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A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics : the case of NPC1 deficiency

Arun Kumar Tharkeshwar Raghunath, Jesse Trekker, Wendy Vermeire, Jarne Pauwels UGent, Ragna Sannerud, David A Priestman, Danielle te Vruchte, Katlijn Vints, Pieter Baatsen, Jean-Paul Decuypere, et al. (2017) SCIENTIFIC REPORTS. 7.
abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
NIEMANN-PICK C1, IRON-OXIDE NANOPARTICLES, STABILIZED MAGNETIC FLUIDS, CELL-LINE, ORGANELLAR PROTEOMICS, PROTEIN LOCALIZATION, STORAGE DISORDERS, MEMBRANE-PROTEINS, DISEASE, SURFACE
journal title
SCIENTIFIC REPORTS
Sci. Rep.
volume
7
article number
41408
pages
20 pages
Web of Science type
Article
Web of Science id
000392854700001
ISSN
2045-2322
DOI
10.1038/srep41408
language
English
UGent publication?
yes
classification
A1
copyright statement
Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
id
8508277
handle
http://hdl.handle.net/1854/LU-8508277
date created
2017-02-08 13:51:43
date last changed
2017-03-03 11:10:09
@article{8508277,
  abstract     = {Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.},
  articleno    = {41408},
  author       = {Tharkeshwar Raghunath, Arun Kumar and Trekker, Jesse and Vermeire, Wendy and Pauwels, Jarne and Sannerud, Ragna and Priestman, David A and te Vruchte, Danielle and Vints, Katlijn and Baatsen, Pieter and Decuypere, Jean-Paul and Lu, Huiqi and Martin, Shaun and Vangheluwe, Peter and Swinnen, Johannes V and Lagae, Liesbet and Impens, Francis and Platt, Frances M and Gevaert, Kris and Annaert, Wim},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keyword      = {NIEMANN-PICK C1,IRON-OXIDE NANOPARTICLES,STABILIZED MAGNETIC FLUIDS,CELL-LINE,ORGANELLAR PROTEOMICS,PROTEIN LOCALIZATION,STORAGE DISORDERS,MEMBRANE-PROTEINS,DISEASE,SURFACE},
  language     = {eng},
  pages        = {20},
  title        = {A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics : the case of NPC1 deficiency},
  url          = {http://dx.doi.org/10.1038/srep41408},
  volume       = {7},
  year         = {2017},
}

Chicago
Tharkeshwar Raghunath, Arun Kumar, Jesse Trekker, Wendy Vermeire, Jarne Pauwels, Ragna Sannerud, David A Priestman, Danielle te Vruchte, et al. 2017. “A Novel Approach to Analyze Lysosomal Dysfunctions Through Subcellular Proteomics and Lipidomics : the Case of NPC1 Deficiency.” Scientific Reports 7.
APA
Tharkeshwar Raghunath, A. K., Trekker, J., Vermeire, W., Pauwels, J., Sannerud, R., Priestman, D. A., te Vruchte, D., et al. (2017). A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics : the case of NPC1 deficiency. SCIENTIFIC REPORTS, 7.
Vancouver
1.
Tharkeshwar Raghunath AK, Trekker J, Vermeire W, Pauwels J, Sannerud R, Priestman DA, et al. A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics : the case of NPC1 deficiency. SCIENTIFIC REPORTS. 2017;7.
MLA
Tharkeshwar Raghunath, Arun Kumar, Jesse Trekker, Wendy Vermeire, et al. “A Novel Approach to Analyze Lysosomal Dysfunctions Through Subcellular Proteomics and Lipidomics : the Case of NPC1 Deficiency.” SCIENTIFIC REPORTS 7 (2017): n. pag. Print.