Summary of Study ST001429
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 PR000981. The data can be accessed directly via it's Project DOI: 10.21228/M8WD7R 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 | ST001429 |
| Study Title | MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with Host Cell Factor-1 |
| Study Summary | MYC is an oncoprotein transcription factor that is overexpressed in the majority cancers. Although MYC itself is considered undruggable, it may be possible to inhibit MYC by targeting the co-factors it uses to drive oncogenic gene expression patterns. Here, we use loss- and gain- of function approaches to interrogate how one MYC co-factor—Host Cell Factor (HCF)-1—contributes to MYC activity in a Burkitt lymphoma setting. We identify high-confidence direct targets of the MYC–HCF-1 interaction that are regulated through a recruitment-independent mechanism, including genes that control mitochondrial function and rate-limiting steps for ribosome biogenesis and translation. We describe how these gene expression events impact cell growth and metabolism, and demonstrate that the MYC–HCF-1 interaction is essential for tumor maintenance in vivo. This work highlights the MYC–HCF-1 interaction as a focal point for development of novel anti-cancer therapies. |
| Institute | Vanderbilt University |
| Last Name | Codreanu |
| First Name | Simona |
| Address | 1234 Stevenson Center Lane |
| simona.codreanu@vanderbilt.edu | |
| Phone | 6158758422 |
| Submit Date | 2020-07-15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-01-19 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000981 |
| Project DOI: | doi: 10.21228/M8WD7R |
| Project Title: | MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with Host Cell Factor-1 |
| Project Summary: | MYC is an oncoprotein transcription factor that is overexpressed in the majority cancers. Although MYC itself is considered undruggable, it may be possible to inhibit MYC by targeting the co-factors it uses to drive oncogenic gene expression patterns. Here, we use loss- and gain- of function approaches to interrogate how one MYC co-factor—Host Cell Factor (HCF)-1—contributes to MYC activity in a Burkitt lymphoma setting. We identify high-confidence direct targets of the MYC–HCF-1 interaction that are regulated through a recruitment-independent mechanism, including genes that control mitochondrial function and rate-limiting steps for ribosome biogenesis and translation. We describe how these gene expression events impact cell growth and metabolism, and demonstrate that the MYC–HCF-1 interaction is essential for tumor maintenance in vivo. This work highlights the MYC–HCF-1 interaction as a focal point for development of novel anti-cancer therapies. |
| Institute: | Vanderbilt University |
| Last Name: | Codreanu |
| First Name: | Simona |
| Address: | 1234 Stevenson Center Lane |
| Email: | simona.codreanu@vanderbilt.edu |
| Phone: | 6158758422 |
Subject:
| Subject ID: | SU001503 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | Burkitt lymphoma cell line, wild type and two mutants, 4A and VP16 |
| Gender: | Not applicable |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | genotype |
|---|---|---|
| SA120690 | 4A-2 | 4A |
| SA120691 | 4A-4 | 4A |
| SA120692 | 4A-5 | 4A |
| SA120693 | 4A-1 | 4A |
| SA120694 | 4A-3 | 4A |
| SA120695 | VP-3 | VP |
| SA120696 | VP-4 | VP |
| SA120697 | VP-5 | VP |
| SA120698 | VP-2 | VP |
| SA120699 | VP-1 | VP |
| SA120700 | WT-2 | WT |
| SA120701 | WT-1 | WT |
| SA120702 | WT-4 | WT |
| SA120703 | WT-3 | WT |
| SA120704 | WT-5 | WT |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO001498 |
| Collection Summary: | To understand the cellular consequences of modulating the MYC–HCF-1 interaction, we engineered a system that allows us to express the 4A or VP16 HBM mutant MYC proteins as the sole form of MYC in a cell. We chose Ramos cells, a Burkitt lymphoma (BL)-derived line in which a t(8;14) translocation places one c-MYC allele under regulatory control of the immunoglobulin heavy chain enhancer. The untranslocated c-MYC allele is not expressed in these cells. Because sequences encoding the MYC HBM are contained within exon 3, we used CRISPR/Cas9-triggered homologous recombination of the translocated MYC allele to integrate an exon 3 switchable cassette for wild-type (WT) MYC, 4A, or VP16 HBM mutants, and confirmed appropriate integration by Southern blotting. Thus, we successfully generated a system for inducible, selective, and bidirectional modulation of the MYC−HCF-1 interaction in the context of an archetypal MYC-driven cancer cell line. |
