Summary of Study ST002276

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 PR001457. The data can be accessed directly via it's Project DOI: 10.21228/M8D133 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.

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Study IDST002276
Study TitleMachine Learning Reveals Lipidome Dynamics in a Mouse Model of Ovarian Cancer
Study SummaryOvarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It presents little or no symptoms at the early stages, and typically unspecific symptoms at later stages. Of the OC subtypes, high-grade serous carcinoma (HGSC) is responsible for most OC deaths. However, very little is known about the metabolic course of this disease. In this longitudinal study, we investigated the temporal course of lipidome changes in a Dicer-Pten Double-Knockout (DKO) HGSC mouse model using machine and statistical learning approaches. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages were marked by more diverse lipids alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations provided evidence of perturbations in cell membrane stability, proliferation, and survival and candidates for early-stage and prognostic markers in humans.
Institute
Georgia Institute of Technology
DepartmentChemistry and Biochemistry
LaboratoryFernandez group
Last NameSah
First NameSamyukta
Address901 Atlantic Dr NW, Atlanta, GA, 30332, USA
Emailssah9@gatech.edu
Phone5746780124
Submit Date2022-09-01
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-09-28
Release Version1
Samyukta Sah Samyukta Sah
https://dx.doi.org/10.21228/M8D133
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001457
Project DOI:doi: 10.21228/M8D133
Project Title:Machine Learning Reveals Lipidome Dynamics in a Mouse Model of Ovarian Cancer
Project Summary:Ovarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It presents little or no symptoms at the early stages, and typically unspecific symptoms at later stages. Of the OC subtypes, high-grade serous carcinoma (HGSC) is responsible for most OC deaths. However, very little is known about the metabolic course of this disease. In this longitudinal study, we investigated the temporal course of lipidome changes in a Dicer-Pten Double-Knockout (DKO) HGSC mouse model using machine and statistical learning approaches. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages were marked by more diverse lipids alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations provided evidence of perturbations in cell membrane stability, proliferation, and survival and candidates for early-stage and prognostic markers in humans.
Institute:Georgia Institute of Technology
Department:Chemistry and Biochemistry
Laboratory:Fernandez group
Last Name:Sah
First Name:Samyukta
Address:901 Atlantic Dr NW, Atlanta, GA, 30332, USA
Email:ssah9@gatech.edu
Phone:5746780124

Subject:

Subject ID:SU002362
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 phenotype
SA218095NC20_T7control
SA218096NC20_T6control
SA218097NC20_T5control
SA218098NC20_T8control
SA218099NC20_T11control
SA218100NC20_T4control
SA218101NC20_T10control
SA218102NC20_T9control
SA218103NC20_T3control
SA218104NC7_T13control
SA218105NC7_T14control
SA218106NC7_T12control
SA218107NC7_T11control
SA218108NC7_T9control
SA218109NC7_T10control
SA218110NC7_T15control
SA218111NC7_T16control
SA218112NC8_T1control
SA218113NC8_T2control
SA218114NC7_T19control
SA218115NC7_T18control
SA218116NC7_T17control
SA218117NC7_T8control
SA218118NC7_T7control
SA218119NC6_T17control
SA218120NC6_T18control
SA218121NC6_T16control
SA218122NC6_T15control
SA218123NC6_T14control
SA218124NC6_T19control
SA218125NC7_T1control
SA218126NC7_T5control
SA218127NC7_T6control
SA218128NC7_T4control
SA218129NC7_T3control
SA218130NC7_T2control
SA218131NC8_T3control
SA218132NC8_T4control
SA218133NC9_T9control
SA218134NC9_T10control
SA218135NC9_T8control
SA218136NC9_T7control
SA218137NC9_T5control
SA218138NC9_T6control
SA218139NC9_T11control
SA218140NC9_T12control
SA218141NC10_T2control
SA218142NC10_T3control
SA218143NC10_T1control
SA218144NC9_T15control
SA218145NC9_T13control
SA218146NC9_T4control
SA218147NC9_T3control
SA218148NC8_T8control
SA218149NC8_T9control
SA218150NC8_T7control
SA218151NC8_T6control
SA218152NC8_T5control
SA218153NC8_T10control
SA218154NC8_T11control
SA218155NC9_T1control
SA218156NC9_T2control
SA218157NC8_T15control
SA218158NC8_T13control
SA218159NC8_T12control
SA218160NC6_T13control
SA218161NC6_T12control
SA218162NC2_T7control
SA218163NC2_T8control
SA218164NC2_T6control
SA218165NC2_T5control
SA218166NC2_T3control
SA218167NC2_T4control
SA218168NC2_T9control
SA218169NC2_T10control
SA218170NC4_T1control
SA218171NC4_T2control
SA218172NC2_T13control
SA218173NC2_T12control
SA218174NC2_T11control
SA218175NC2_T2control
SA218176NC2_T1control
SA218177NC1_T5control
SA218178NC1_T6control
SA218179NC1_T4control
SA218180NC1_T3control
SA218181NC1_T2control
SA218182NC1_T7control
SA218183NC1_T8control
SA218184NC1_T12control
SA218185NC1_T13control
SA218186NC1_T11control
SA218187NC1_T10control
SA218188NC1_T9control
SA218189NC4_T3control
SA218190NC4_T4control
SA218191NC6_T3control
SA218192NC6_T4control
SA218193NC6_T2control
SA218194NC6_T1control
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Collection:

