Summary of study ST001819

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 PR001150. The data can be accessed directly via it's Project DOI: 10.21228/M82690 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001819
Study TitleEC and PVC from 14-15 month-old APOE3/3, APOE3/4 and APOE4/4 mice
Study SummaryWe performed a targeted lipidomic analysis on EC and PVC tissue from 14-15 month old APOE3/3, APOE3/4, and APOE4/4 mice.
Institute
Columbia University
Last NameNuriel
First NameTal
Address630 W 168th St., P&S 12-430
Emailtn2283@cumc.columbia.edu
Phone2123045683
Submit Date2021-06-02
Analysis Type DetailLC-MS
Release Date2021-06-10
Release Version1
Tal Nuriel Tal Nuriel
https://dx.doi.org/10.21228/M82690
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001150
Project DOI:doi: 10.21228/M82690
Project Title:APOE4-associated differences in lipidomics signatures in mouse brain and cultured neurons
Project Type:Lipidomics analysis
Project Summary:Apolipoprotein E ε4 (APOE4) is the primary genetic risk factor for the late-onset form of Alzheimer's disease (AD). Although the reason for this association is not completely understood, researchers have uncovered numerous effects of APOE4 expression on AD-relevant brain processes, including amyloid beta (Aβ) accumulation, lipid metabolism, endosomal-lysosomal processing and bioenergetics. In this study, we aimed to determine the effect of APOE4 allelic dosage on regional brain lipid composition in aged mice, as well as in cultured neurons. We performed a targeted lipidomic analysis on the entorhinal cortex (EC) and primary visual cortex (PVC) from 14–15 month-old APOE3/3, APOE3/4, and APOE4/4 targeted replacement mice, as well as on WT neurons cultured with conditioned media from APOE3/3 or APOE4/4 astrocytes. Our results reveal that the EC possesses increased susceptibility to APOE4-associated lipid alterations compared to the PVC. In the EC, APOE4 expression showed a dominant effect in decreasing diacylglycerol (DAG) levels, and a semi-dominant additive effect in the upregulation of multiple ceramide, glycosylated sphingolipid and bis(monoacylglycerol)phosphate (BMP) species, lipids known to accumulate as a result of endosomal-lysosomal dysfunction and defective lysosomal clearance. Neurons treated with conditioned media from APOE4 vs. APOE3 astrocytes also showed similar alterations of DAG and BMP species as those observed in the mouse EC. Our results suggest that APOE4 expression differentially modulates regional and neuronal lipid signatures, which may underlie the increased susceptibility of EC-localized neurons to AD pathology.
Institute:Columbia University
Last Name:Nuriel
First Name:Tal
Address:630 W 168th St., P&S 12-430
Email:tn2283@cumc.columbia.edu
Phone:2123045683

Subject:

Subject ID:SU001896
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:14-15 month-old
Gender:Male

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Region Genotype
SA169061EC8EC E3/3
SA169062EC1EC E3/3
SA169063EC7EC E3/3
SA169064EC6EC E3/3
SA169065EC2EC E3/3
SA169066EC3EC E3/3
SA169067EC4EC E3/3
SA169068EC5EC E3/3
SA169069EC16EC E3/4
SA169070EC14EC E3/4
SA169071EC15EC E3/4
SA169072EC12EC E3/4
SA169073EC10EC E3/4
SA169074EC13EC E3/4
SA169075EC23EC E4/4
SA169076EC24EC E4/4
SA169077EC22EC E4/4
SA169078EC21EC E4/4
SA169079EC17EC E4/4
SA169080EC19EC E4/4
SA169081EC18EC E4/4
SA169082EC20EC E4/4
SA169083PVC6PVC E3/3
SA169084PVC7PVC E3/3
SA169085PVC5PVC E3/3
SA169086PVC1PVC E3/3
SA169087PVC4PVC E3/3
SA169088PVC2PVC E3/3
SA169089PVC3PVC E3/3
SA169090PVC14PVC E3/4
SA169091PVC16PVC E3/4
SA169092PVC13PVC E3/4
SA169093PVC15PVC E3/4
SA169094PVC12PVC E3/4
SA169095PVC10PVC E3/4
SA169096PVC9PVC E3/4
SA169097PVC11PVC E3/4
SA169098PVC23PVC E4/4
SA169099PVC24PVC E4/4
SA169100PVC22PVC E4/4
SA169101PVC20PVC E4/4
SA169102PVC17PVC E4/4
SA169103PVC19PVC E4/4
SA169104PVC21PVC E4/4
Showing results 1 to 44 of 44

Collection:

Collection ID:CO001889
Collection Summary:Mice were sacrificed by cervical dislocation to maintain the brain environment, and individual brain regions were immediately removed and snap-frozen on dry ice. Tissues were stored at -80°C for prior to extraction.
Sample Type:Brain

Treatment:

Treatment ID:TR001909
Treatment Summary:No treatments were made. Mice were either APOE3/3, APOE3/4 or APOE4/4 gentoype.

