Summary of Study ST003267
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 PR002029. The data can be accessed directly via it's Project DOI: 10.21228/M8BJ9X 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 | ST003267 |
| Study Title | FDX2-KO induces global down-regulation of iron-sulfur cluster-containing proteins and senescence-like growth arrest or death in ovarian cancer cells |
| Study Summary | Recent studies report molecular mechanisms underlying iron-sulfur cluster (Fe-S) biosynthesis and suggest its importance in health and disease. However, a role for Fe-S biosynthesis in cancer contexts remains unclear. Here we report that FDX2, an Fe-S assembly factor, is indispensable for maintenance of cellular Fe-S-containing proteins (Fe-S protein(s)) and proliferation of ovarian cancer (OVC) cells. CRISPR-screening of all metabolism-related genes in OVC cells identified several Fe-S assembly genes as essential for OVC growth. Using an inducible FDX2-KO OVC line, we found that FDX2 loss promotes either senescence-like growth arrest or cell death, depending on TP53 status. Mechanistically, FDX2-loss caused global but differential post transcriptional down-regulation of Fe-S proteins, in turn perturbing respiration, iron-regulation and redox homeostasis, all associated with DNA damage. These results demonstrate significant roles for Fe-S biosynthesis in OVC proliferation and survival and provide information about how the cellular Fe-S-protein network responds to disruptions in Fe-S assembly. |
| Institute | Tohoku University |
| Department | Graduate School of Medicine |
| Laboratory | Department of Biochemical Oncology |
| Last Name | Tanuma |
| First Name | Nobu-hiro |
| Address | 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan |
| nobuhiro.tanuma.c7@tohoku.ac.jp | |
| Phone | +81-22-381-1165 |
| Submit Date | 2023-10-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | CE-MS |
| Release Date | 2024-08-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002029 |
| Project DOI: | doi: 10.21228/M8BJ9X |
| Project Title: | FDX2-KO induces global down-regulation of iron-sulfur cluster-containing proteins and senescence-like growth arrest or death in ovarian cancer cells |
| Project Summary: | Recent studies report molecular mechanisms underlying iron-sulfur cluster (Fe-S) biosynthesis and suggest its importance in health and disease. However, a role for Fe-S biosynthesis in cancer contexts remains unclear. Here we report that FDX2, an Fe-S assembly factor, is indispensable for maintenance of cellular Fe-S-containing proteins (Fe-S protein(s)) and proliferation of ovarian cancer (OVC) cells. CRISPR-screening of all metabolism-related genes in OVC cells identified several Fe-S assembly genes as essential for OVC growth. Using an inducible FDX2-KO OVC line, we found that FDX2 loss promotes either senescence-like growth arrest or cell death, depending on TP53 status. Mechanistically, FDX2-loss caused global but differential post transcriptional down-regulation of Fe-S proteins, in turn perturbing respiration, iron-regulation and redox homeostasis, all associated with DNA damage. These results demonstrate significant roles for Fe-S biosynthesis in OVC proliferation and survival and provide information about how the cellular Fe-S-protein network responds to disruptions in Fe-S assembly. |
| Institute: | Tohoku University |
| Department: | Graduate School of Medicine |
| Laboratory: | Department of Biochemical Oncology |
| Last Name: | Tanuma |
| First Name: | Nobu-hiro |
| Address: | 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan |
| Email: | nobuhiro.tanuma.c7@tohoku.ac.jp |
| Phone: | +81-22-381-1165 |
| Publications: | https://doi.org/10.1016/j.jbc.2024.107678, https://www.jbc.org/article/S0021-9258(24)02179-3/fulltext, https://pubmed.ncbi.nlm.nih.gov/39151727/ |
Subject:
| Subject ID: | SU003387 |
| 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 | Sample source | DOX |
|---|---|---|---|
| SA354345 | 5 | Ovarian cancer cells | OFF |
| SA354346 | 6 | Ovarian cancer cells | OFF |
| SA354347 | 7 | Ovarian cancer cells | OFF |
| SA354348 | 8 | Ovarian cancer cells | OFF |
| SA354349 | 1 | Ovarian cancer cells | On |
| SA354350 | 2 | Ovarian cancer cells | On |
| SA354351 | 3 | Ovarian cancer cells | On |
| SA354352 | 4 | Ovarian cancer cells | On |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO003380 |
