Summary of Study ST003953
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 PR002476. The data can be accessed directly via it's Project DOI: 10.21228/M8KV7F 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 | ST003953 |
| Study Title | Metabolomic Profiling of Gastric Cancer Post-ESRP1 Gene Knockout |
| Study Summary | Therapeutic resistance represents a bottleneck to treatment in advanced gastric cancer (GC). Ferroptosis is an iron-dependent form of non-apoptotic cell death and is associated with anti-cancer therapeutic efficacy. Further investigations are required to clarify the underlying mechanisms. Ferroptosis-resistant GC cell lines are constructed. Dysregulated mRNAs between ferroptosis-resistant and parental cell lines are identified. The expression of ESRP1/SCAF1 is manipulated in GC cell lines where relevant biological and molecular analyses are performed. Molecular docking and computational screening are performed to screen potential inhibitors of ESRP1. We show that ESRP1 boosts protein remodeling of electron transport chain (ETC) complexes by directly transactivating SCAF1. This leads to increased supercomplexes (SCs) assembly, mitochondrial respiration, mitochondrial energetics and chemo- and immune-resistance. Zanamivir, reverts the ferroptosis-resistant phenotype via directly targeting ESRP1 and promoting TRIM25-mediated ubiquitination and degradation of ESRP1. Here we show, ESRP1/SCAF1 are important in ferroptosis-resistance, and targeting ESRP1 with zanamivir has therapeutic potential. We conducted untargeted metabolomic analysis of Erastin-resis SNU-668 cells transfected with shRNA-ESRP1 or shRNA-NC. |
| Institute | Fudan University Shanghai Cancer Center |
| Department | Department of Gastric Surgery |
| Last Name | Mingzhe |
| First Name | Ma |
| Address | building 18, 29 Nong Linling Road, Xuhui district, Shanghai, 200024, China |
| mmz666@163.com, ding@bioinformatics.com.cn | |
| Phone | 13917006049 |
| Submit Date | 2025-05-29 |
| Num Groups | 2 |
| Total Subjects | 2 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-06-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002476 |
| Project DOI: | doi: 10.21228/M8KV7F |
| Project Title: | Targeting ESRP1 inhibits the assembly of respiratory chain supercomplexes to overcome ferroptosis-resistance in gastric cancer |
| Project Summary: | Therapeutic resistance represents a bottleneck to treatment in advanced gastric cancer (GC). Ferroptosis is an iron-dependent form of non-apoptotic cell death and is associated with anti-cancer therapeutic efficacy. Further investigations are required to clarify the underlying mechanisms. Ferroptosis-resistant GC cell lines are constructed. Dysregulated mRNAs between ferroptosis-resistant and parental cell lines are identified. The expression of ESRP1/SCAF1 is manipulated in GC cell lines where relevant biological and molecular analyses are performed. Molecular docking and computational screening are performed to screen potential inhibitors of ESRP1. We show that ESRP1 boosts protein remodeling of electron transport chain (ETC) complexes by directly transactivating SCAF1. This leads to increased supercomplexes (SCs) assembly, mitochondrial respiration, mitochondrial energetics and chemo- and immune-resistance. Zanamivir, reverts the ferroptosis-resistant phenotype via directly targeting ESRP1 and promoting TRIM25-mediated ubiquitination and degradation of ESRP1. Here we show, ESRP1/SCAF1 are important in ferroptosis-resistance, and targeting ESRP1 with zanamivir has therapeutic potential. We conducted untargeted metabolomic analysis of Erastin-resis SNU-668 cells transfected with shRNA-ESRP1 or shRNA-NC. |
| Institute: | Fudan University Shanghai Cancer Center |
| Department: | Department of Gastric Surgery |
| Last Name: | Mingzhe |
| First Name: | Ma |
| Address: | building 18, 29 Nong Linling Road, Xuhui district, Shanghai, 200024, China |
| Email: | mmz666@163.com, ding@bioinformatics.com.cn |
| Phone: | 13917006049 |
Subject:
| Subject ID: | SU004090 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Treatment |
|---|---|---|---|---|
| SA452608 | NC1 | NC1 | Control | Control |
| SA452609 | NC2 | NC2 | Control | Control |
| SA452610 | NC3 | NC3 | Control | Control |
