and accumulate time-dependently in late endosomes and lysosomes, while cationic aminolipid-coated SPIONs surprisingly strongly reside considerably at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for late endosomes/lysosomes and plasma membranes with as consolidated by biochemical, ultrastructural analyses, and to a yield and purity allowing subsequent proteomic and lipidomic profiling. We validated the strength of our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and HeLa to those of HeLa cells deficient in Niemann-Pick disease type C1 (NPC1) deficient HeLa cells expression. While the plasma membrane composition remaineds largely unaltered, pronounced alterations in several protein and lipid species including cholesterol wereare observed in isolated lysosomes reflecting vesicular transport obstruction jamming and deficient lysosomal turnover resulting from NPC1 deficiency. The technology thus allows high-resolution analysis of proteins and lipids. It also, and provides a major advance step forward in fingerprinting subcellular compartments, with an increased potential to identify subtle alterations in biomolecular compositions of lysosomes and/or plasma membranes.
HostingRepository	PRIDE
AnnounceDate	2017-02-01
AnnouncementXML	Submission_2017-02-06_01:13:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jarne Pauwels
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-03 03:12:33	ID requested
1	2017-02-01 11:58:44	announced
⏵ 2	2017-02-06 01:13:29	announced	Updated publication reference for PubMed record(s): 28134274.

Tharkeshwar AK, Trekker J, Vermeire W, Pauwels J, Sannerud R, Priestman DA, Te Vruchte D, Vints K, Baatsen P, Decuypere JP, Lu H, Martin S, Vangheluwe P, Swinnen JV, Lagae L, Impens F, Platt FM, Gevaert K, Annaert W, A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency. Sci Rep, 7():41408(2017) [pubmed]

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

curator keyword: Biological

submitter keyword: Niemann-Pick disease type C1, lysosomal fraction, superparamegnetic iron oxide nanoparticles, label-free quantification

Wim Annaert
contact affiliation	Laboratory for Membrane Trafficking Center for Human Genetics (KULeuven) & VIB-Center for the Biology of Disease
contact email	wim.annaert@cme.vib-kuleuven.be
lab head
Jarne Pauwels
contact affiliation	VIB-Ugent
contact email	jarne.pauwels@vib-ugent.be
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/2017/02/PXD004273

PRIDE project URI

• PRIDE
  1. PXD004273
     1. Label: PRIDE project
     2. Name: LFQ comparison of total cell lysate, lysosomal and plasma membrane fraction of WT and NPC1 KO cells