Summary of Study ST002835
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 | ST002835 |
| Study Title | Investigation of FGFR signaling controlled metabolism in FGFR2-fusion+ intrahepatic cholangiocarcinoma |
| 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. Elucidating the FGFR2-driven oncogenic program and the adaptions to FGFR inhibition is needed to gain insight into the biology of these tumors and inform future therapeutic development. Here, we conducted 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-fusion+ ICC maintains a highly glycolytic phenotype in FGFR2+ ICC. Conversely, FGFR inhibition blocks glucose uptake and glycolysis, while inciting a series of adaptive changes. Thus, we show that glycolysis is a key downstream effector of oncogenic FGFR2 signaling in ICC, and that pronounced 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 | 2023-08-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| 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: | SU002945 |
| 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 | cell line | treatment | labeling status |
|---|---|---|---|---|
| SA307239 | SUB11589p2_Spl09 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 0h as ctrl |
| SA307240 | SUB11589p2_Spl07 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 0h as ctrl |
| SA307241 | SUB11589p2_Spl08 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 0h as ctrl |
| SA307242 | SUB11589p2_Spl15 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 1h |
| SA307243 | SUB11589p2_Spl14 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 1h |
| SA307244 | SUB11589p2_Spl16 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 1h |
| SA307245 | SUB11589p2_Spl20 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 24h |
| SA307246 | SUB11589p2_Spl21 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 24h |
| SA307247 | SUB11589p2_Spl22 | ICC13-7 | control | 13C6-Glucose Isotopic tracing 24h |
| SA307230 | SUB11589p2_Spl12 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 0h as ctrl |
| SA307231 | SUB11589p2_Spl10 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 0h as ctrl |
| SA307232 | SUB11589p2_Spl11 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 0h as ctrl |
| SA307233 | SUB11589p2_Spl17 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 1h |
| SA307234 | SUB11589p2_Spl18 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 1h |
| SA307235 | SUB11589p2_Spl19 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 1h |
| SA307236 | SUB11589p2_Spl24 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 24h |
| SA307237 | SUB11589p2_Spl25 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 24h |
| SA307238 | SUB11589p2_Spl23 | ICC13-7 | Infigratinib | 13C6-Glucose Isotopic tracing 24h |
| SA307248 | SUB11589p2_Spl32 | ICC21 | Afatinib | N/A |
| SA307249 | SUB11589p2_Spl33 | ICC21 | Afatinib | N/A |
| SA307250 | SUB11589p2_Spl34 | ICC21 | Afatinib | N/A |
| SA307251 | SUB11589p2_Spl36 | ICC21 | Combo | N/A |
| SA307252 | SUB11589p2_Spl37 | ICC21 | Combo | N/A |
| SA307253 | SUB11589p2_Spl35 | ICC21 | Combo | N/A |
| SA307257 | SUB11589p2_Spl28 | ICC21 | control | N/A |
| SA307258 | SUB11589p2_Spl26 | ICC21 | control | N/A |
| SA307259 | SUB11589p2_Spl27 | ICC21 | control | N/A |
| SA307254 | SUB11589p2_Spl29 | ICC21 | Infigratinib | N/A |
| SA307255 | SUB11589p2_Spl30 | ICC21 | Infigratinib | N/A |
| SA307256 | SUB11589p2_Spl31 | ICC21 | Infigratinib | N/A |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO002938 |
| Collection Summary: | 1 million ICC cells were seeded in 6 cm dishes under indicated treatments with triplicates to identify metabolic characteristics. Fresh media was provided 2 hours before harvest. For metabolite collection, 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: | Tumor cells |
Treatment:
| Treatment ID: | TR002954 |
| Treatment Summary: | ICC13-7 cells were treated with DMSO or 100 nM infigratinib for 24 hours, then labeled with 13C6-Glucose for indicated time points (0,1,24 hours). ICC21 cells were treated with DMSO, 100 nM infigratinib, 100 nM afatinib or combo for 24 hours. |
Sample Preparation:
| Sampleprep ID: | SP002951 |
| Sampleprep Summary: | Samples were dried under N2 flow. Samples were resuspended in acetonitrile 50% in water. The volume was scaled to the biomass. 15ul was used for the lowest biomass, and all other were scaled accordingly. Standard mixes were prepared at 100uM and run after the samples to allow for identification of the targets |
Combined analysis:
| Analysis ID | AN004631 | AN004632 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo BETASIL Diol (150 x 2.1mm,5um) | Thermo BETASIL Diol (150 x 2.1mm,5um) |
| 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 | area analyzed by Compound discoverer (counts x seconds) | area analyzed by Compound discoverer (counts x seconds) |
Chromatography:
| Chromatography ID: | CH003485 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo BETASIL Diol (150 x 2.1mm,5um) |
| Column Temperature: | 40 |
| Flow Gradient: | The LC program was as follow: starting at 93% B, to 40% B in 19 min, then to 0% B in 9 min, maintained at 0% B for 5 min, then back to 93% B in 3 min and re-equilibrated at 93% B for 9 min. |
| Flow Rate: | The flow rate was maintained at 0.15 mL/min, except for the first 30 seconds where the flow rate was uniformly ramped from 0.05 to 0.15 mL/ min. |
| Solvent A: | 20 mMAmmonium Carbonate, 0.1% Ammonium hydroxide, in Water |
| Solvent B: | Acetonitrile 97%, in water |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004378 |
| Analysis ID: | AN004631 |
| 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: | POSITIVE |
| MS ID: | MS004379 |
| Analysis ID: | AN004632 |
| 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. 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: | NEGATIVE |
