Summary of Study ST002408
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 PR001550. The data can be accessed directly via it's Project DOI: 10.21228/M8BM6G 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 | ST002408 |
| Study Title | Multi-omic Analysis of ClpP Activation in Triple-Negative Breast Cancer Cells |
| Study Summary | The ClpP activators ONC201 and related small molecules (TR compounds, Madera Therapeutics), have demonstrated significant anti-cancer potential in an array of in vitro cell models and in vivo studies, including clinical trials for refractory solid tumors. Though progress has been made in identifying specific phenotypic outcomes following ClpP activation, the exact mechanism by which ClpP activation leads to broad anti-cancer activity has yet to be fully elucidated. In this study, we utilized a multi-omics approach to identify the ClpP-dependent proteomic, transcriptomic, and metabolomic changes resulting from ONC201 or the TR compound TR-57 in triple-negative breast cancer cells (TNBC). Applying mass spectrometry- based methods of proteomics and metabolomics, we identified ~8000 proteins and 588 metabolites, respectively. From proteomics data, approximately 3400 (ONC201) and 3000 (TR-57) proteins increased and ~4600 (ONC201) and ~4800 (TR-57) proteins decreased in this study. Additionally, gene ontological analysis revealed strong similarities between proteins up- or downregulated by ONC201 or TR-57 treatment. Notably, this included the downregulation of many mitochondrial processes and proteins, including mitochondrial translation and mitochondrial matrix proteins. We also performed a large-scale transcriptomic analysis of WT SUM159 cells, identifying ~7700 transcripts (~3600 and 3800 increasing, ~4000 and 3900 decreasing in ONC201 and TR-57 treated cells, respectively). Less than 21% of these genes were affected by these compounds in ClpP null cells. Gene ontological analysis of these data demonstrated additional similarity of response to ONC201 and TR-57. Many of the same gene ontology processes and cellular components were identified, including a decrease in transcripts related to the mitochondrial inner membrane and matrix, the cell cycle, and the nucleus, as well as increases in other nuclear transcripts and transcripts related to metal-ion binding. Comparative analysis demonstrated a highly analogous response in all -omics datasets. Analysis of metabolites also revealed significant similarities between ONC201 and TR-57 with increases in α-ketoglutarate and 2-hydroxyglutaric acid and decreased levels of ureidosuccinic acid, L-ascorbic acid, L-serine, and cytidine observed following ClpP activation in TNBC cells. Further analysis identified multiple pathways that were specifically impacted by ClpP activation, including ATF4 activation, heme biosynthesis, and the citrulline/urea cycle. In summary the results of our studies demonstrate that ONC201 and TR-57 induce highly similar and broad effects against multiple mitochondrial processes required for cell proliferation. |
| Institute | University of North Carolina at Chapel Hill |
| Last Name | Graves |
| First Name | Lee |
| Address | 4111 Genetic Medicine Building, 120 Mason Farm Rd, Chapel Hill, NC 27514 |
| lmg@med.unc.edu | |
| Phone | (919) 966-0915 |
| Submit Date | 2022-12-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-12-18 |
| Release Version | 1 |
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Collection:
| Collection ID: | CO002490 |
| Collection Summary: | The human triple-negative breast cancer (TNBC) cell line SUM159 was cultured in Dulbecco’s modified Eagle’s medium: Nutrient Mixture F-12 (DMEM/F-12, Gibco, 11330-032) supplemented with 5% fetal bovine serum (VWR-Seradigm, 97068-085), 1% antibiotic/antimycotic (ThermoFisher Scientific, 15240062), 5 μg/mL insulin (Gibco, 12585014), and 1 μg/mL hydrocortisone. CRISPRi was used to generate CLPP-knockout SUM159 cells. WT MDA-MB-231 cells were cultured in RPMI 1640 media (Gibco, 11875-093) supplemented with 10% FBS and 1% antibiotic/antimycotic. Cells were incubated at 5% CO2 and 37°C and periodically tested for mycoplasma. |
| Sample Type: | Cultured cells |
