Summary of Study ST003597
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 PR002225. The data can be accessed directly via it's Project DOI: 10.21228/M81833 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 | ST003597 |
| Study Title | Metabolic regulation of RNA methylation by the m6A-reader IGF2BP3 |
| Study Summary | The interplay of RNA modifications – deposited by “writers”, removed by “erasers” and identified by RNA binding proteins known as “readers” – forms the basis of the epitranscriptomic gene regulation hypothesis. Recent studies have identified the oncofetal RNA-binding protein IGF2BP3 as a “reader” of the N6-methyladenosine (m6A) modification and crucial for regulating gene expression. Here, we report the novel finding that the “reader” IGF2BP3 changes cellular metabolism, resulting in an altered ability of the “writers” to modify the epitranscriptome. Specifically, loss of IGF2BP3 caused a reduction in glycolytic flux and one-carbon metabolism, leading to decreased production of S-adenosyl methionine, a key substrate for methylation reactions within the cell. |
| Institute | University of California, Los Angeles |
| Last Name | Rao |
| First Name | Dinesh S |
| Address | 12-272, Factor Building, 650 Charles E Young Drive, UCLA, USA 90095 |
| gunjansharma@mednet.ucla.edu | |
| Phone | 3108252548 |
| Submit Date | 2024-11-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002225 |
| Project DOI: | doi: 10.21228/M81833 |
| Project Title: | Metabolic regulation of RNA methylation by the m6A-reader IGF2BP3 |
| Project Summary: | The interplay of RNA modifications – deposited by “writers”, removed by “erasers” and identified by RNA binding proteins known as “readers” – forms the basis of the epitranscriptomic gene regulation hypothesis. Recent studies have identified the oncofetal RNA-binding protein IGF2BP3 as a “reader” of the N6-methyladenosine (m6A) modification and crucial for regulating gene expression. Here, we report the novel finding that the “reader” IGF2BP3 changes cellular metabolism, resulting in an altered ability of the “writers” to modify the epitranscriptome. Specifically, loss of IGF2BP3 caused a reduction in glycolytic flux and one-carbon metabolism, leading to decreased production of S-adenosyl methionine, a key substrate for methylation reactions within the cell. |
| Institute: | University of California, Los Angeles |
| Last Name: | Rao |
| First Name: | Dinesh S |
| Address: | 12-272, Factor Building, 650 Charles E Young Drive, UCLA, USA 90095 |
| Email: | gunjansharma@mednet.ucla.edu |
| Phone: | 3108252548 |
Subject:
| Subject ID: | SU003726 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment |
|---|---|---|---|
| SA392347 | GS-004 | KO | Knockout |
| SA392348 | GS-005 | KO | Knockout |
| SA392349 | GS-006 | KO | Knockout |
| SA392350 | GS-010 | KO | Knockout |
| SA392351 | GS-011 | KO | Knockout |
| SA392352 | GS-012 | KO | Knockout |
| SA392353 | GS-001 | WT | Control |
| SA392354 | GS-002 | WT | Control |
| SA392355 | GS-003 | WT | Control |
| SA392356 | GS-007 | WT | Control |
| SA392357 | GS-008 | WT | Control |
| SA392358 | GS-009 | WT | Control |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003719 |
| Collection Summary: | 5e6 cells were collected, rinsed with PBS, and immediately extracted in 1 mL ice-cold 80% methanol (Optima* LC/MS, Fisher Scientific). As an internal standard, 1 µM norvaline (Sigma-Aldrich) was added to each sample. Samples were then vortexed every 5 min, three times and clarified at top speed for 5 min at 4°C. The supernatants was transferred to a new microcentrifuge tube and dried overnight using a refrigerated CentriVap vacuum concentrator (LabConco). Extracted metabolite samples were stored at -80°C. The insoluble pellets were resuspended in 0.5 M NaOH for protein estimation. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003735 |
| Treatment Summary: | Cells of the control and IGF2BP3 knocked out cell lines were plated in triplicates and cultured in their regular culture medium without glucose but supplemented with 13C6 Glucose (10 mM, Cambridge Isotope Laboratories, Inc.) for 24 hours prior to metabolite extraction. |
Sample Preparation:
| Sampleprep ID: | SP003733 |
| Sampleprep Summary: | Dried metabolites were resuspended in 100 µl 50% ACN:water and 5 µL was loaded onto a Luna 3µm NH2 100A (150 × 2.0 mm) column (Phenomenex). The chromatographic separation was performed on a Vanquish Flex (Thermo Scientific) with mobile phases A (5 mM NH4AcO pH 9.9) and B (ACN) and a flow rate of 200 μL/min. A linear gradient from 15% A to 95% A over 18 min was followed by 7 min isocratic flow at 95% A and re-equilibration to 15% A. Metabolites were detected with a Thermo Scientific Q Exactive mass spectrometer run with polarity switching in full scan mode with an m/z range of 70-975 and 70.000 resolution. |
Chromatography:
| Chromatography ID: | CH004486 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Synergi Hydro RP 100 A (100 x 2mm,2.5um) |
| Column Temperature: | 27ºC |
| Flow Gradient: | The chromatographic separation was performed on a Vanquish Flex (Thermo Scientific) with mobile phases A (5 mM NH4AcO pH 9.9) and B (ACN) and a flow rate of 200 μl/min. A linear gradient from 15% A to 95% A over 18 min was followed by 7 min isocratic flow at 95% A and re-equilibration to 15% A |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 100% Water; 5 mM Ammonium acetate (pH 9.9) |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN005908 |
| Analysis Type: | MS |
| Chromatography ID: | CH004486 |
| Num Factors: | 2 |
| Num Metabolites: | 203 |
| Units: | peak area |
| Analysis ID: | AN005909 |
| Analysis Type: | MS |
| Chromatography ID: | CH004486 |
| Num Factors: | 2 |
| Num Metabolites: | 247 |
| Units: | peak area |