Collection ID:CO002355
Collection Summary:Serum samples were collected from Dicerflox/flox Ptenflox/flox Amhr2cre/+ (DKO) and Dicerflox/flox Ptenflox/flox without Amhr2cre/+ (Control) mice every two weeks until humane end point for sacrifice or development of ascites. Samples from 15 DKO mice (n = 231) and 15 control mice (n = 238) were used for lipidomics analyses.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002374
Treatment Summary:Dicerflox/flox Ptenflox/flox without Amhr2cre/+ (DKO Control mice) Dicerflox/flox Ptenflox/flox (DKO mice with high grade serous carcinoma )

Sample Preparation:

Sampleprep ID:SP002368
Sampleprep Summary:The lipid extraction solvent was prepared by adding 700 µL of the isotopically labeled lipid standard mixture to 42 mL of 2-propanol. Serum samples were thawed on ice, followed by extraction of non-polar metabolites. The extraction procedure was carried out by adding the prepared extraction solvent to 10-25 µL serum sample in a 3:1 ratio. Following this step, samples were vortex-mixed for 30 s and centrifuged at 13,000 rpm for 7 min. The resulting supernatant was transferred to LC vials and stored at -80 °C until analysis, which was performed within a week. A blank sample, prepared with LC-MS grade water, underwent the same sample preparation process as the serum samples. A pooled quality control (QC) sample was prepared by adding 2-5 µL aliquot of supernatant to each serum sample. This QC sample was analyzed every 10 runs to assess LC-MS instrument stability through the course of the experiment. Samples were run in a randomized order on consecutive days.

Combined analysis:

Analysis ID AN003719 AN003720
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Accucore C30 (150 × 2.1mm,2.6um Thermo Accucore C30 (150 × 2.1mm,2.6um
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap ID-X tribrid Thermo Orbitrap ID-X tribrid
Ion Mode POSITIVE NEGATIVE
Units chromatographic peak area chromatographic peak area

Chromatography:

Chromatography ID:CH002755
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore C30 (150 × 2.1mm,2.6um
Chromatography Type:Reversed phase

MS:

MS ID:MS003468
Analysis ID:AN003719
Instrument Name:Thermo Orbitrap ID-X tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Spectral features (described as retention time, m/z pairs) were extracted with Compound Discoverer v3.2 (ThermoFisher Scientific) from the LC-MS datasets.
Ion Mode:POSITIVE
  
MS ID:MS003469
Analysis ID:AN003720
Instrument Name:Thermo Orbitrap ID-X tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:spectral features (described as retention time, m/z pairs) were extracted with Compound Discoverer v3.2 (ThermoFisher Scientific) from the LC-MS datasets.
Ion Mode:NEGATIVE
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