Summary of Study ST003106
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 PR001775. The data can be accessed directly via it's Project DOI: http://dx.doi.org/10.21228/M88M6V 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 | ST003106 |
| Study Title | 13C-palmitate labeling experiment in ICC13-7 treated with DMSO or Infigratinib |
| Study Summary | Genomic alterations that activate FGFR2 are common in intrahepatic cholangiocarcinoma (ICC) and confer sensitivity to treatment with FGFR inhibitors. However, the depth and duration of responses are often limited. Here, we conducted integrative transcriptomic and metabolomic analysis of patient-derived models to define the pathways that fuel tumor growth downstream of oncogenic FGFR2 signaling in ICC and to uncover compensatory mechanisms associated with pathway inhibition. We find FGFR2-mediated activation of NF-B maintains a highly glycolytic phenotype. Conversely, FGFR inhibition blocks glucose uptake and glycolysis while inciting a series of adaptive changes, including switching fuel source utilization to favor fatty acid oxidation and increasing mitochondrial fusion and autophagy. Accordingly, FGFR inhibitor efficacy is potentiated by combined mitochondrial targeting, an effect enhanced in xenograft models by intermittent fasting. Thus, we show that oncogenic FGFR2 signaling drives NF-kB-dependent glycolysis in ICC and that metabolic reprogramming in response to FGFR inhibition confers new targetable vulnerabilities. |
| Institute | Massachusetts General Hospital |
| Last Name | Zhen |
| First Name | Yuanli |
| Address | 185 cambridge street, room 4100 |
| yzhen1@mgh.harvard.edu | |
| Phone | 4698792279 |
| Submit Date | 2024-01-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-03-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001775 |
| Project DOI: | http://dx.doi.org/10.21228/M88M6V |
| Project Title: | FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma |
| Project Summary: | Genomic alterations that activate FGFR2 are common in intrahepatic cholangiocarcinoma (ICC) and confer sensitivity to FGFR inhibitor treatment. However, the depth and duration of responses are often limited. Here, we conducted integrative transcriptomics, metabolomics, and phosphoproteomics analysis of patient-derived models to define the pathways that fuel tumor growth downstream of oncogenic FGFR2 signaling in ICC and to uncover compensatory mechanisms associated with pathway inhibition. We find FGFR2-mediated activation of NF-kB maintains a highly glycolytic phenotype. Conversely, FGFR inhibition blocks glucose uptake and glycolysis while inciting a series of adaptive changes, including switching fuel source utilization to favor fatty acid oxidation and increasing mitochondrial fusion and autophagy. Accordingly, FGFR inhibitor efficacy is potentiated by combined mitochondrial targeting, an effect enhanced in xenograft models by intermittent fasting. Thus, we show that oncogenic FGFR2 signaling drives NF-kB-dependent glycolysis in ICC and that metabolic reprogramming in response to FGFR inhibition confers new targetable vulnerabilities. |
| Institute: | mgh |
| Last Name: | Zhen |
| First Name: | Yuanli |
| Address: | 185 cambridge street, room 4100 |
| Email: | yzhen1@mgh.harvard.edu |
| Phone: | 4698792279 |
Subject:
| Subject ID: | SU003221 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Sample source |
|---|---|---|---|
| SA333652 | SUB13607p4_SPL07 | DMSO | ICC13-7 cells |
| SA333653 | SUB13607p4_SPL09 | DMSO | ICC13-7 cells |
| SA333654 | SUB13607p4_SPL08 | DMSO | ICC13-7 cells |
| SA333655 | SUB13607p4_SPL12 | Infigratinib | ICC13-7 cells |
| SA333656 | SUB13607p4_SPL10 | Infigratinib | ICC13-7 cells |
| SA333657 | SUB13607p4_SPL11 | Infigratinib | ICC13-7 cells |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003214 |
| Collection Summary: | media was completely aspirated, and cells were washed with ice-cold saline quickly. After washing, fully remove saline and cells can be scrapped in 1 ml pre-cooled methanol (-20°C) with internal standards (Cambridge Isotope Laboratories, MSK-A2-1.2), and transferred to glass vials, stored at -80°C until extraction. |
| Sample Type: | ICC13-7 |
Treatment:
| Treatment ID: | TR003230 |
| Treatment Summary: | Cells were pretreated with DMSO or 100nM Infigratinib for 24h in lipid-depleted media. Then they were changed to 13C-Plamitate labeling media for 8h (with DMSO or infigratinib) before harvesting cells. |
Sample Preparation:
| Sampleprep ID: | SP003227 |
| Sampleprep Summary: | extractions were conducted following the biphasic extraction protocol. Basically, add cold chloroform to samples (in methanol) with a ratio of 2:1. Vortex samples for 1 minute to homogenize. Add 1 fraction of water, and vortex samples again. Glass vials were centrifuged at 3000 rcf for 10 minutes for phase separation. The aqueous phase was transferred to a new glass vial for metabolomics and the remaining interphase was used for protein quantification. The aqueous phase was evaporated under nitrogen flow. Samples were resuspended in 50% acetonitrile, and the volume was scaled according to the protein amounts. 15ul was used for the lowest biomass, and all others were scaled accordingly. Standard mixes were prepared at 100 uM and run after the samples to allow for the identification of the targets. |
Combined analysis:
| Analysis ID | AN005085 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X tribrid |
| Ion Mode | UNSPECIFIED |
| Units | area analyzed by Compound discoverer (counts x seconds) |
Chromatography:
| Chromatography ID: | CH003841 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 40 |
| Flow Gradient: | Started at 93% B and 7% A ; 40% B/60% A in 19 min; 100% A in 9 min; 100% A for 5 min; back to 93% B/7% A in 3 min; re-equilibration at 93% B/7% A for 9 min. |
| Flow Rate: | 0.05 to 0.15 mL/min in 30 sec; then held at 0.15mL/min |
| Solvent A: | 100% Water; 20 mMAmmonium Carbonate, 0.1% Ammonium hydroxide |
| Solvent B: | Acetonitrile 97%, 3% water |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004822 |
| Analysis ID: | AN005085 |
| Instrument Name: | Thermo Orbitrap ID-X tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data was acquired on the ID-X in switching polarities at 120000 resolution, with an AGC target of 1e5, and a m/z range of 65 to 1000. MS1 data is acquired in switching polarities for all samples.Data is analyzed in Compound Discoverer 3.3 (CD, ThermoFisher Scientific). A mix of standard of each target was run along the samples and used as the unlabeled reference for the CD labelling workflow. Isotopomer distribution is found in the exchange column, as % of 0 labelled carbon, 1 labelled carbon, 2 labelled carbon, etc. Those are corrected for natural abundance. For the compounds that couldn’t be analyzed by CD, the areas have been extracted with Tracefinder manually. |
| Ion Mode: | UNSPECIFIED |
