Summary of Study ST002851

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 PR001785. The data can be accessed directly via it's Project DOI: 10.21228/M8043D 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 IDST002851
Study TitleMetabolic caracterization of liver metastasis organotropism
Study SummaryTranscriptomic and metabolomic analyses in animals revealed distinct metabolic adaptations, particularly related to the TCA cycle and OxPhos, specific to liver metastases compared to concurrent lung metastases. This finding was substantiated by analyzing RNA-seq data from a considerable number of patient metastases across various cancer types. Further analysis of exome/RNA-seq data from melanoma patients indicated more frequent PIK3CA mutations, lower transcript levels of PIP4K2C, and enrichment of TCA cycle and OxPhos pathways in liver metastases.
Institute
Columbia University
DepartmentDepartment of Medicine
LaboratoryDivision of Hematology/Oncology
Last NameIzar
First NameBenjamin
AddressColumbia University Irving Medical Center, New York, NY, USA
Emailbi2175@cumc.columbia.edu
Phone0123456789
Submit Date2023-08-31
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-10-02
Release Version1
Benjamin Izar Benjamin Izar
https://dx.doi.org/10.21228/M8043D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001785
Project DOI:doi: 10.21228/M8043D
Project Title:A genetic-metabolic axis confers liver-metastatic organotropism
Project Summary:Transcriptomic and metabolomic analyses in animals revealed distinct metabolic adaptations, particularly related to the TCA cycle and OxPhos, specific to liver metastases compared to concurrent lung metastases. This finding was substantiated by analyzing RNA-seq data from a considerable number of patient metastases across various cancer types. Further analysis of exome/RNA-seq data from melanoma patients indicated more frequent PIK3CA mutations, lower transcript levels of PIP4K2C, and enrichment of TCA cycle and OxPhos pathways in liver metastases.
Institute:Columbia University - Medical Center
Department:Department of Medicine
Laboratory:Division of Hematology/Oncology
Last Name:Izar
First Name:Benjamin
Address:Columbia University Irving Medical Center, New York, NY, USA
Email:bi2175@cumc.columbia.edu
Phone:0123456789

Subject:

Subject ID:SU002963
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Organism part
SA308612ExtractionBlank_002blank
SA308613ExtractionBlank_001blank
SA308614ExtractionBlank_003blank
SA308615QC_Lung_001control
SA308616QC_Mix_003control
SA308617QC_Mix_001control
SA308618QC_Lung_002control
SA308619QC_Mix_002control
SA308620QC_Liver_001control
SA308621QC_Liver_003control
SA308622QC_Lung_003control
SA308623QC_Liver_002control
SA308624KO_Liver_MR18liver
SA308625KO_Liver_MR17liver
SA308626KO_Liver_MR16liver
SA308627KO_Liver_MR15liver
SA308628KO_Liver_MR14liver
SA308629WT_Lung_MR05lung
SA308630WT_Liver_MR06lung
SA308631WT_Lung_MR04lung
SA308632WT_Lung_MR02lung
SA308633WT_Liver_MR07lung
SA308634WT_Lung_MR03lung
SA308635KO_Lung_MR09lung
SA308636KO_Lung_MR12lung
SA308637KO_Lung_MR13lung
SA308638KO_Lung_MR11lung
SA308639KO_Lung_MR10lung
SA308640WT_Lung_MR01lung
SA308641WT_Liver_MR08lung
Showing results 1 to 30 of 30

Collection:

Collection ID:CO002956
Collection Summary:Briefly, 6-8-week-old female NOD/SCID/IL2gR mice (005557 Jackson Laboratory) were injected via tail vein with 1 x 10^5 A375 human melanoma cell line of indicated genotypes, n=5/group. Mice were monitored over 3-4 weeks. When mice showed signs of sickness, 20% of weight loss, impaired activity, hunching and limb paralysis, animals were euthanized, and organs were harvested for evaluation on metastasis presence, liver and lung metastasis were snap frozen and subjected to downstream analysis.
Sample Type:Biopsy
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002972
Treatment Summary:Briefly, 6-8-week-old female NOD/SCID/IL2gR mice (005557 Jackson Laboratory) were injected via tail vein with 1 x 10^5 A375 human melanoma cell line of indicated genotypes, n=5/group.
Animal Endp Euthanasia:When mice showed signs of sickness, 20% of weight loss, impaired activity, hunching and limb paralysis.

