Summary of Study ST002999
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 PR001869. The data can be accessed directly via it's Project DOI: 10.21228/M84F0M 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 | ST002999 |
| Study Title | Metabolomics and glucose and glutamine labeled isotope tracing analysis in murine lung adenocarcinoma cells in the context of normal or active NRF2 pathway as well as HDAC and glutaminase inhibitor treatment. |
| Study Summary | Interplay between metabolism and chromatin signaling are implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDAC). This association is observed across cultured cells, mouse models and patient-derived xenografts. Integrative epigenomic, transcriptomic and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors. In this metabolomics experiment we characterize the changes in metabolic pathway flux in KP LUAD cells in response to HDAC and glutaminase inhibition. This dataset includes metabolomics of U-C13 glucose tracing (1h and 24h) and U-C13 glutamine (8h) of mouse LUAD cell lines with Kras overexpression and p53 knock-out (KP), carrying empty vector (EV) or overexpression of NRF2dNeh2 (NRF2) and treated with DMSO, Romidepsin or CB-839. 3 technical replicates were done per condition in 2 separate experiments, 1: glucose tracing and 2: glutamine tracing. |
| Institute | Columbia University - Medical Center |
| Department | Genetics and Development |
| Laboratory | Chao Lu |
| Last Name | Dimitris |
| First Name | Karagiannis |
| Address | 622 W 168th St, New York, NY 10032 |
| karagiannis_dimitrios@yahoo.gr | |
| Phone | +30 6982804931 |
| Submit Date | 2023-12-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-12-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001869 |
| Project DOI: | doi: 10.21228/M84F0M |
| Project Title: | Metabolic Reprogramming by Histone Deacetylase Inhibition Preferentially Targets NRF2-activated tumors |
| Project Summary: | Interplay between metabolism and chromatin signaling are implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDAC). This association is observed across cultured cells, mouse models and patient-derived xenografts. Integrative epigenomic, transcriptomic and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors. |
| Institute: | Columbia University Medical Center |
| Department: | Genetics and Development |
| Laboratory: | Chao Lu |
| Last Name: | Karagiannis |
| First Name: | Dimitris |
| Address: | 630 West 168th Street, NEW YORK, NY, 10032, USA |
| Email: | karagiannis_dimitrios@yahoo.gr |
| Phone: | +30 6982804931 |
Subject:
| Subject ID: | SU003112 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment | Timepoint | Tracer |
|---|---|---|---|---|---|
| SA326444 | EV_CB839_Gln_2 | Empty vector | CB-839 | 8 hours | U-C13 Glutamine |
| SA326445 | EV_CB839_Gln_3 | Empty vector | CB-839 | 8 hours | U-C13 Glutamine |
| SA326446 | EV_CB839_Gln_1 | Empty vector | CB-839 | 8 hours | U-C13 Glutamine |
| SA326447 | EV_DMSO_1h_3 | Empty vector | DMSO | 1 hour | U-C13 Glucose |
| SA326448 | EV_DMSO_1h_1 | Empty vector | DMSO | 1 hour | U-C13 Glucose |
| SA326449 | EV_DMSO_1h_2 | Empty vector | DMSO | 1 hour | U-C13 Glucose |
| SA326450 | EV_DMSO_24h_2 | Empty vector | DMSO | 24 hours | U-C13 Glucose |
| SA326451 | EV_DMSO_24h_1 | Empty vector | DMSO | 24 hours | U-C13 Glucose |
| SA326452 | EV_DMSO_24h_3 | Empty vector | DMSO | 24 hours | U-C13 Glucose |
| SA326453 | EV_DMSO_Gln_3 | Empty vector | DMSO | 8 hours | U-C13 Glutamine |
