Dataset Information

LFQ comparison of total cell lysate, lysosomal and plasma membrane fraction of WT and NPC1 KO cells

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

DISEASE(S): Niemann-pick Disease

SUBMITTER: Jarne Pauwels

LAB HEAD: Wim Annaert

PROVIDER: PXD004273 | Pride | 2017-02-01

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	H00425_5461_Arun_WT_TCL_run1.raw	Raw
	H00427_5461_Arun_WT_TCL_run2.raw	Raw
	H00430_5461_Arun_KO1_TCL_run1_IT80.raw	Raw
	H00432_5461_Arun_KO1_TCL_run2_IT80.raw	Raw
	H00435_5461_Arun_KO2_TCL_run1_IT80.raw	Raw

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Publications

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

Tharkeshwar Arun Kumar AK Trekker Jesse J Vermeire Wendy W Pauwels Jarne J Sannerud Ragna R Priestman David A DA Te Vruchte Danielle D Vints Katlijn K Baatsen Pieter P Decuypere Jean-Paul JP Lu Huiqi H Martin Shaun S Vangheluwe Peter P Swinnen Johannes V JV Lagae Liesbet L Impens Francis F Platt Frances M FM Gevaert Kris K Annaert Wim W

Scientific reports 20170130

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 pro ...[more]

PMID: 28134274

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Project description:Niemann-Pick Type C (NPC) disease is a rare, genetic, lysosomal disorder with progressive neurodegeneration. Poor understanding of the pathophysiology and lack of blood-based diagnostic markers are major hurdles in the treatment and management of NPC and several additional neurological, lysosomal disorders. To identify disease severity correlates, we undertook whole genome expression profiling of sentinel organs, brain, liver, and spleen of Balb/c Npc1-/- mice (Npc1nih)relative to Npc1+/- at an asymptomatic stage, as well as early- and late-symptomatic stages. Unexpectedly, we found prominent up regulation of innate immunity genes with age-dependent change in their expression, in all three organs. We shortlisted a set of 12 secretory genes whose expression steadily increased with age in both brain and liver, as potential plasma correlates for the neurological disease. Ten were innate immune genes with eight ascribed to lysosomes. Several are known to be elevated in diseased organs of murine models of other lysosomal diseases including GaucherM-bM-^@M-^Ys disease, Sandhoff disease and MPSIIIB. We validated the top candidate lysozyme, in the plasma of Npc1-/- as well as Balb/c Npc1nmf164 mice (bearing a point mutation closer to human disease mutants) and show its reduction in response to an emerging therapeutic. We further established elevation of innate immunity in Npc1-/- mice through multiple functional assays including inhibition of bacterial infection as well as cellular analysis and immunohistochemistry. We used microarrays on the diseased organs, brain, liver and spleen of the Npc1-/- mice to unserstand the molecular changes occur during the progression of NPC diseases. From the data, we have identified 12 potential genes which can be potentially developed as blood-based biomarker. We have also discovered up regulation of innate iimunity genes in all three organs of Npc1-/- mice and functionally validated them in liver and spleen. Brain from 11 female Npc1M-bM-^HM-^R/M-bM-^HM-^R and 16 control female mice (Npc1+/+ and Npc1+/M-bM-^HM-^R) from 6 age groups (20-25, 37-40, 54-55, 59-62, 67-71 and 81-84 days) were surgically harvested. Liver and spleen from 6 Npc1-/- and 6 Npc1+/- female mice from three age group ( 20-25, 54-55 and 67-71 days) were surgically harvested. Organs were kept in RNA later and stored at -20 M-BM-0C until used. RNA was isolated and Affymetrix mouse 430 2.0 array hybridizations were performed by M-bM-^@M-^XUCLA Clinical Microarray CoreM-bM-^@M-^Y, UCLA, Los Angeles, CA, USA. Subsequent raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. Data from Npc1-/- mice from all age groups were compared to control mice (Npc1+/- and/or Npc1-/- mice) from all age groups separately for brain, liver and spleen. 'Matrix Table1' corrsponds for brain, 'Matrix Table2' corresponds for liver and 'Matrix Table3' corresponds for spleen. Thresholds for selecting significant genes were set at a relative difference M-BM-31.5-fold, absolute difference M-BM-3100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.