{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002851","ANALYSIS_ID":"AN004671","VERSION":"1","CREATED_ON":"September 6, 2023, 11:19 pm"},

"PROJECT":{"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"},

"STUDY":{"STUDY_TITLE":"Metabolic caracterization of liver metastasis organotropism","STUDY_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","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_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WT_Lung_MR01",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Lung_MR01"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Lung_MR02",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Lung_MR02"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Lung_MR03",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Lung_MR03"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Lung_MR04",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Lung_MR04"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Lung_MR05",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Lung_MR05"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Liver_MR06",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Liver_MR06"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Liver_MR07",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Liver_MR07"}
},
{
"Subject ID":"-",
"Sample ID":"WT_Liver_MR08",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"WT NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"WT_Liver_MR08"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Lung_MR09",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Lung_MR09"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Lung_MR10",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Lung_MR10"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Lung_MR11",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Lung_MR11"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Lung_MR12",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Lung_MR12"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Lung_MR13",
"Factors":{"Organism":"Mus musculus","Organism part":"lung","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Lung_MR13"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Liver_MR14",
"Factors":{"Organism":"Mus musculus","Organism part":"liver","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Liver_MR14"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Liver_MR15",
"Factors":{"Organism":"Mus musculus","Organism part":"liver","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Liver_MR15"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Liver_MR16",
"Factors":{"Organism":"Mus musculus","Organism part":"liver","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Liver_MR16"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Liver_MR17",
"Factors":{"Organism":"Mus musculus","Organism part":"liver","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Liver_MR17"}
},
{
"Subject ID":"-",
"Sample ID":"KO_Liver_MR18",
"Factors":{"Organism":"Mus musculus","Organism part":"liver","Variant":"KN NOD/SCID/IL2gR"},
"Additional sample data":{"Sample type":"experimental sample","RAW_FILE_NAME":"KO_Liver_MR18"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Mix_001",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Mix_001"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Mix_002",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Mix_002"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Mix_003",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Mix_003"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Lung_001",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Lung_001"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Lung_002",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Lung_002"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Lung_003",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Lung_003"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Liver_001",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Liver_001"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Liver_002",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Liver_002"}
},
{
"Subject ID":"-",
"Sample ID":"QC_Liver_003",
"Factors":{"Organism":"Mus musculus","Organism part":"control","Variant":"-"},
"Additional sample data":{"Sample type":"pooled quality control sample","RAW_FILE_NAME":"QC_Liver_003"}
},
{
"Subject ID":"-",
"Sample ID":"ExtractionBlank_001",
"Factors":{"Organism":"blank","Organism part":"blank","Variant":"-"},
"Additional sample data":{"Sample type":"experimental blank","RAW_FILE_NAME":"ExtractionBlank_001"}
},
{
"Subject ID":"-",
"Sample ID":"ExtractionBlank_002",
"Factors":{"Organism":"blank","Organism part":"blank","Variant":"-"},
"Additional sample data":{"Sample type":"experimental blank","RAW_FILE_NAME":"ExtractionBlank_002"}
},
{
"Subject ID":"-",
"Sample ID":"ExtractionBlank_003",
"Factors":{"Organism":"blank","Organism part":"blank","Variant":"-"},
"Additional sample data":{"Sample type":"experimental blank","RAW_FILE_NAME":"ExtractionBlank_003"}
}
],
"COLLECTION":{"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_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."},

"SAMPLEPREP":{"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℃"},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1290 Infinity II Bio LC system","COLUMN_NAME":"AdvanceBio MS Spent Media (150 x 2.1 mm, 2.7 µm)","SOLVENT_A":"water (10 mM ammonium acetate pH 9)","SOLVENT_B":"acetonitrile/water (90/10; v/v; 10 mM ammonium acetate pH 9)","FLOW_GRADIENT":"none","FLOW_RATE":"250 μL/min","COLUMN_TEMPERATURE":"35 °C"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Data were analyszed in both positive and negative ion mode separately. MS-Dial version 4.9 was used for feature analysis.","MS_RESULTS_FILE":"ST002851_AN004671_Results.txt UNITS:Peak Area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}