Summary of Study ST002720
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 PR001307. The data can be accessed directly via it's Project DOI: 10.21228/M8S124 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 | ST002720 |
| Study Title | Metabolic characterization of the polar endometabolome of Triple-Negative Breast Cancer parental and cDDP-resistant cells |
| Study Type | NMR-based metabolomics |
| Study Summary | Platinum (Pt(II)) drugs, e.g. cisplatin (cDDP), are some of the most used chemotherapeutic agents, yet tumor acquired resistance and high toxicity are still current drawbacks. Metabolomics can measure the metabolic response of drug-exposed cells, unveiling insight into drug mechanisms and metabolic markers of drug efficacy, toxicity and resistance. The present 1H NMR metabolomics study aims to describe the polar endometabolome of both MDA-MB-231 parental and cDDP-resistant cells (MDA-MB-231\R), which are representative of Triple-Negative Breast Cancer, aiding the current knowledge about the resistant cells metabolism rewiring and disclosing metabolic hotspots as possible targets to counteract the therapy resistance. |
| Institute | University of Aveiro |
| Department | Department of Chemistry and CICECO-Aveiro Institute of Materials |
| Laboratory | Metabolomics from Ana M. Gil |
| Last Name | Carneiro |
| First Name | Tatiana João |
| Address | Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal |
| tatiana.joao@ua.pt | |
| Phone | +351926369478 |
| Submit Date | 2023-05-30 |
| Num Groups | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2024-01-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001307 |
| Project DOI: | doi: 10.21228/M8S124 |
| Project Title: | Biochemical Impact of Platinum and Palladium-based Anticancer Agents – BioIMPACT |
| Project Type: | NMR-based metabolomics |
| Project Summary: | Platinum (Pt(II)) drugs, e.g. cisplatin (cDDP), are some of the most used chemotherapeutic agents, yet tumor acquired resistance and high toxicity are still current drawbacks. Palladium (Pd(II))-complexes are alternatives due to similar metal coordination and promising cytotoxic properties. Metabolomics can measure the metabolic response of drug-exposed tissues, unveiling insight into drug mechanisms and new markers of drug efficacy/toxicity. The present 1H NMR metabolomics study aims to characterize the in vivo response of the impact of a Pd(II)-complex with polyamine spermine (Pd2Spm), compared to cDDP, on the metabolism of several organs from healthy mice. |
| Institute: | University of Aveiro |
| Department: | Department of Chemistry and CICECO-Aveiro Institute of Materials |
| Laboratory: | Metabolomics from Ana M. Gil |
| Last Name: | Carneiro |
| First Name: | Tatiana J. |
| Address: | Campus Universitário de Santiago, Aveiro, Aveiro, 3810-193, Portugal |
| Email: | tatiana.joao@ua.pt |
| Phone: | +351926369478 |
| Funding Source: | This research was developed within the scope of the CICECO—Aveiro Institute of Materials, with references UIDB/50011/2020 and UIDP/50011/2020, financed by national funds through the Por-tuguese Foundation for Science and Technology (FCT/MEC) and when appropriate co-financed by European Regional Development Fund (FEDER) under the PT2020 Partnership Agreement. This work was also funded by the FCT through LAQV/REQUIMTE FCT UIDB/50006/2020 (C.D.), UIDB/00070/2020 (A.L.M.B.d.C and M.P.M.M.), POCI-01-0145-FEDER-0016786, and Cen-tro-01-0145-FEDER-029956 (co-financed by COMPETE 2020, Portugal 2020 and European Com-munity through FEDER). We also acknowledge the Portuguese National NMR Network (PTNMR), supported by FCT funds as the NMR spectrometer used is part of PTNMR and partially supported by Infrastructure Project Nº 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL, and the FCT through PIDDAC). M.V. thanks the FCT and the PhD Program in Medicines and Pharmaceutical Innovation (i3DU) for his PhD grant PD/BD/135460/2017 and T.J.C. thanks FCT for her PhD grant SFRH/BD/145920/2019; both grants were funded by the European Social Fund of the European Union and national funds FCT/MCTES. |
