Summary of Study ST002234
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 PR001424. The data can be accessed directly via it's Project DOI: 10.21228/M8NM68 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002234 |
| Study Title | A metabolic map of the DNA damage response identifies PRDX1 in nuclear ROS scavenging and aspartate synthesis |
| Study Type | Targetted metabolomics in U2OS PRDX1 WT and PRDX1-/- |
| Study Summary | Targetted metabolomics in U2OS PRDX1 WT and PRDX1-/- While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential when cells are exposed to DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Subsequent analysis identified Peroxiredoxin 1, PRDX1, as fundamental for DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it is required to reduce DNA damage-induced nuclear reactive oxygen species levels. Moreover, PRDX1 controls aspartate availability, which is required for the DNA damage repair-induced upregulation of de novo nucleotide synthesis. Loss of PRDX1 leads to an impairment in the clearance of γΗ2ΑΧ nuclear foci, accumulation of replicative stress and cell proliferation defects, thus revealing a crucial role for PRDX1 as a DNA damage surveillance factor. |
| Institute | CRG |
| Department | GRSC |
| Laboratory | Sdelci_lab |
| Last Name | Kourtis |
| First Name | Savvas |
| Address | Carrer del Dr. Aiguader, 88, 08003 Barcelona, Barcelona, barcelona, 08003, Spain |
| savvas.kourtis@crg.eu | |
| Phone | 653549060 |
| Submit Date | 2022-07-19 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-03 |
| Release Version | 1 |
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Combined analysis:
| Analysis ID | AN003644 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II |
| Column | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6470 TQ |
| Ion Mode | NEGATIVE |
| Units | au |
Chromatography:
| Chromatography ID: | CH002698 |
| Chromatography Summary: | A 1290 Infinity II UHPLC system (Agilent Technologies) coupled with a 6470 triple quadrupole mass spectrometer (Agilent Technologies) was used for the LC-MS/MS analysis. The chromatographic separation for samples was carried out on a ZORBAX RRHD Extend-C18, 2.1 x 150 mm, 1.8 µm analytical column (Agilent Technologies). The column was maintained at a temperature of 40°C and 4 µL of sample was injected per run. The mobile phase A was 3% methanol (v/v), 10 mM tributylamine, 15 mM acetic acid in water and mobile phase B was 10 mM tributylamine, 15 mM acetic acid in methanol. The gradient elution with a flow rate of 0.25 mL/min was performed for a total time of 24 min. Afterwards back-flushing of the column using a 6port/2-position divert valve was carried out for 8 min using acetonitrile, followed by 8 min of column equilibration with 100% mobile phase A. The triple quadrupole mass spectrometer was operated in negative electrospray ionization mode, spray voltage 2 kV, gas temperature 150 °C, gas flow 1.3 L/min, nebulizer 45 psi, sheath gas temperature 325 °C, sheath gas flow 12 L/min. The metabolites of interest were detected using a dynamic MRM mode. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | The gradient elution with a flow rate of 0.25 mL/min was performed for a total time of 24 mi |
| Flow Rate: | 0.25ml/min |
| Solvent A: | 3% methanol/97% water; 15 mM acetic acid; 10 mM tributylamine |
| Solvent B: | 100% methanol; 15 mM acetic acid |
| Chromatography Type: | Reversed phase |