| Collection Summary: | Cells were maintained in DMEM medium (high glucose) in the presence of doxycycline (DOX). For metabolome analysis, cells were seeded to new dishes at day 0 and cultured in the presence or absence of Dox for 4 days. At day 4, cells were replenished with fresh medium (with or without Dox) and cultured for additional one day. At day 5, cells were washed with PBS twice and detached from dishes using cell scraper into PBS. The detached cells were collected by centrifugation, snap-frozen by liquid nitrogen, and stored at -80 oC until metabolite extraction. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003396 |
| Treatment Summary: | FDX2-iKO JHOC5 cells were cultured 5 days with or without doxycycline (30 ng/ml) and collected. Metabolome data were normalized to protein amounts of cells (shown in "Study design") used for the metabolite extraction. |
Sample Preparation:
| Sampleprep ID: | SP003394 |
| Sampleprep Summary: | The cell extracts were centrifugally concentrated for 2.5 hours using a LABCONCO centrifugal concentrator with cooling function (LABCONCO corporation). |
Combined analysis:
| Analysis ID | AN005352 | AN005353 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | CE | CE |
| Chromatography system | Agilent 7100 CE | Agilent 7100 CE |
| Column | Molex Fused silica capillary tubing (100cm x 50um) | Nacalai Tesque COSMO(+)Capillary (105cm x 50um) |
| MS Type | ESI | ESI |
| MS instrument type | TOF | TOF |
| MS instrument name | Agilent 6230 TOF | Agilent 6210 TOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | μmol/g of protein | μmol/g of protein |
Chromatography:
| Chromatography ID: | CH004053 |
| Chromatography Summary: | Column information: Fused silica capillary tubing 50 um i.d. x 200 cm (cut to 100 cm for analysis), Manufacturer: Molex, Material number: 106815-0017, Product description: TSP050375, Lot: CHCC04A |
| Instrument Name: | Agilent 7100 CE |
| Column Name: | Molex Fused silica capillary tubing (100cm x 50um) |
| Column Temperature: | 20 |
| Flow Gradient: | (Not applicable) |
| Flow Rate: | 10 uL/min |
| Internal Standard: | Methionine sulfone |
| Sample Injection: | Pressure injection 50 mbar, 5 sec (approximately 5 nL) |
| Solvent A: | (Not applicable) |
| Solvent B: | (Not applicable) |
| Capillary Voltage: | Positive, 30 kV |
| Running Buffer: | 1 M formic acid |
| Sheath Liquid: | 50% (v/v) methanol-water containing 0.01 uM hexakis(2,2-difluoroethoxy)phosphazene |
| Chromatography Type: | CE |
| Chromatography ID: | CH004054 |
| Chromatography Summary: | Column information: COSMO(+)Capillary, 50 um i.d. x 120 cm (cut to 105 cm for analysis), Manufacturer: Nacalai Tesque，Product No: 07584-44，Lot: P23753 |
| Instrument Name: | Agilent 7100 CE |
| Column Name: | Nacalai Tesque COSMO(+)Capillary (105cm x 50um) |
| Column Temperature: | 20 |
| Flow Gradient: | (Not applicable) |
| Flow Rate: | 10 uL / min |
| Internal Standard: | CAS |
| Sample Injection: | Pressure injection 50 mbar, 30 sec (approximately 30 nL) |
| Solvent A: | (Not applicable) |
| Solvent B: | (Not applicable) |
| Capillary Voltage: | Negative, 30 kV |
| Running Buffer: | 50 mM ammonium acetate, pH 8.5 |
| Sheath Liquid: | 5 mM ammonium acetate in 50% (v/v) methanol-water containing 0.1 uM hexakis(2,2-difluoroethoxy)phosphazene |
| Chromatography Type: | CE |
MS:
| MS ID: | MS005082 |
| Analysis ID: | AN005352 |
| Instrument Name: | Agilent 6230 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | ESI-TOFMS was performed in positive ion mode. Automatic recalibration of each acquired spectrum was achieved using the masses of the reference standards (13C isotopic ion of a protonated methanol dimer, m/z 66.0631) and (protonated ion of hexakis(2,2-difluoroethoxy)phosphazene, m/z 622.0290). For system control and data acquisition we used the MassHunter workstation software for Agilent CE-TOFMS. CE-TOFMS raw data were analyzed using our proprietary software MasterHands (ver, 2.20.0.3). |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 4,000 V |
| Dry Gas Flow: | Nitrogen, 10 L/min |
| Dry Gas Temp: | 300℃ |
| Fragment Voltage: | 75 V |
| Ionization: | ESI |
| Octpole Voltage: | 500 V |
| MS ID: | MS005083 |
| Analysis ID: | AN005353 |
| Instrument Name: | Agilent 6210 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | ESI-TOFMS was performed in negative ion mode. Automatic recalibration of each acquired spectrum was performed using reference masses of standards, i.e., (13C isotopic ion of deprotonated acetatic acid dimer, m/z 120.0383) and ([hexakis(2,2-difluoroethoxy)phosphazene + deprotonated acetic acid, m/z 680.0355). For system control and data acquisition we used the MassHunter workstation software for Agilent CE-TOFMS. CE-TOFMS raw data were analyzed using our proprietary software MasterHands (ver, 2.20.0.3). |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3,500 V |
| Dry Gas Flow: | Nitrogen, 10 L/min |
| Dry Gas Temp: | 300℃ |
| Fragment Voltage: | 100 V |
| Ionization: | ESI |
| Octpole Voltage: | 200 V |
