Summary of Study ST002173
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 PR001382. The data can be accessed directly via it's Project DOI: 10.21228/M8312X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002173 |
| Study Title | Unveiling the mechanism of action of nature-inspired anti-cancer compounds using a multi-Omics approach |
| Study Summary | Novel anti-cancer compounds SIMR-3058 and SIMR-3066 were tested against MCF-7. The 2020 global cancer registry has ranked breast cancer (BCa) as the most commonly diagnosed type of cancer and the most common cause of cancer-related deaths, especially in women worldwide. Increased resistance and significant side effects continue to limit the efficacy of anti-BCa drugs, hence the need to identify new drug targets and to develop novel compounds to overcome these limitations. Nature-inspired anti-cancer compounds are becoming increasingly popular since they often provide a relatively safe and effective alternative. In this study, we employed multi-omics techniques to gain insights into the novel and potentially relevant mechanism of action of two recently identified nature- inspired anti-cancer compounds (SIMR 3066 and SIMR 3058). Discovery proteomics analysis combined with LC-MS/MS-based untargeted metabolomics analysis was performed on compound-treated vs. DMSO-treated control MCF-7 cells. Downstream protein functional analysis showed that most of the responsive proteins were functionally associated with antigen processing and neutrophil degranulation, RNA catabolism and protein folding as well as cytoplasmic vesicle lumen and mitochondrial matrix formation. Consistent with the proteomics findings, metabolomic pathway analysis suggested that SIMR compounds could alter metabolic pathways such as glycolysis, the Krebs cycle and oxidative phosphorylation. Furthermore, metabolomics-based enriched-for-action pathway analysis showed that the of two SIMR compounds associate with mercaptopurine and thioguanine and azathiprine. Lastly, joint proteomics and metabolomics analysis revealed that treatment of BCa with SIMR3066 disrupts several signaling pathways including such p53-mediated apoptosis and the circadian entertainment pathway. Overall, the multi-omics we used in this study seems potent at probing the mechanism of action of novel anti-cancer agents. |
| Institute | University of Sharjah |
| Department | Sharjah Institute for Medical Research |
| Laboratory | Biomarker Discovery Group |
| Last Name | Giddey |
| First Name | Alexander |
| Address | Sharjah |
| agiddey@sharjah.ac.ae | |
| Phone | +971 6 5057417 |
| Submit Date | 2022-04-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-05-01 |
| Release Version | 1 |
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Project:
| Project ID: | PR001382 |
| Project DOI: | doi: 10.21228/M8312X |
| Project Title: | Unveiling the mechanism of action of nature-inspired anti-cancer compounds using a multi-Omics approach |
| Project Type: | LC-MS/MS |
| Project Summary: | The 2020 global cancer registry has ranked breast cancer (BCa) as the most commonly diagnosed type of cancer and the most common cause of cancer-related deaths, especially in women worldwide. Increased resistance and significant side effects continue to limit the efficacy of anti-BCa drugs, hence the need to identify new drug targets and to develop novel compounds to overcome these limitations. Nature-inspired anti-cancer compounds are becoming increasingly popular since they often provide a relatively safe and effective alternative. In this study, we employed multi-omics techniques to gain insights into the novel and potentially relevant mechanism of action of two recently identified nature- inspired anti-cancer compounds (SIMR 3066 and SIMR 3058). Discovery proteomics analysis combined with LC-MS/MS-based untargeted metabolomics analysis was performed on compound-treated vs. DMSO-treated control MCF-7 cells. Downstream protein functional analysis showed that most of the responsive proteins were functionally associated with antigen processing and neutrophil degranulation, RNA catabolism and protein folding as well as cytoplasmic vesicle lumen and mitochondrial matrix formation. Consistent with the proteomics findings, metabolomic pathway analysis suggested that SIMR compounds could alter metabolic pathways such as glycolysis, the Krebs cycle and oxidative phosphorylation. Furthermore, metabolomics-based enriched-for-action pathway analysis showed that the of two SIMR compounds associate with mercaptopurine and thioguanine and azathiprine. Lastly, joint proteomics and metabolomics analysis revealed that treatment of BCa with SIMR3066 disrupts several signaling pathways including such p53-mediated apoptosis and the circadian entertainment pathway. Overall, the multi-omics we used in this study seems potent at probing the mechanism of action of novel anti-cancer agents. |
| Institute: | University of Sharjah |
| Department: | Sharjah Institute for Medical Research |
| Laboratory: | Biomarker Discovery Group |
| Last Name: | Giddey |
| First Name: | Alexander |
| Address: | Sharjah |
| Email: | agiddey@sharjah.ac.ae |
| Phone: | +971 6 5057417 |
Subject:
| Subject ID: | SU002259 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Strain Details: | MCF-7 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA208924 | 3058(4)-02_15_1_755 | 3058 |
| SA208925 | 3058(2)-02_13_1_751 | 3058 |
| SA208926 | 3058(5)-02_16_1_757 | 3058 |
| SA208927 | 3058(4)-01_15_1_754 | 3058 |
| SA208928 | 3058(3)-02_14_1_753 | 3058 |
| SA208929 | 3058(1)-02_12_1_749 | 3058 |
| SA208930 | 3058(2)-01_13_1_750 | 3058 |