Subject:
| Subject ID: | SU002826 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | MDA-MB-231 cells |
| Gender: | Not applicable |
| Cell Biosource Or Supplier: | ATCC (Manassas, VA, USA); ATCC HTB-26 |
| Cell Strain Details: | Epithelial breast cancer cells; absence of estrogen and progesterone receptors, HER2 overexpression |
| Cell Passage Number: | Between 5 to 10 |
| Cell Counts: | 5 M |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment_group |
|---|---|---|
| SA273752 | R_C0h_EA_32_1_2 | Resistant_Controls_0h |
| SA273753 | R_C0h_EA_33_1_2 | Resistant_Controls_0h |
| SA273754 | R_C0h_EA_23_1_2 | Resistant_Controls_0h |
| SA273755 | R_C0h_EA_11_1_2 | Resistant_Controls_0h |
| SA273756 | R_C0h_EA_31_1_2 | Resistant_Controls_0h |
| SA273757 | R_C0h_EA_12_1_2 | Resistant_Controls_0h |
| SA273758 | R_C0h_EA_21_1_2 | Resistant_Controls_0h |
| SA273759 | R_C0h_EA_13_1_2 | Resistant_Controls_0h |
| SA273760 | R_C0h_EA_22_1_2 | Resistant_Controls_0h |
| SA273761 | R_C24h_EA_32_1_2 | Resistant_Controls_24h |
| SA273762 | R_C24h_EA_33_1_2 | Resistant_Controls_24h |
| SA273763 | R_C24h_EA_23_1_2 | Resistant_Controls_24h |
| SA273764 | R_C24h_EA_31_1_2 | Resistant_Controls_24h |
| SA273765 | R_C24h_EA_22_1_2 | Resistant_Controls_24h |
| SA273766 | R_C24h_EA_13_1_2 | Resistant_Controls_24h |
| SA273767 | R_C24h_EA_12_1_2 | Resistant_Controls_24h |
| SA273768 | R_C24h_EA_21_1_2 | Resistant_Controls_24h |
| SA273769 | R_C24h_EA_11_1_2 | Resistant_Controls_24h |
| SA273770 | R_C48h_EA_31_1_2 | Resistant_Controls_48h |
| SA273771 | R_C48h_EA_33_1_2 | Resistant_Controls_48h |
| SA273772 | R_C48h_EA_23b_1_2 | Resistant_Controls_48h |
| SA273773 | R_C48h_EA_32_1_2 | Resistant_Controls_48h |
| SA273774 | R_C48h_EA_22_1_2 | Resistant_Controls_48h |
| SA273775 | R_C48h_EA_21_1_2 | Resistant_Controls_48h |
| SA273776 | R_C48h_EA_12_1_2 | Resistant_Controls_48h |
| SA273777 | R_C48h_EA_11_1_2 | Resistant_Controls_48h |
| SA273778 | R_C48h_EA_13_1_2 | Resistant_Controls_48h |
| SA273779 | S_C0h_EA_31_1_2 | Sensitive_Controls_0h |
| SA273780 | S_C0h_EA_32_1_2 | Sensitive_Controls_0h |
| SA273781 | S_C0h_EA_33_1_2 | Sensitive_Controls_0h |
| SA273782 | S_C0h_EA_23_1_2 | Sensitive_Controls_0h |
| SA273783 | S_C0h_EA_11_1_2 | Sensitive_Controls_0h |
| SA273784 | S_C0h_EA_22_1_2 | Sensitive_Controls_0h |
| SA273785 | S_C0h_EA_13_1_2 | Sensitive_Controls_0h |
| SA273786 | S_C0h_EA_12_1_2 | Sensitive_Controls_0h |
| SA273787 | S_C0h_EA_21_1_2 | Sensitive_Controls_0h |
| SA273788 | S_C24h_EA_31_1_2 | Sensitive_Controls_24h |
| SA273789 | S_C24h_EA_33_1_2 | Sensitive_Controls_24h |
| SA273790 | S_C24h_EA_23_1_2 | Sensitive_Controls_24h |
| SA273791 | S_C24h_EA_32_1_2 | Sensitive_Controls_24h |
| SA273792 | S_C24h_EA_22_1_2 | Sensitive_Controls_24h |
| SA273793 | S_C24h_EA_12_1_2 | Sensitive_Controls_24h |
| SA273794 | S_C24h_EA_11_1_2 | Sensitive_Controls_24h |
| SA273795 | S_C24h_EA_21_1_2 | Sensitive_Controls_24h |
| SA273796 | S_C24h_EA_13_1_2 | Sensitive_Controls_24h |
| SA273797 | S_C48h_EA_31_1_2 | Sensitive_Controls_48h |
| SA273798 | S_C48h_EA_32_1_2 | Sensitive_Controls_48h |
| SA273799 | S_C48h_EA_33_1_2 | Sensitive_Controls_48h |