Sample Preparation:

Sampleprep ID:SP002969
Sampleprep Summary:Metabolites were extracted by a two-step liquid extraction adapted from Sellik et al.[1], 50 mg of frozen tissue was used and 500 µL of prechilled methanol (-80 °C) was added. For quantification and data normalization, 25 µL of internal standard solution containing 13C6-L-Arginine, 13C5 L Valine, 13C2-Citric acid, 2H4-Succinic acid and 13C6-Fructose-6-phosphate at a concentration of 100 µM was added. This results in a concentration of 10 µM in the final extract. The sample was homogenized by a tissue slicer and the extract was vortexed for 2 min until no larger cell clusters were visible. Afterward, the sample was sonicated for 2 min in a chilled (0 °C) ultrasonic bath. The cells were kept at -80 °C for 5 min and subsequently thawed. The thawed cells were vortexed and sonicated for 2 min each and centrifuged at 3000 x g for 5 min. The supernatant was collected and 250 µL of water acidified with 0.1 % acetic acid (LC-MS grade) was added. The sample was vortexed and sonicated for 2 min and subject to the same freezing-thawing cycle described before. The samples were centrifuged at 3000 x g for 5 min and the supernatant was collected. The combined supernatant was dried in a vacuum-centrifuge for 45 min. The residue was resuspended in 250 µL acetonitrile/water (50/50; v/v) by sonicating and vortexing for 2 min each. To remove remaining proteins or other cell debris the extracts have been centrifuged at 12,000 rpm for 2 min and filtered using Nanosep 3KDa Omega centrifugal filters (Pall, Port Washington, USA). After the extraction pooled QC samples were generated for the whole sample set as well as for each investigated sample group and analyzed along the study samples to monitor the analytical quality. Ref: [1] (Sellick CA, Hansen R, Stephens GM, Goodacre R, Dickson AJ. Metabolite extraction from suspension-cultured mammalian cells for global metabolite profiling. Nat Protoc. 2011 28;6(8):1241-9. doi: 10.1038/nprot.2011.366)
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004670 AN004671
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1290 Infinity II Bio LC system Agilent 1290 Infinity II Bio LC system
Column Agilent AdvanceBio MS Spent Media (150 x 2.1mm, 2.7um) Agilent AdvanceBio MS Spent Media (150 x 2.1mm, 2.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak Area Peak Area

Chromatography:

Chromatography ID:CH003515
Chromatography Summary:For liquid chromatography, an Agilent 1290 Infinity II Bio LC system (Agilent Technologies Inc., Waldbronn, Germany) consisting of a 1290 Bio High-Speed Pump, a 1290 Bio Multisampler and a 1290 MCT with an AdvanceBio MS Spent Media (150 x 2.1 mm, 2.7 µm; Agilent Technologies Inc., Waldbronn, Germany) were used. The elution was carried out by utilizing a gradient at a flow rate of 250 μL/min with water (10 mM ammonium acetate pH 9) as solvent A and acetonitrile/water (90/10; v/v; 10 mM ammonium acetate pH 9) as solvent B. The linear gradient was: 0 min, 90% B; 2 min, 90% B; 12 min, 40% B; 13 min, 20% B; 16 min, 20% B; followed by 9 min at initial condition for re-equilibration. Column temperature was 35 °C, injection volume 5 µL.
Instrument Name:Agilent 1290 Infinity II Bio LC system
Column Name:Agilent AdvanceBio MS Spent Media (150 x 2.1mm, 2.7um)
Column Temperature:35 °C
Flow Gradient:none
Flow Rate:250 μL/min
Solvent A:water (10 mM ammonium acetate pH 9)
Solvent B:acetonitrile/water (90/10; v/v; 10 mM ammonium acetate pH 9)
Chromatography Type:HILIC

MS:

MS ID:MS004417
Analysis ID:AN004670
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were analyszed in both positive and negative ion mode separately. MS-Dial version 4.9 was used for feature analysis.
Ion Mode:POSITIVE
  
MS ID:MS004418
Analysis ID:AN004671
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were analyszed in both positive and negative ion mode separately. MS-Dial version 4.9 was used for feature analysis.
Ion Mode:NEGATIVE
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