Summary of Study ST002334
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, 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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST002334 |
| Study Title | Phospholipase D3 impact on the endolysosomal lipidome |
| Study Summary | Neurons 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). |
| Institute | VIB-KU Leuven |
| Department | Center for Brain & Disease Research |
| Laboratory | Laboratory for Membrane Trafficking |
| Last Name | Van Acker |
| First Name | Zoë |
| Address | Herestraat 49 - box 602, 3000 Leuven, Belgium |
| zoe.vanacker@kuleuven.vib.be | |
| Phone | +3216320784 |
| Submit Date | 2022-10-27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-11-25 |
| Release Version | 1 |
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 Type | ESI | ESI |
| 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 |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | nmol lipid per mg protein | nmol lipid per mg protein |
Chromatography:
| Chromatography ID: | CH002819 |
| Chromatography Summary: | Chromatographic separation was performed on a XBridge amide column (150 mm × 4.6 mm, 3.5 μm; Waters) maintained at 35°C using mobile phase A [1 mM ammonium acetate in water-acetonitrile 5:95 (v/v)] and mobile phase B [1 mM ammonium acetate in water-acetonitrile 50:50 (v/v)] in the following gradient: (0-6 min: 0% B - 6% B; 6-10 min: 6% B - 25% B; 10-11 min: 25% B - 98% B; 11-13 min: 98% B - 100% B; 13-19 min: 100% B; 19-24 min: 0% B) at a flow rate of 0.7 mL/min, which was increased to 1.5 mL/min from 13 minutes onwards. |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| Column Temperature: | 35 |
| Flow Gradient: | 0-6 min: 0% B - 6% B; 6-10 min: 6% B - 25% B; 10-11 min: 25% B - 98% B; 11-13 min: 98% B - 100% B; 13-19 min: 100% B; 19-24 min: 0% B |
| Flow Rate: | 0.7 mL/min, which was increased to 1.5 mL/min from 13 minutes onwards |
| Solvent A: | 5% water/95% acetonitrile; 1 mM ammonium acetate |
| Solvent B: | 50% water/50% acetonitrile; 1 mM ammonium acetate |
| Chromatography Type: | HILIC |