| SA326454 | EV_DMSO_Gln_2 | Empty vector | DMSO | 8 hours | U-C13 Glutamine |
| SA326455 | EV_DMSO_Gln_1 | Empty vector | DMSO | 8 hours | U-C13 Glutamine |
| SA326456 | EV_Rom_1h_2 | Empty vector | Romidepsin | 1 hour | U-C13 Glucose |
| SA326457 | EV_Rom_1h_1 | Empty vector | Romidepsin | 1 hour | U-C13 Glucose |
| SA326458 | EV_Rom_1h_3 | Empty vector | Romidepsin | 1 hour | U-C13 Glucose |
| SA326459 | EV_Rom_24h_2 | Empty vector | Romidepsin | 24 hours | U-C13 Glucose |
| SA326460 | EV_Rom_24h_3 | Empty vector | Romidepsin | 24 hours | U-C13 Glucose |
| SA326461 | EV_Rom_24h_1 | Empty vector | Romidepsin | 24 hours | U-C13 Glucose |
| SA326462 | EV_ROM_Gln_2 | Empty vector | Romidepsin | 8 hours | U-C13 Glutamine |
| SA326463 | EV_ROM_Gln_1 | Empty vector | Romidepsin | 8 hours | U-C13 Glutamine |
| SA326464 | EV_ROM_Gln_3 | Empty vector | Romidepsin | 8 hours | U-C13 Glutamine |
| SA326465 | QC2 | NA | NA | NA | NA |
| SA326466 | QC3 | NA | NA | NA | NA |
| SA326467 | QC4 | NA | NA | NA | NA |
| SA326468 | QC1 | NA | NA | NA | NA |
| SA326469 | QC_4 | NA | NA | NA | NA |
| SA326470 | QC_2 | NA | NA | NA | NA |
| SA326471 | QC5 | NA | NA | NA | NA |
| SA326472 | QC_3 | NA | NA | NA | NA |
| SA326473 | blank1 | NA | NA | NA | NA |
| SA326474 | blank4 | NA | NA | NA | NA |
| SA326475 | Blank_1 | NA | NA | NA | NA |
| SA326476 | QC_1 | NA | NA | NA | NA |
| SA326477 | blank2 | NA | NA | NA | NA |
| SA326478 | blank3 | NA | NA | NA | NA |
| SA326479 | NRF2_CB839_Gln_3 | NRF2 overexpression | CB-839 | 8 hours | U-C13 Glutamine |
| SA326480 | NRF2_CB839_Gln_2 | NRF2 overexpression | CB-839 | 8 hours | U-C13 Glutamine |
| SA326481 | NRF2_CB839_Gln_1 | NRF2 overexpression | CB-839 | 8 hours | U-C13 Glutamine |
| SA326482 | NRF2_DMSO_1h_1 | NRF2 overexpression | DMSO | 1 hour | U-C13 Glucose |
| SA326483 | NRF2_DMSO_1h_3 | NRF2 overexpression | DMSO | 1 hour | U-C13 Glucose |
| SA326484 | NRF2_DMSO_1h_2 | NRF2 overexpression | DMSO | 1 hour | U-C13 Glucose |
| SA326485 | NRF2_DMSO_24h_3 | NRF2 overexpression | DMSO | 24 hours | U-C13 Glucose |
| SA326486 | NRF2_DMSO_24h_2 | NRF2 overexpression | DMSO | 24 hours | U-C13 Glucose |
| SA326487 | NRF2_DMSO_24h_1 | NRF2 overexpression | DMSO | 24 hours | U-C13 Glucose |
| SA326488 | NRF2_DMSO_Gln_2 | NRF2 overexpression | DMSO | 8 hours | U-C13 Glutamine |
| SA326489 | NRF2_DMSO_Gln_1 | NRF2 overexpression | DMSO | 8 hours | U-C13 Glutamine |
| SA326490 | NRF2_DMSO_Gln_3 | NRF2 overexpression | DMSO | 8 hours | U-C13 Glutamine |
| SA326491 | NRF2_Rom_1h_1 | NRF2 overexpression | Romidepsin | 1 hour | U-C13 Glucose |
| SA326492 | NRF2_Rom_1h_2 | NRF2 overexpression | Romidepsin | 1 hour | U-C13 Glucose |
| SA326493 | NRF2_Rom_1h_3 | NRF2 overexpression | Romidepsin | 1 hour | U-C13 Glucose |
| SA326494 | NRF2_Rom_24h_2 | NRF2 overexpression | Romidepsin | 24 hours | U-C13 Glucose |
| SA326495 | NRF2_Rom_24h_1 | NRF2 overexpression | Romidepsin | 24 hours | U-C13 Glucose |
| SA326496 | NRF2_Rom_24h_3 | NRF2 overexpression | Romidepsin | 24 hours | U-C13 Glucose |
| SA326497 | NRF2_ROM_Gln_3 | NRF2 overexpression | Romidepsin | 8 hours | U-C13 Glutamine |
| SA326498 | NRF2_ROM_Gln_2 | NRF2 overexpression | Romidepsin | 8 hours | U-C13 Glutamine |
| SA326499 | NRF2_ROM_Gln_1 | NRF2 overexpression | Romidepsin | 8 hours | U-C13 Glutamine |
| Showing results 1 to 56 of 56 |
Collection:
| Collection ID: | CO003105 |
