Summary of Study ST004207
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 PR002652. The data can be accessed directly via it's Project DOI: 10.21228/M8VC26 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004207 |
| Study Title | Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma |
| Study Summary | Study conditions Human studies: Five patients with clear cell renal cell carcinoma undergoing a radical nephrectomy were infused with 13C6 glucose from time of anaesthetic induction to sampling of tissues at time point 1 (95-145 minutes). At time point 1, tissue samples (between 1-3 samples) were taken from each patient's tumour and adjacent healthy kidney. After the kidney was surgically removed (detached from blood supply), repeat tissue samples (between 1-3 samples) were taken from each patient's tumour and adjacent healthy kidney. Mouse studies: All experiments were conducted in strict accordance with the UK Animals (Scientific Procedures) Act 1986 by personnel with the appropriate personal licence. Eleven healthy male NSG mice (Charles River Laboratories, UK) were orthotopically xenografted with 786-O human ccRCC cells at between 8-13 weeks of age. All mice were housed in specific-pathogen-free animal facilities with ad libitum access to food and water. Mice were infused with 13C6 glucose for 60 minutes. Mice were euthanised at the end of the infusion and tissues immediately harvested. Tissue samples (both kidney and 786-O tumour) were divided into 4 equal pieces, one piece was immediately flash frozen in liquid nitrogen and the other pieces left at room temperature in a petri dish for 5, 30, or 60 mins prior to freezing. Study summary: Human isotopic tracer studies are becoming the gold standard for studying cancer metabolism in vivo. Analysed tissues are typically retrieved after surgical resection exposing them to variable amounts of warm ischaemia. Although standardised protocols are emerging, the effects of sampling conditions on the tissue metabolome remain understudied. Here, we perform a 13C-glucose study coupled with metabolomic, transcriptomic, and proteomic profiling in patients with clear cell renal cell carcinoma (ccRCC) to assess the impact of ischaemia on tissues sampled intraoperatively (blood supply intact) and post-surgical resection (tissues exposed to ischaemia). Although several metabolic features were preserved, we demonstrate that ischaemia significantly impacted other metabolic phenotypes of ccRCC, masking key features such as suppressed gluconeogenesis. Notably, kidneys were more metabolically susceptible to ischaemia than these VHL-mutant ccRCC tumours. Despite the overall stability of the proteome and transcription, we also identified subtle degrees of ischaemia-induced perturbations. Using orthotopic ccRCC-derived xenografts, we evidenced that prolonged exposure to ischaemia disrupted the tissue metabolome stability. Overall, minimising tissue ischaemia is pivotal in accurately profiling cancer metabolism in these important and resource-intense patient studies. |
| Institute | University of Cambridge |
| Last Name | Yong |
| First Name | Cissy |
| Address | Cambridge University Hospitals, Hills Road, CB2 0QQ |
| cy295@cam.ac.uk | |
| Phone | +49 221 478- 84308 |
| Submit Date | 2025-09-17 |
| Num Groups | 1 |
| Total Subjects | 5 |
| Num Males | 5 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN006997 |
|---|---|
| Chromatography ID | CH005313 |
| MS ID | MS006694 |
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Q Exactive Hydrid Quadrupole-Orbitrap Mass spectrometer (Thermo Scientific, USA) coupled to a Dionex Ultimate 3000 UHPLC |
| Column | Millipore Sequant ZIC-pHILIC analytical column (150 x 2.1 mm, 5 µm) |
| MS Type | Other |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | normalized total ion count |
Chromatography:
| Chromatography ID: | CH005313 |
| Instrument Name: | Q Exactive Hydrid Quadrupole-Orbitrap Mass spectrometer (Thermo Scientific, USA) coupled to a Dionex Ultimate 3000 UHPLC |
| Column Name: | Millipore Sequant ZIC-pHILIC analytical column (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; 17.1-22.5 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 |
