Summary of Study ST003381

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 PR002085. The data can be accessed directly via it's Project DOI: 10.21228/M83R6P 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	ST003381
Study Title	Impact of high-fat diet enriched in cis or trans fatty acids and myriocin on newly synthesized sphingolipids from D2O in circulation in Ldlr-/- mice
Study Summary	We analyzed newly synthesized DHCer (dihydroceramides), Cer (ceramides), and SM (sphingomyelin) in plasma of Ldlr-/- mice fed 1) Cis HFD (high-fat diet), 2) Cis HFD + Myriocin, 3) Trans HFD, or 4) Trans HFD + Myriocin. We aimed to determine how dietary cis and trans monounsaturated fatty acids impact hepatic secretion of newly synthesized sphingolipids into circulation while pharmacologically inhibiting the initial rate-limiting enzyme of sphingolipid biosynthesis, serine palmitoyltransferase (SPT), via myriocin.
Institute	Salk Institute for Biological Studies
Last Name	Gengatharan
First Name	Jivani
Address	10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
Email	jivani14@gmail.com
Phone	(858) 453-4100
Submit Date	2024-08-02
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2024-08-12
Release Version	1

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Project:

Project ID:	PR002085
Project DOI:	doi: 10.21228/M83R6P
Project Title:	Altered sphingolipid biosynthetic flux and lipoprotein trafficking contribute to trans fat-induced atherosclerosis
Project Summary:	The goal of the project is to determine the role of sphingolipid metabolism in atherosclerosis induced by dietary trans fat. We analyzed lipid metabolites in Huh7 cells following various fatty acid treatments, with specific focus on cis and trans unsaturated fatty acids. Additionally, we analyzed lipid metabolites in plasma and liver of Ldlr-/- mice fed high-fat diets enriched in cis or trans fatty acids in the presence or absence of myriocin, a pharmacological inhibitor of Serine palmitoyltransferase (SPT), the initial rate-limiting enzyme of sphingolipid biosynthesis.
Institute:	Salk Institute for Biological Studies
Last Name:	Gengatharan
First Name:	Jivani
Address:	10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
Email:	jivani14@gmail.com
Phone:	(858) 453-4100

Subject:

Subject ID:	SU003502
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

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

mb_sample_id	local_sample_id	Genotype	Sample source	Group
SA367324	PlasmaD2O_CisHFD_152_MS2_top12	Ldlr-/-	Mouse plasma	Cis HFD D2O
SA367325	PlasmaD2O_CisHFD_72	Ldlr-/-	Mouse plasma	Cis HFD D2O
SA367326	PlasmaD2O_CisHFD_71	Ldlr-/-	Mouse plasma	Cis HFD D2O
SA367327	PlasmaD2O_CisHFD_75	Ldlr-/-	Mouse plasma	Cis HFD D2O
SA367328	PlasmaD2O_CisHFD_74	Ldlr-/-	Mouse plasma	Cis HFD D2O
SA367329	PlasmaD2O_CisHFD_73	Ldlr-/-	Mouse plasma	Cis HFD D2O
SA367319	PlasmaD2O_CisHFDMyr_114	Ldlr-/-	Mouse plasma	Cis HFD + Myriocin D2O
SA367320	PlasmaD2O_CisHFDMyr_115	Ldlr-/-	Mouse plasma	Cis HFD + Myriocin D2O
SA367321	PlasmaD2O_CisHFDMyr_111	Ldlr-/-	Mouse plasma	Cis HFD + Myriocin D2O
SA367322	PlasmaD2O_CisHFDMyr_112	Ldlr-/-	Mouse plasma	Cis HFD + Myriocin D2O
SA367323	PlasmaD2O_CisHFDMyr_113	Ldlr-/-	Mouse plasma	Cis HFD + Myriocin D2O
SA367336	PlasmaD2O_TransHFD_21	Ldlr-/-	Mouse plasma	Trans HFD D2O
SA367337	PlasmaD2O_TransHFD_22	Ldlr-/-	Mouse plasma	Trans HFD D2O
SA367338	PlasmaD2O_TransHFD_24	Ldlr-/-	Mouse plasma	Trans HFD D2O
SA367339	PlasmaD2O_TransHFD_25	Ldlr-/-	Mouse plasma	Trans HFD D2O
SA367340	PlasmaD2O_TransHFD_22_MS2_top12	Ldlr-/-	Mouse plasma	Trans HFD D2O
SA367341	PlasmaD2O_TransHFD_23	Ldlr-/-	Mouse plasma	Trans HFD D2O
SA367330	PlasmaD2O_TransHFDMyr_51	Ldlr-/-	Mouse plasma	Trans HFD + Myriocin D2O
SA367331	PlasmaD2O_TransHFDMyr_52	Ldlr-/-	Mouse plasma	Trans HFD + Myriocin D2O
SA367332	PlasmaD2O_TransHFDMyr_53	Ldlr-/-	Mouse plasma	Trans HFD + Myriocin D2O
SA367333	PlasmaD2O_TransHFDMyr_54	Ldlr-/-	Mouse plasma	Trans HFD + Myriocin D2O
SA367334	PlasmaD2O_TransHFDMyr_55	Ldlr-/-	Mouse plasma	Trans HFD + Myriocin D2O
SA367335	PlasmaD2O_TransHFDMyr_52_MS2_top12	Ldlr-/-	Mouse plasma	Trans HFD + Myriocin D2O

Showing results 1 to 23 of 23

Showing results 1 to 23 of 23

Collection:

