Summary of Study ST004110

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 PR002572. The data can be accessed directly via it's Project DOI: 10.21228/M86540 This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST004110
Study TitleLipidomics characterization from plasma VLDL fractions isolated from human PNPLA3 wild type and human PNPLA3(I148M) knock in mice.
Study TypeLipidomics
Study SummaryWe conducted lipidomics experiments comparing the lipidomics profiles of plasma VLDL fractions isolated from PNPLA3(I148M) and PNPLA3 wild type mice. These experiments were conducted to understand the relative abundance of triglycerides in VLDL fractions from the PNPLA3 mutant and wild type mice to identify differences in VLDL secretion in mutant mice.
Institute
Amgen
Last NameLaGory
First NameEdward
Address750 Gateway Blvd, South San Francisco, CA 94080
Emailelagory@amgen.com
Phone1 (650) 244-2333
Submit Date2025-08-03
Num Groups4
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-08-14
Release Version1
Edward LaGory Edward LaGory
https://dx.doi.org/10.21228/M86540
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002572
Project DOI:doi: 10.21228/M86540
Project Title:Lipidomics analysis of PNPLA3 wild type and PNPLA3 I148M mutant Hep3B cells.
Project Type:Lipidomics
Project Summary:The PNPLA3(I148M) mutation is associated with increased risk of developing metabolic dysfunction-associated steatotic liver disease (MASLD). To better understand how PNPLA3(I148M) mutation impacts hepatic lipid metabolism, we conducted lipidomics analysis from Hep3B cells expressing wild type or I148M mutant PNPLA3 and cultured in media plus or minus oleic acid. Our studies revealed widespread changes in the lipidomic profiles of Hep3B cells expressing PNPLA3(I148M) compared to Hep3B cells expressing wild type PNPLA3, particularly after exposure to exogenous oleic acid in the culture media. Of particular note, we report decreases in the relative abundance of phosphatidylcholines and other phospholipids containing polyunsaturated fatty acids (PUFA) like arachidonic acid. These changes in phospholipid PUFA content lead to changes in membrane fluidity that impact the ability of cells carrying the PNPLA3(I148M) to secrete apolipoprotein B (apoB)-rich very low density lipoproteins. This impaired lipid secretory phenotype leads to an accumulation of triglycerides, which was verified by our lipidomics observation that Hep3B cells expressing PNPLA3(I148M) contain increases in the relative abundance of many triglycerides relative to PNPLA3 wild type Hep3B cells.
Institute:Amgen
Last Name:LaGory
First Name:Edward
Address:750 Gateway Blvd, South San Francisco, CA 94080
Email:elagory@amgen.com
Phone:+1 (650) 244-2333

Subject:

Subject ID:SU004257
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:PNPLA3 wild type, PNPLA3(I148M)

Factors:

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

mb_sample_id local_sample_id Sample source SEC Fraction Genotype
SA475014blank04blank blank NA
SA475015blank03blank blank NA
SA475016blank02_20230417115938blank blank NA
SA475017blank_5blank blank NA
SA474967A_10Plasma VLDL Fraction 10 PNPLA3(I148M)
SA474966E_10Plasma VLDL Fraction 10 PNPLA3 WT
SA474969A_11Plasma VLDL Fraction 11 PNPLA3(I148M)
SA474968E_11Plasma VLDL Fraction 11 PNPLA3 WT
SA474971A_12Plasma VLDL Fraction 12 PNPLA3(I148M)
SA474970E_12Plasma VLDL Fraction 12 PNPLA3 WT
SA474973A_13Plasma VLDL Fraction 13 PNPLA3(I148M)
SA474972E_13Plasma VLDL Fraction 13 PNPLA3 WT
SA474975A_14Plasma VLDL Fraction 14 PNPLA3(I148M)
SA474974E_14Plasma VLDL Fraction 14 PNPLA3 WT
SA474977A_15Plasma VLDL Fraction 15 PNPLA3(I148M)
SA474976E_15Plasma VLDL Fraction 15 PNPLA3 WT
SA474979A_16Plasma VLDL Fraction 16 PNPLA3(I148M)
SA474978E_16Plasma VLDL Fraction 16 PNPLA3 WT
SA474981A_17Plasma VLDL Fraction 17 PNPLA3(I148M)
SA474980E_17Plasma VLDL Fraction 17 PNPLA3 WT
SA474983A_18Plasma VLDL Fraction 18 PNPLA3(I148M)
SA474982E_18Plasma VLDL Fraction 18 PNPLA3 WT
SA474985A_19Plasma VLDL Fraction 19 PNPLA3(I148M)
SA474984E_19Plasma VLDL Fraction 19 PNPLA3 WT
SA474987A_20Plasma VLDL Fraction 20 PNPLA3(I148M)
SA474986E_20Plasma VLDL Fraction 20 PNPLA3 WT
SA474989A_21Plasma VLDL Fraction 21 PNPLA3(I148M)
SA474988E_21Plasma VLDL Fraction 21 PNPLA3 WT
SA474991A_22Plasma VLDL Fraction 22 PNPLA3(I148M)
SA474990E_22Plasma VLDL Fraction 22 PNPLA3 WT
SA474993A_23Plasma VLDL Fraction 23 PNPLA3(I148M)
SA474992E_23Plasma VLDL Fraction 23 PNPLA3 WT
SA474995A_24Plasma VLDL Fraction 24 PNPLA3(I148M)
SA474994E_24Plasma VLDL Fraction 24 PNPLA3 WT
SA474997A_25Plasma VLDL Fraction 25 PNPLA3(I148M)
SA474996E_25Plasma VLDL Fraction 25 PNPLA3 WT
SA474999A_26Plasma VLDL Fraction 26 PNPLA3(I148M)
SA474998E_26Plasma VLDL Fraction 26 PNPLA3 WT
SA475001A_27Plasma VLDL Fraction 27 PNPLA3(I148M)
SA475000E_27Plasma VLDL Fraction 27 PNPLA3 WT
SA475003A_28Plasma VLDL Fraction 28 PNPLA3(I148M)
SA475002E_28Plasma VLDL Fraction 28 PNPLA3 WT
SA475005A_8Plasma VLDL Fraction 8 PNPLA3(I148M)
SA475004E_8Plasma VLDL Fraction 8 PNPLA3 WT
SA475007A_9Plasma VLDL Fraction 9 PNPLA3(I148M)
SA475006E_9Plasma VLDL Fraction 9 PNPLA3 WT
SA475008QC_MS2_PosPlasma VLDL Fraction QC Pool NA
SA475009QC_MS2_NegPlasma VLDL Fraction QC Pool NA
SA475010QC_MS1Plasma VLDL Fraction QC Pool NA
SA475011QC_MS1_2Plasma VLDL Fraction QC Pool NA
SA475012BIODEV_QC_MSMS_NegPlasma VLDL Fraction QC Pool NA
SA475013BIODEV_QC_MSMS_PosPlasma VLDL Fraction QC Pool NA
Showing results 1 to 52 of 52

Collection:

Collection ID:CO004250
Collection Summary:Plasma lipoprotein particles were isolated using an AKTA Purifier FPLC System. Sample volumes from 100 – 450 µL were loaded onto a Superose 6 Increase 10/300 GL column (Cytiva, #29-0915-96) using an A-905 Autosampler (Amersham). Fractionation was performed in PBS with 3 mM EDTA using a flow rate of 0.5 mL/min. 200 – 400 µL fractions were collected in 96-well plates using a Frac-950 automated fraction collector (GE AKTA). Additional separation resolution on large particles was accomplished utilizing the same protocol with a Sephacryl S-500 HR column (Cytiva, #17-0613-10). Fractions were subject to analytic assays to measure cholesterol, TG, and ApoB content.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR004266
Treatment Summary:Plasma samples were collected from transgenic mice expressing human PNPLA3(I148M) or human PNPLA3 WT in place of the mouse PNPLA3 gene.

Sample Preparation:

Sampleprep ID:SP004263
Sampleprep Summary:Lipids were extracted by mixing 100 µL of the VLDL isolate with 225 µL methanol, and the resulting suspension was transferred to a glass culture tube. 10 µL of lipidomics internal standard (SPLASH® LIPIDOMIX® Mass Spec Standard) was spiked into each sample, followed by vortexing and addition of 750 µL methyl-tert-butyl ether (MTBE). Samples were incubated on ice for 20 min, vortexed, and 188 µL water was added, followed by another round of vortexing. Samples were then centrifuged for 10 min at 3,200 x g and the top layer was transferred to a glass autosampler vial and evaporated under a stream of nitrogen gas. Dried samples were reconstituted in isopropanol and subjected to LC-MS for analysis.

Chromatography:

Chromatography ID:CH005176
Instrument Name:Waters Acquity I-Class
Column Name:Thermo Accucore C30 (150 x 2.1 mm, 2.6 µm)
Column Temperature:40°C
Flow Gradient:The initial mobile phase composition was 30% B and was increased to 43% B by 5 min, 50% B by 5.1 min, 70% B by 14 min, 99% B by 21 min, then held at 99% B until 24 min, followed by column equilibration at initial mobile phase conditions for 6 minutes.
Flow Rate:0.35 mL/min
Solvent A:60% Acetonitrile/40% Water; 10mM Ammonium Formate; 0.1% Formic Acid
Solvent B:90% Isopropanol/8% Acetonitrile/2% Water; 10mM Ammonium Formate; 0.1% Formic Acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006813
Analysis Type:MS
Chromatography ID:CH005176
Num Factors:44
Num Metabolites:227
Units:Area
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