| Collection Summary: | Mouse lung adenocarcinoma (LUAD) cell lines were established as in a previous study by the Papagiannakopoulos lab (Romero et al. Nature Medicine 2017). Briefly, KrasLSL-G12D/+; p53flox/flox genetically engineered mice were intratracheally infected with pSECC lentiviral vectors expressing sgRNAs against Keap1 or tdTomato as a control. The mice developed LUAD tumors and cell lines were derived from them. In this experiment we used a cell line derived from control tumors (KP: Kras-mutant, p53-null). In this cell line we overexpressed an active form of NRF2 (NRF2) or introduced the empty vector (EV). |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR003121 |
| Treatment Summary: | For glucose tracing analysis, 2x105 KP cells (n=3) were plated in 6-well plates overnight in RPMI medium (Sigma). After 24 hours, the media was replaced with fresh RPMI medium containing DMSO or Romidepsin. At 48 hours the media was replaced with fresh glucose-free RPMI medium (Sigma) containing 10% dialyzed fetal bovine serum (Gibco), 2.0 g/L 13C6-glucose (Sigma) and DMSO or 5nM Romidepsin. Cells were harvested at 49 and 72 hours and processed as described below. For glutamine tracing, 2x105 KP cells (n=3) were plated in 6-well plates overnight in RPMI medium (Sigma). After 24 hours, the media was replaced with fresh RPMI medium containing DMSO, 1nM Romidepsin or 150nM CB-839. At 48 hours the media was replaced with fresh glutamine-free RPMI medium (Sigma) containing 10% dialyzed fetal bovine serum (Gibco), 2.0 g/L 13C6-glutamine (Cambridge Isotope Laboratories) and DMSO, 1nM Romidepsin or 150nM CB-839 |
Sample Preparation:
| Sampleprep ID: | SP003118 |
| Sampleprep Summary: | Cells were washed with cold PBS, lysed in 80% Ultra LC-MS acetonitrile (Thermo Scientific) supplemented with 20 µM deuterated 2-hydroxyglutarate (D-2-hydroxyglutaric-2,3,3,4,4-d5 acid (d5-2HG), Cambridge Isotope Laboratories) as an internal standard on ice for 15 minutes, and centrifuged for 10 minutes at 20,000 x g at 4 °C. 200 µL of supernatants were subjected to mass spectrometry analysis. |
Combined analysis:
| Analysis ID | AN004926 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 1290 Infinity |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6545 QTOF |
| Ion Mode | NEGATIVE |
| Units | Abundance (Extracted ion chromatogram core area) |
Chromatography:
| Chromatography ID: | CH003718 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 35 |
| Flow Gradient: | 0-1.5 min, 80% B; 1.5-7 min, 80% B to 50% B, 7-8.5 min, 50% B; 8.5-8.7 min, 50% B to 80% B, 8.7-13 min, 80% B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 25 mM ammonium carbonate in water |
| Solvent B: | acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004669 |
| Analysis ID: | AN004926 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The overall runtime was 13 minutes, and the injection volume was 5 µL. The Agilent Q-TOF was operated in negative mode and the relevant parameters were as listed: ion spray voltage, 3500 V; nozzle voltage, 1000 V; fragmentor voltage, 125 V; drying gas flow, 11 L/min; capillary temperature, 325 °C; drying gas temperature, 350 °C; and nebulizer pressure, 40 psi. A full scan range was set at 50 to 1600 (m/z). The reference masses were 119.0363 and 980.0164. The acquisition rate was 2 spectra/s. Targeted analysis, isotopologues extraction (for the metabolic tracing study), and natural isotope abundance correction were performed by the Agilent Profinder B.10.00 Software (Agilent Technologies). |
| Ion Mode: | NEGATIVE |