| SA273800 | S_C48h_EA_23_1_2 | Sensitive_Controls_48h |
| SA273801 | S_C48h_EA_13_1_2 | Sensitive_Controls_48h |
| SA273802 | S_C48h_EA_11_1_2 | Sensitive_Controls_48h |
| SA273803 | S_C48h_EA_12_1_2 | Sensitive_Controls_48h |
| SA273804 | S_C48h_EA_21_1_2 | Sensitive_Controls_48h |
| SA273805 | S_C48h_EA_22_1_2 | Sensitive_Controls_48h |
| Showing results 1 to 54 of 54 |
Collection:
| Collection ID: | CO002819 |
| Collection Summary: | MDA-MB-231 parental and resistant (MDA-MB-231/R) cells were seeded at a density of 3 × 10^4 cells/cm2 onto 13.55 cm diameter Petri dishes, cultured in a humidified atmosphere of 5% CO2 at 37 ◦C and allowed to adhere for 24 h. After this, cells were incubated and collected at 0, 24 and 48 h, with basis on the population (25.5 ± 0.9 h and 30.6 ± 1.1 h for MDA-MB-231 and MDA-MB-231/R cells, respectively). At each time-point, cells were harvested using a 0.25% (v/v) trypsin-EDTA solution, washed twice with PBS and centrifuged (300 g, 5 min, 20 ◦C). The cell pellet was directly stored at − 80 ◦C until analysis. Three independent experiments with triplicates were performed for each cell type and time-point. |
| Sample Type: | Breast cancer cells |
| Collection Duration: | Between 2 and 5 minutes |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002835 |
| Treatment Summary: | In this study, both cell types (MDA-MB-231 and MDA-MB-231/R) correspond to controls, so no treatment was applied to these two groups. |
Sample Preparation:
| Sampleprep ID: | SP002832 |
| Sampleprep Summary: | The cellular polar extracts were extracted using a biphasic extraction method of methanol/chloroform/water. Basically, cell pellets were resuspended in 650 µL of 80% (v/v) methanol-miliQ water solution, transferred to microcentrifuge tubes with 150 mg of glass beads, and vortexed for 5 min. Subsequently, 260 µL of 100% chloroform and 260 µL of 100% chloroform plus 220 µL MiliQ water were added to samples, which were vortexed for 5 min between solvents addition. The samples were kept at − 20 °C for 10 min and centrifuged. The aqueous phase of the resulting extract was collected into a new tube, vacuum-dried and stored at − 80 °C until the NMR analysis. Previously to NMR spectra acquision, the dry aqueous extracts were suspended in 650 µL of 100 mM sodium phosphate buffer (pH 7.4, in D2O containing 0.25% 3-(trimethylsilyl)-propionic-2,2,3,3-d4 acid (TSP) for chemical shift referencing) and transferred into 5 mm NMR tubes |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Biphasic method (methanol/ chloroform/ water) |
| Extract Storage: | -80℃ |
Analysis:
| Analysis ID: | AN004410 |
| Laboratory Name: | Metabolomics Ana M. Gil |
| Analysis Type: | NMR |
| Acquisition Date: | February 2023 |
| Software Version: | Topspin 3.2 |
| Results File: | ST002720_AN004410_Results.txt |
| Units: | ppm |
NMR:
| NMR ID: | NM000265 |
| Analysis ID: | AN004410 |
| Instrument Name: | Avance III TM HD 500MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| NMR Comments: | On folder 1 and folder pdata: 1st subfolder contains raw spectra; 2nd subfolder contains manually processed spectra |
| Field Frequency Lock: | Deuterium |
| Spectrometer Frequency: | 500MHz |
| NMR Probe: | TXI |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm |
| Shimming Method: | Topshim |
| Receiver Gain: | 203 |
| Temperature: | 298K |
| Number Of Scans: | 512 |
| Acquisition Time: | 2.34s |
| Relaxation Delay: | 2s |
| Spectral Width: | 7002.801 |
| Zero Filling: | 64k |
| Baseline Correction Method: | Manual |
| Chemical Shift Ref Std: | TSP (3-(trimethylsilyl)-propionic-2,2,3,3-d4 acid) |