Sample Preparation:

Sampleprep ID:SP001902
Sampleprep Summary:Lipid and small-molecule metabolite extraction was performed using a methyl tert-butyl ether (MTBE)/methanol extraction protocol modified from previous reports (40, 41), as we have described previously (34). Briefly, individual EC or PVC tissues were homogenized in 400 ul of ice-cold methanol using a bead mill homogenizer (TissueLyser II, Qiagen) at 25 beats/sec, 2x for 45 sec each. Following homogenization, samples were incubated in 1200 ul of MTBE for 1 hr at room temperature to separate organic-soluble lipids from aqueous-soluble lipids and other small-molecules. Finally, 360 ul of ultrapure water was added (for a final ratio of 3:1:0.9 MTBE:methanol:water) to resolve the two liquid phases, and each samples were centrifuged at 10,000 x g for 10 min. For this experiment, the upper organic phase was collected from each sample and stored in a separate tube, and the remaining protein pellets were resuspended in 25 mM ammonium bicarbonate, pH 8, with 2.5% SDS. A BCA protein assay was performed on each protein fraction, and the organic phase was normalized to their protein concentration equivalent with 100% methanol. All samples were then stored at -80°C prior to analysis.

Combined analysis:

Analysis ID AN002951 AN002952 AN002953
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase Normal phase
Chromatography system Agilent 1260 Agilent 1260 Agilent 1260
Column Agilent Eclipse XDB-C18 (100 x 3.0mm) Agilent Eclipse XDB-C18 (100 x 3.0mm) Phenomenex Luna NH2 (150 x 2.1mm, 3um)
MS Type ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name Agilent 6490 QQQ Agilent 6490 QQQ Agilent 6490 QQQ
Ion Mode NEGATIVE POSITIVE POSITIVE
Units area under the curve area under the curve area under the curve

Chromatography:

Chromatography ID:CH002186
Chromatography Summary:Reverse phase negative mode
Instrument Name:Agilent 1260
Column Name:Agilent Eclipse XDB-C18 (100 x 3.0mm)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002187
Chromatography Summary:Normal phase
Instrument Name:Agilent 1260
Column Name:Phenomenex Luna NH2 (150 x 2.1mm, 3um)
Chromatography Type:Normal phase

MS:

MS ID:MS002741
Analysis ID:AN002951
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Lipid profiling was performed using an Agilent 1260 HPLC coupled to an Agilent 6490 triple quadrupole (QQQ) mass spectrometer (41). Each sample was run through three separate chromatographic conditions (reverse-phase negative mode, reverse-phase positive mode and normal-phase positive mode) for the effective quantification of 337 distinct lipids from 28 lipid subclasses, as previously described (41). Individual lipid species were measured by multiple reaction monitoring transitions.
Ion Mode:NEGATIVE
  
MS ID:MS002742
Analysis ID:AN002952
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Lipid profiling was performed using an Agilent 1260 HPLC coupled to an Agilent 6490 triple quadrupole (QQQ) mass spectrometer (41). Each sample was run through three separate chromatographic conditions (reverse-phase negative mode, reverse-phase positive mode and normal-phase positive mode) for the effective quantification of 337 distinct lipids from 28 lipid subclasses, as previously described (41). Individual lipid species were measured by multiple reaction monitoring transitions.
Ion Mode:POSITIVE
  
MS ID:MS002743
Analysis ID:AN002953
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Lipid profiling was performed using an Agilent 1260 HPLC coupled to an Agilent 6490 triple quadrupole (QQQ) mass spectrometer (41). Each sample was run through three separate chromatographic conditions (reverse-phase negative mode, reverse-phase positive mode and normal-phase positive mode) for the effective quantification of 337 distinct lipids from 28 lipid subclasses, as previously described (41). Individual lipid species were measured by multiple reaction monitoring transitions.
Ion Mode:POSITIVE
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