Summary of Study ST002334

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001497. The data can be accessed directly via it's Project DOI: 10.21228/M8740F This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002334
Study TitlePhospholipase D3 impact on the endolysosomal lipidome
Study SummaryNeurons rely on the endo-lysosomal network for the maintenance of lipid turnover, removal of dysfunctional organelles and the recycling of proteins. These mechanisms appear to go awry in late-onset Alzheimer’s disease (LOAD). Interestingly, GWA-studies identified risk genes for LOAD linked to endocytic transport regulation (BIN1-CD2AP-PICALM-RIN3-SORL1) and lysosomes (PLD3). Phospholipase D3, also known as PLD3, is a single-pass type II membrane protein that is majorly localized to lysosomes, making it one of the few (or only) risk factors that potentially links lysosomal dysfunction directly to LOAD initiation and progression. CRISPR/Cas9 gene editing was used to generate PLD3 knockout SH-SY5Y cells that were subsequently stably rescued with wild-type PLD3 and coding-variants (M6R & V232M). All cell lines were evaluated for morphological and functional alterations of the endolysosomal compartment, including lipid profiling of endolysosomes magnetically isolated from the different cell lines, as previously described (DOI: 10.1016/j.xpro.2020.100122). A prior isolation step has the unique advantage that it provides spatial resolution to the identified dysregulated networks or compositions. We observe a marked accumulation of storage lipids in endolysosomal isolates; chiefly attributed to cholesterol ester (CE) accretion. A significantly lowered monoacylglycerol level and increased phosphatidylinositol level point to an affected transport/sorting (vesicle/tubule formation).
VIB-KU Leuven
DepartmentCenter for Brain & Disease Research
LaboratoryLaboratory for Membrane Trafficking
Last NameVan Acker
First NameZoë
AddressHerestraat 49 - box 602, 3000 Leuven, Belgium
Submit Date2022-10-27
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2022-11-25
Release Version1
Zoë Van Acker Zoë Van Acker application/zip

Select appropriate tab below to view additional metadata details:

Combined analysis:

Analysis ID AN003810 AN003811
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um)
MS instrument type hybrid triple quadrupole/linear ion trap hybrid triple quadrupole/linear ion trap
MS instrument name ABI Sciex 6500 QTrap ABI Sciex 6500 QTrap
Units nmol lipid per mg protein nmol lipid per mg protein


MS ID:MS003552
Analysis ID:AN003810
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:hybrid triple quadrupole/linear ion trap
MS Comments:SM, CE, CER, DCER, HCER, LCER were measured in positive ion mode with a precursor scan of 184.1, 369.4, 264.4, 266.4, 264.4 and 264.4 respectively. TAG, DAG and MAG were measured in positive ion mode with a neutral loss scan for one of the fatty acyl moieties.
MS ID:MS003553
Analysis ID:AN003811
Instrument Name:ABI Sciex 6500 QTrap
Instrument Type:hybrid triple quadrupole/linear ion trap
MS Comments:PC, LPC, PE, LPE, PG, PI and PS were measured in negative ion mode by fatty acyl fragment ions. Lipid quantification was performed by scheduled multiple reactions monitoring (MRM), the transitions being based on the neutral losses or the typical product ions as described above. The instrument parameters were as follows: Curtain Gas = 35 psi; Collision Gas = 8 a.u. (medium); IonSpray Voltage = 5500 V and −4,500 V; Temperature = 550°C; Ion Source Gas 1 = 50 psi; Ion Source Gas 2 = 60 psi; Declustering Potential = 60 V and −80 V; Entrance Potential = 10 V and −10 V; Collision Cell Exit Potential = 15 V and −15 V.