Summary of Study ST004120
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 PR002590. The data can be accessed directly via it's Project DOI: 10.21228/M8VN87 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 | ST004120 |
| Study Title | Assessing the dependence of murine WT and Crebbp-/- tumour B cells on glucose to fuel Oxidative Phosphorylation. |
| Study Summary | The objective of this experiment was to compare the oxidation of glucose by murine WT and Crebbp-/- tumour B cells by examining the relative incorporation of glucose into TCA cycle-derived intermediates in these cells. To perform this experiment we cultured CD19+ splenocytes isolated from WT and Crebbp-/- tumour mice for 4 hours in Seahorse RPMI with U13C-labelled glucose stable isotope tracer. Data were generated from 5 independent cultures. |
| Institute | Cambridge Stem Cell Institute |
| Last Name | Horton |
| First Name | Sarah |
| Address | Puddicombe Way, Cambridge, Cambridgeshire, CB2 0AW, United Kingdom |
| sjh244@cam.ac.uk | |
| Phone | +44 1223 763368. |
| Submit Date | 2025-07-31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002590 |
| Project DOI: | doi: 10.21228/M8VN87 |
| Project Title: | CREBBP-loss confers metabolic and epigenetic vulnerabilities upon lymphoma cells. |
| Project Summary: | Inactivating-mutations of CREBBP are common in diffuse large B-cell lymphoma (DLBCL). We previously demonstrated that Crebbp-/- mice develop mature B-cell malignancies preceded by a pre-malignant phase. Using single-cell RNA-seq of WT and Crebbp-/- B-cells from distinct stages of disease evolution, we discovered expansion of aberrant germinal center B-cells during disease progression. Both Crebbp-/- murine and human CRISPR-engineered isogenic CREBBP-null cells displayed reduced expression of BCR-signaling genes and increased OXPHOS transcriptional programs, a finding recapitulated in DLBCL patients with low CREBBP expression. Mechanistically, BCR-signaling decreased upon CREBBP loss, alleviating p65-mediated repression of the transcriptional coactivator PGC1β, resulting in enhanced OXPHOS transcriptional programs. This metabolic vulnerability could be targeted therapeutically. Furthermore, CREBBP-loss also conferred an epigenetic vulnerability by altering the landscape of acetylated transcription factors, including BET proteins, at super-enhancers. Combined inhibition of complex I and BET proteins exploited the metabolic and epigenetic vulnerabilities of Crebbp-/- tumors, extending lymphoma survival in vivo. |
| Institute: | Cambridge Stem Cell Institute |
| Department: | Haematology |
| Laboratory: | Huntly / Frezza |
| Last Name: | Horton |
| First Name: | Sarah |
| Address: | Puddicombe Way, Cambridge, Cambridgeshire, CB2 0AW, United Kingdom |
| Email: | sjh244@cam.ac.uk |
| Phone: | +44 1223 763368 |
Subject:
| Subject ID: | SU004269 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Sample source |
|---|---|---|---|
| SA476350 | SH_248 | Crebbp-/- Tumour | Spleen cells |
| SA476351 | SH_247 | Crebbp-/- Tumour | Spleen cells |
| SA476352 | SH_249 | Crebbp-/- Tumour | Spleen cells |
| SA476353 | SH_250 | Crebbp-/- Tumour | Spleen cells |
| SA476354 | SH_251 | Crebbp-/- Tumour | Spleen cells |
| SA476349 | - | - | - |
| SA476355 | SH_237 | WT | Spleen cells |
| SA476356 | SH_238 | WT | Spleen cells |
| SA476357 | SH_239 | WT | Spleen cells |
| SA476358 | SH_240 | WT | Spleen cells |
| SA476359 | SH_241 | WT | Spleen cells |
| Showing results 1 to 11 of 11 |
Collection:
| Collection ID: | CO004262 |
| Collection Summary: | 1x106 CD19+ splenocytes were plated in 24-well plates in Seahorse RPMI media with U13C-labelled glucose stable isotope tracer (5 replicates for each condition). Before extraction, cells were counted using a separate counting plate. After that, cells were washed at room temperature with PBS twice and then kept on ice prior to adding the metabolite extraction solution. |
| Collection Protocol Filename: | Sample_and_treatment_preparation.pdf |
| Sample Type: | Splenocytes |
Treatment:
| Treatment ID: | TR004278 |
| Treatment Summary: | CD19+ splenocytes were cultured for 4 hours in Seahorse RPMI media supplemented with 10% dialyzed FCS, 2mM glutamine with 1:1000 CD40Ab at a concentration of 1 x 106/mL. For the glucose tracing experiments 50 μM unlabeled palmitate and 11.1 mM D-Glucose tracer were added. |
Sample Preparation:
| Sampleprep ID: | SP004275 |
| Sampleprep Summary: | After the PBS washes, 100 μL metabolite extraction solution (50% methanol, 30% acetonitrile, 20% ultrapure water, 5 μM final concentration valine-d8) was added to each sample. The samples were vortexed for 20 seconds and incubated for 5 minutes in a dry ice / methanol bath and stored at -80°C overnight. The next day the samples were incubated at 4°C with shaking for 15 minutes and then centrifuged for 20 minutes at maximum speed at 4°C. The top 80% of supernatant was then transferred to individual autosampler vials and stored at -80°C prior to analysis. |
Chromatography:
| Chromatography ID: | CH005188 |
| Chromatography Summary: | Chromatographic separation of polar metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A was 20 mM ammonium carbonate, 0.05% ammonium hydroxide; Solvent B was acetonitrile. The column oven and autosampler tray were held at 40 °C and 4°C, respectively. The chromatographic gradient was run at a flow rate of 0.200 mL/min as follows: 0–2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-22.5 min: hold at 80% B. Samples were randomized and analyzed with LC–MS in a blinded manner with an injection volume was 5 µL. Pooled samples were generated from an equal mixture of all individual samples and analyzed interspersed at regular intervals within sample sequence as a quality control. |
| Methods Filename: | Chromatography_and_MS.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1 mm, 5 µm) |
| Column Temperature: | 40°C |
| Flow Gradient: | 0-2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B. |
| Flow Rate: | 0.200 mL/min |
| Solvent A: | 100% Water; 20 mM ammonium carbonate; 0.05% ammonium hydroxide |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006832 |
| Analysis Type: | MS |
| Chromatography ID: | CH005188 |
| Num Factors: | 3 |
| Num Metabolites: | 274 |
| Units: | peak area |