Collection ID:	CO003495
Collection Summary:	Blood was collected in EDTA-coated tubes (Sarstedt Inc.) and centrifuged at 2000g for 5 min. The plasma supernatant was transferred to a new Eppendorf tube and stored at -80°C until analysis.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR003511
Treatment Summary:	Four-five-week-old Ldlr-/- C57BL/6J male and female mice (JAX# 002207) were fed with irradiated 60% high fat diets (HFD) prepared by Dyets for 16 weeks. These diets include Cis Unsaturated HFD (105063GI), Cis Unsaturated HFD with 2.2 mg/kg Myriocin Added (105064GI), Trans Unsaturated HFD (105061GI), and Trans Unsaturated HFD with 2.2 mg/kg Myriocin Added (105061GI). The Trans Unsaturated HFD was designed with 100% Primex, a partially hydrogenated vegetable oil, and the Cis Unsaturated HFD was designed with 34% lard and 66% olive oil. Following 16 weeks of diet administration, mice were administered D2O in 0.9% NaCl at a dose of 0.027 mL/g body weight via intraperitoneal injection. Drinking water was replaced with 8% D2O drinking water for 30 hours. 24 hours post-injection, mice were fasted for 6 hours with 8% D2O drinking water provided ad libitum. Blood were collected as described above.

Treatment ID:

TR003511

Treatment Summary:

Four-five-week-old Ldlr-/- C57BL/6J male and female mice (JAX# 002207) were fed with irradiated 60% high fat diets (HFD) prepared by Dyets for 16 weeks. These diets include Cis Unsaturated HFD (105063GI), Cis Unsaturated HFD with 2.2 mg/kg Myriocin Added (105064GI), Trans Unsaturated HFD (105061GI), and Trans Unsaturated HFD with 2.2 mg/kg Myriocin Added (105061GI). The Trans Unsaturated HFD was designed with 100% Primex, a partially hydrogenated vegetable oil, and the Cis Unsaturated HFD was designed with 34% lard and 66% olive oil. Following 16 weeks of diet administration, mice were administered D2O in 0.9% NaCl at a dose of 0.027 mL/g body weight via intraperitoneal injection. Drinking water was replaced with 8% D2O drinking water for 30 hours. 24 hours post-injection, mice were fasted for 6 hours with 8% D2O drinking water provided ad libitum. Blood were collected as described above.

Sample Preparation:

Sampleprep ID:	SP003509
Sampleprep Summary:	Sphingolipid biosynthesis via 2H2O enrichment in plasma was quantified by spiking 10 µL of plasma with internal standards 100 pmol d18:0-d7/13:0 dihydroceramide (Avanti Polar Lipids, Cat# 330726), 200 pmol d18:1-d7/15:0 ceramide (Avanti Polar Lipids, Cat# 860681), and 1 ug 15:0-18:1(d7) phosphatidylcholine (Avanti Polar Lipids, Cat #791637). 0.5 mL methanol, 0.5 mL H2O, and 1 mL chloroform were added directly. Samples were vortexed for 5 min, centrifuged for 5 min at 4 ˚C at 15,000g. The organic phase was collected and 2 μL of formic acid was added to the remaining polar phase which was re-extracted with 1 mL of chloroform. Combined organic phases were dried under nitrogen. After dried extracts for plasma were resuspended in 60 µl MeOH, 5 µL of sample was injected.

Sampleprep ID:

SP003509

Sampleprep Summary:

Sphingolipid biosynthesis via 2H2O enrichment in plasma was quantified by spiking 10 µL of plasma with internal standards 100 pmol d18:0-d7/13:0 dihydroceramide (Avanti Polar Lipids, Cat# 330726), 200 pmol d18:1-d7/15:0 ceramide (Avanti Polar Lipids, Cat# 860681), and 1 ug 15:0-18:1(d7) phosphatidylcholine (Avanti Polar Lipids, Cat #791637). 0.5 mL methanol, 0.5 mL H2O, and 1 mL chloroform were added directly. Samples were vortexed for 5 min, centrifuged for 5 min at 4 ˚C at 15,000g. The organic phase was collected and 2 μL of formic acid was added to the remaining polar phase which was re-extracted with 1 mL of chloroform. Combined organic phases were dried under nitrogen. After dried extracts for plasma were resuspended in 60 µl MeOH, 5 µL of sample was injected.

Combined analysis:

Analysis ID	AN005539
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Vanquish
Column	Phenomenex Kinetex C18 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE
Units	Peak area

Chromatography:

Chromatography ID:	CH004211
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (100 x 2.1mm,1.7um)
Column Temperature:	35˚C
Flow Gradient:	0 min, 30%B; 1 min, 30%B; 2 min, 70%B; 11 min, 95%B; 17 min, 30%B; 21.5 min, 30%B; 27 min, 30%B.
Flow Rate:	0.2 mL/min
Solvent A:	98% Water/2% Methanol; 5 mM ammonium acetate
Solvent B:	50% Methanol/50% Isopropanol; 5 mM ammonium acetate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005264
Analysis ID:	AN005539
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Lipids were identified in EL-MAVEN using exact mass of precursor ion in MS1 chromatogram and product ion in MS2 spectra. Lipids were quantified using peak areas in MS1 chromatogram. Relative abundance of lipids was calculated by normalizing to internal standard specific to lipid class and volume of plasma. Sphingomyelin was normalized to 15:0-18:1(d7) phosphatidylcholine as a deuterated sphingomyelin standard would have interfered with the mass isotopologue distribution of specific sphingomyelin species. The percent isotopologue distribution of each sphingolipid was determined and corrected for natural 13C abundance, the most abundant natural stable isotope, using in-house algorithms adapted from a previous report.
Ion Mode:	POSITIVE