| SA208931 | 3058(1)-01_12_1_748 | 3058 |
| SA208932 | 3058(3)-01_14_1_752 | 3058 |
| SA208933 | 3058(5)-01_16_1_756 | 3058 |
| SA208934 | 3066(2)-01_8_1_740 | 3066 |
| SA208935 | 3066(1)-01_7_1_738 | 3066 |
| SA208936 | 3066(3)-02_9_1_743 | 3066 |
| SA208937 | 3066(3)-01_9_1_742 | 3066 |
| SA208938 | 3066(2)-02_8_1_741 | 3066 |
| SA208939 | 3066(4)-01_10_1_744 | 3066 |
| SA208940 | 3066(4)-02_10_1_745 | 3066 |
| SA208941 | 3066(5)-02_11_1_747 | 3066 |
| SA208942 | 3066(5)-01_11_1_746 | 3066 |
| SA208943 | 3066(1)-02_7_1_739 | 3066 |
| SA208944 | CR4-02_5_1_735 | Control |
| SA208945 | CR2-01_3_1_730 | Control |
| SA208946 | CR1-02_2_1_729 | Control |
| SA208947 | CR1-01_2_1_728 | Control |
| SA208948 | CR2-02_3_1_731 | Control |
| SA208949 | CR3-01_4_1_732 | Control |
| SA208950 | CR5-01_6_1_736 | Control |
| SA208951 | CR4-01_5_1_734 | Control |
| SA208952 | CR3-02_4_1_733 | Control |
| SA208953 | CR5-02_6_1_737 | Control |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO002252 |
| Collection Summary: | Around 2x106 MCF-7 cells were plated per flask and then separately treated with SIMR3058 or SIMR3066 compounds for 12 hrs to perform proteomic analysis; the uniform number of cells per flask for each sample was to avoid the effect of variable cell number on the outcome of the specific experiment. A volume of 1 mL of the extraction solvent (methanol + 0.1% formic acid) was added to the cells, which quenched cellular metabolic activity. The cells were vortexed for 2 min to ensure the quantitative extraction of metabolites and stored in ice for 1 hr. After this, the insoluble cell matrices were subjected to intermittent ultrasonication using the COPLEY sonicator (QSONICA SONICATOR, USA) under 30% amplifier and for 30 seconds with an ice bath employed throughout the process. Following that, cells debris were centrifuged (15000 rpm, 10 min, -4 °C), and the supernatants were collected and processed for proteomics and metabolomics analysis. |
| Sample Type: | Breast cancer cells |
Treatment:
| Treatment ID: | TR002271 |
| Treatment Summary: | Around 2x106 MCF-7 cells were plated per flask and then separately treated with SIMR3058 or SIMR3066 compounds for 12 hrs to perform proteomic analysis; the uniform number of cells per flask for each sample was to avoid the effect of variable cell number on the outcome of the specific experiment. A volume of 1 mL of the extraction solvent (methanol + 0.1% formic acid) was added to the cells, which quenched cellular metabolic activity. The cells were vortexed for 2 min to ensure the quantitative extraction of metabolites and stored in ice for 1 hr. After this, the insoluble cell matrices were subjected to intermittent ultrasonication using the COPLEY sonicator (QSONICA SONICATOR, USA) under 30% amplifier and for 30 seconds with an ice bath employed throughout the process. Following that, cells debris were centrifuged (15000 rpm, 10 min, -4 °C), and the supernatants were collected and processed for proteomics and metabolomics analysis. |
Sample Preparation:
| Sampleprep ID: | SP002265 |
| Sampleprep Summary: | Around 2x106 MCF-7 cells were plated per flask and then separately treated with SIMR3058 or SIMR3066 compounds for 12 hrs to perform proteomic analysis; the uniform number of cells per flask for each sample was to avoid the effect of variable cell number on the outcome of the specific experiment. A volume of 1 mL of the extraction solvent (methanol + 0.1% formic acid) was added to the cells, which quenched cellular metabolic activity. The cells were vortexed for 2 min to ensure the quantitative extraction of metabolites and stored in ice for 1 hr. After this, the insoluble cell matrices were subjected to intermittent ultrasonication using the COPLEY sonicator (QSONICA SONICATOR, USA) under 30% amplifier and for 30 seconds with an ice bath employed throughout the process. Following that, cells debris were centrifuged (15000 rpm, 10 min, -4 °C), and the supernatants were collected and processed for proteomics and metabolomics analysis. |
Combined analysis:
| Analysis ID | AN003561 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Bruker Elute |
| Column | Hamilton Intensity Solo 2 C18 |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker timsTOF |
| Ion Mode | POSITIVE |
| Units | AU |
Chromatography:
| Chromatography ID: | CH002632 |
| Chromatography Summary: | Samples were chromatographically separated using a Hamilton® Intensity Solo 2 C18 column (100 mm x 2.1 mm x 1.8 µm) and eluted using 0.1% formic acid in water (A) and 0.1% formic acid in ACN (B) using the following gradient: at a flow rate of 0.250 ml/min 1% B from 0-2 min, then gradient elution to 99% B from 2-17 min, held at 99% B from 17-20 min, then re-equilibrated to 1% B from 20-30 min using a flow rate of 0.350 ml/min. The autosampler temperature was set at 8℃ and the column oven temperature at 35℃. |
| Instrument Name: | Bruker Elute |
| Column Name: | Hamilton Intensity Solo 2 C18 |
| Column Temperature: | 35 |
| Flow Gradient: | 1%B to 99%B in 15 min |
| Flow Rate: | 250 uL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003318 |
| Analysis ID: | AN003561 |
| Instrument Name: | Bruker timsTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Auto MS/MS mode with 0.5 second cycle time. The ESI source with dry nitrogen gas was 10 L/min, and the drying temperature was equal to 220℃ with nebulizer gas pressure set to 2.2 bar. The capillary voltage of the ESI was 4500 V and the Plate Offset 500 V. MS acquisition scan was set from 20-1300 m/z and the collision energy to 7 eV. |
| Ion Mode: | POSITIVE |