| SA452611 | NC4 | NC4 | Control | Control |
| SA452612 | NC5 | NC5 | Control | Control |
| SA452613 | NC6 | NC6 | Control | Control |
| SA452614 | siESRP1_1 | siESRP1_1 | Knockout | Knockout |
| SA452615 | siESRP1_2 | siESRP1_2 | Knockout | Knockout |
| SA452616 | siESRP1_3 | siESRP1_3 | Knockout | Knockout |
| SA452617 | siESRP1_4 | siESRP1_4 | Knockout | Knockout |
| SA452618 | siESRP1_5 | siESRP1_5 | Knockout | Knockout |
| SA452619 | siESRP1_6 | siESRP1_6 | Knockout | Knockout |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO004083 |
| Collection Summary: | Erastinresis SNU-668 cells transfected with shRNA-NC, n = 12 Erastin-resis SNU-668 cells transfected with shRNA-ESRP1 or shRNA-NC. 2 × 105 cells of adherent cells were harvested in six-well plates. When collected, cellswerewashed by cold PBS buffer twice and immediately quenched in liquid nitrogen. Tumor samples were weighed and pulverized. All samples were lysed in 1ml of −80 °C extraction solvent (80% methanol/ water). After centrifugation (20,000 g, 4 °C, 15min), supernatant was transferred to a new tube, and samples were dried using a vacuum centrifugal concentrator. Blood samples from patients and mice were collected into BD Vacutainer blood collection tubes and placed on ice. Serum was isolated by centrifugation (15,000 g, 4 °C, 10min), and aliquots of 100 μl of supernatant were frozen immediately at −80 °C. Metabolites were reconstituted in 150 μl of 80% acetonitrile/water, vortexed, and centrifuged to remove insoluble material. All samples were stored at −80 °C before LC-MS/MS analysis. |
| Sample Type: | SNU-668 Erastin-resistant cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004099 |
| Treatment Summary: | Stable knockdown of ESRP1 in GC cell lines was generated by lentiviral-based shRNA delivery. Specific target shRNAs were subcloned into lentiviral vector pLKO.1 (Shanghai Genechem), while a non-target shRNA was used as a negative control. The shRNAs were designed and synthesized by GenePharma (Shanghai, China) to suppress the gene expression. The design of the shRNAs was assisted by the use of web-based software provided by Invitrogen (http://rnaidesigner.invitrogen.com/rnaiexpress/). Blast searches were performed using the National Center for Biotechnology Information expressed sequence tag database to ensure that the shRNA construct only targeted human ESRP1 expression. Erastin-resis SNU-668 cells transfected with shRNA-NC, or shRNA-ESRP1. |
Sample Preparation:
| Sampleprep ID: | SP004096 |
| Sampleprep Summary: | For untargeted metabolomics, a total of 12 samples were analyzed (n=6 Erastinresis SNU-668 cells transfected with shRNA-NC, n=12 Erastinresis SNU-668 cells transfected with shRNA-ESRP1). Transfer all samples to a 2 mL centrifuge tube and add one grinding bead with a diameter of 6 mm. Add 200 µL of extraction solution (methanol:water = 4:1 (v:v)), containing four internal standards (e.g., L-2-chlorophenylalanine at 0.02 mg/mL). Grind using a cryogenic tissue grinder for 6 minutes (-10°C, 50 Hz). Perform low-temperature ultrasonic extraction for 30 minutes (5°C, 40 kHz). Incubate the samples at -20°C for 30 minutes. Centrifuge for 15 minutes (13,000 g, 4°C), and transfer the supernatant to an injection vial with an insert for analysis. Additionally, transfer 20 µL of the supernatant from each sample into a separate container to create a pooled quality control sample. |
| Processing Storage Conditions: | -80℃ |
Chromatography:
| Chromatography ID: | CH004936 |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1 mm, 1.8 µm) |
| Column Temperature: | 40°C |
| Flow Gradient: | 0.0 min 10% 1.0 min 10% 11.0 min 13% 14.0 min 20% 16.5 min 30% 18.5 min 50% 20.5 |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 95% Water/5% Acetonitrile; 0.1% Formic acid |
| Solvent B: | 47.5% Acetonitrile/47.5% Isopropanol/5% Water; 0.1% Formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006497 |
| Analysis Type: | MS |
| Chromatography ID: | CH004936 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003953_AN006497_Results.txt |
| Units: | peak intensity |
| Analysis ID: | AN006498 |
| Analysis Type: | MS |
| Chromatography ID: | CH004936 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003953_AN006498_Results.txt |
| Units: | peak intensity |