| Sample Type: | Lymphoma cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001518 |
| Treatment Summary: | There is no treatment analyzed by MS in this project. |
Sample Preparation:
| Sampleprep ID: | SP001511 |
| Sampleprep Summary: | The global, untargeted metabolomics study was performed on switchable MYC allele Ramos cell lines treated with 20 nM 4-OHT. Individual cell pellet samples were lysed using 200 µl ice cold lysis buffer (1:1:2, Acetonitrile : Methanol : Ammonium Bicarbonate 0.1 M, pH 8.0, LC-MS grade) and sonicated using a probe tip sonicator, 10 pulses at 30% power, cooling down on ice between samples. A BCA was used to determine the protein concentration for individual samples, and adjusted to 200 µg total protein in 200 µl of lysis buffer. Isotopically labeled standard molecules, Phenylalanine-D8 and Biotin-D2, were added to each sample to assess sample preparation. Samples were subjected to protein precipitation by addition of 800 µL of ice cold methanol (4X by volume), and incubated at -80°C overnight. Samples were centrifuged at 10,000 rpm for 10 minutes to eliminate precipitated proteins and supernatant(s) were transferred to a clean Eppendorf tube and dried down in vacuo. Samples were stored at -80°C until further LC-MS analysis. |
| Sampleprep Protocol ID: | Global untargeted method_MYC_Project |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002389 | AN002390 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C18 (100 x 2.1mm,2.6um) | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | POSITIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH001756 |
| Chromatography Summary: | RPLC analysis metabolite extracts (10 μl injection volume) were separated on a Hypersil Gold, 1.9 μm, 2.1mm x 100 mm column (Thermo Fisher) held at 40°C. Liquid chromatography was performed at a 250 μl/min using solvent A (0.1% formic acid in H2O) and solvent B (0.1% formic acid in acetonitrile) with the following gradient: 5% B for 1 minute, 5-50% B over 9 minutes, 50-70% B over 5 minutes, 70-95% B over 5 minutes, 95% B held 2 minutes, and 95-5% B over 3 minutes, 5% B held 5 minutes (gradient length: 30 minutes). |
| Methods Filename: | Global untargeted method_MYC_Project |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C18 (100 x 2.1mm,2.6um) |
| Column Temperature: | 40 |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile, 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001757 |
| Chromatography Summary: | For HILIC analysis metabolite extracts (10 μl injection volume) were separated on a SeQuant ZIC-HILIC 3.5-μm, 2.1 mm × 100 mm column (Millipore Corporation, Darmstadt, Germany) held at 40°C. Liquid chromatography was performed at a 200 μl min−1 using solvent A (5 mM Ammonium formate in 90% H2O, 10% acetonitrile) and solvent B (5 mM Ammonium formate in 90% acetonitrile, 10% H2O) with the following gradient: 95% B for 2 min, 95-40% B over 16 min, 40% B held 2 min, and 40-95% B over 15 min, 95% B held 10 min (gradient length 45 min). |
| Methods Filename: | Global untargeted method_MYC_Project |
| Instrument Name: | Thermo Vanquish |
| Column Name: | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) |
| Column Temperature: | 40 |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 90% water/10% acetonitrile; 5 mM ammonium formate |
| Solvent B: | 90% acetonitrile/10% water; 5 mM ammonium formate |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002231 |
| Analysis ID: | AN002389 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FMS and DDA acquisition over a mass range of m/z 70-1050 data were imported, processed, normalized and reviewed using Progenesis QI |
| Ion Mode: | POSITIVE |
| MS ID: | MS002232 |
| Analysis ID: | AN002390 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | FMS and DDA acquisition over a mass range of m/z 70-1050 data were imported, processed, normalized and reviewed using Progenesis QI |
| Ion Mode: | POSITIVE |
