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

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	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
Email	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

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Project:

Project ID:	PR002652
Project DOI:	doi: 10.21228/M8VC26
Project Title:	Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma
Project 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:	Hills Road, CAMBRIDGE, England, CB2 0QQ, United Kingdom
Email:	cy295@cam.ac.uk
Phone:	+49 221 478- 84308

Subject:

Subject ID:	SU004359
Subject Type:	Mammal
Subject Species:	Homo Sapiens; Mus musculus
Taxonomy ID:	9606; 10090
Age Or Age Range:	humans 50-80, mice 8-13 weeks
Gender:	Male

Factors:

Subject type: Mammal; Subject species: Homo Sapiens; Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Factor	Sample source
SA484702	EMKC016 T2	in vivo	human ccRCC
SA484703	CY3_112	in vivo	human ccRCC
SA484704	CY3_111	in vivo	human ccRCC
SA484705	CY3_110	in vivo	human ccRCC
SA484706	EMKC016 T1	in vivo	human ccRCC
SA484707	CY3_56	in vivo	human ccRCC
SA484708	CY3_2	in vivo	human ccRCC
SA484709	CY3_32	in vivo	human ccRCC
SA484710	EMKC016 T3	in vivo	human ccRCC
SA484711	CY3_31	in vivo	human ccRCC
SA484712	CY3_3	in vivo	human ccRCC
SA484713	CY3_1	in vivo	human ccRCC
SA484714	EMKC016 K2	in vivo	human kidney
SA484715	EMKC016 K3	in vivo	human kidney
SA484716	CY3_5	in vivo	human kidney
SA484717	CY3_29	in vivo	human kidney
SA484718	CY3_27	in vivo	human kidney
SA484719	CY3_114	in vivo	human kidney
SA484720	CY3_51	in vivo	human kidney
SA484721	CY3_52	in vivo	human kidney
SA484722	EMKC016 K1	in vivo	human kidney
SA484723	CY3_115	in vivo	human kidney
SA484724	CY3_113	in vivo	human kidney
SA484725	CY6_26	in vivo	mouse ccRCC
SA484726	CY6_18	in vivo	mouse ccRCC
SA484727	CY6_34	in vivo	mouse ccRCC
SA484728	CY02_05	in vivo	mouse ccRCC
SA484729	CY6_10	in vivo	mouse ccRCC
SA484730	CY6_22	in vivo	mouse ccRCC
SA484731	CY6_5	in vivo	mouse ccRCC
SA484732	CY6_1	in vivo	mouse ccRCC
SA484733	CY1_01	in vivo	mouse ccRCC
SA484734	CY6_14	in vivo	mouse ccRCC
SA484735	CY6_42	in vivo	mouse ccRCC
SA484736	CY02_01	in vivo	mouse kidney
SA484737	CY6_9	in vivo	mouse kidney
SA484738	CY6_7	in vivo	mouse kidney
SA484739	CY6_3	in vivo	mouse kidney
SA484740	CY6_41	in vivo	mouse kidney
SA484741	CY6_21	in vivo	mouse kidney
SA484742	CY6_33	in vivo	mouse kidney
SA484743	CY1_05	in vivo	mouse kidney
SA484744	CY6_13	in vivo	mouse kidney
SA484745	CY6_25	in vivo	mouse kidney
SA484746	CY6_17	in vivo	mouse kidney
SA484747	CY02_09	in vivo	mouse kidney
SA484637	CY3_116	WIT 10mins	human ccRCC
SA484638	CY3_117	WIT 10mins	human ccRCC
SA484639	CY3_118	WIT 10mins	human kidney
SA484640	CY3_119	WIT 10mins	human kidney
SA484641	CY3_64	WIT 15mins	human ccRCC
SA484642	CY3_65	WIT 15mins	human ccRCC
SA484643	CY3_63	WIT 15mins	human kidney
SA484644	CY3_62	WIT 15mins	human kidney
SA484645	CY6_24	WIT 30mins	mouse ccRCC
SA484646	CY6_38	WIT 30mins	mouse ccRCC
SA484647	CY6_20	WIT 30mins	mouse ccRCC
SA484648	CY6_16	WIT 30mins	mouse ccRCC
SA484649	CY6_46	WIT 30mins	mouse ccRCC
SA484650	CY1_03	WIT 30mins	mouse ccRCC
SA484651	CY02_07	WIT 30mins	mouse ccRCC
SA484652	CY6_2	WIT 30mins	mouse ccRCC
SA484653	CY6_6	WIT 30mins	mouse ccRCC
SA484654	CY6_12	WIT 30mins	mouse ccRCC
SA484655	CY6_30	WIT 30mins	mouse ccRCC
SA484656	CY02_03	WIT 30mins	mouse kidney
SA484657	CY6_19	WIT 30mins	mouse kidney
SA484658	CY6_11	WIT 30mins	mouse kidney
SA484659	CY6_8	WIT 30mins	mouse kidney
SA484660	CY6_4	WIT 30mins	mouse kidney
SA484661	CY6_45	WIT 30mins	mouse kidney
SA484662	CY6_29	WIT 30mins	mouse kidney
SA484663	CY1_07	WIT 30mins	mouse kidney
SA484664	CY6_15	WIT 30mins	mouse kidney
SA484665	CY6_37	WIT 30mins	mouse kidney
SA484666	CY6_23	WIT 30mins	mouse kidney
SA484667	CY02_11	WIT 30mins	mouse kidney
SA484668	CY3_7	WIT 45mins	human ccRCC
SA484669	CY3_6	WIT 45mins	human ccRCC
SA484670	CY3_9	WIT 45mins	human kidney
SA484671	CY3_8	WIT 45mins	human kidney
SA484672	CY1_02	WIT 5mins	mouse ccRCC
SA484673	CY6_28	WIT 5mins	mouse ccRCC
SA484674	CY02_06	WIT 5mins	mouse ccRCC
SA484675	CY6_36	WIT 5mins	mouse ccRCC
SA484676	CY6_44	WIT 5mins	mouse ccRCC
SA484677	CY1_06	WIT 5mins	mouse kidney
SA484678	CY02_02	WIT 5mins	mouse kidney
SA484679	CY6_43	WIT 5mins	mouse kidney
SA484680	CY02_10	WIT 5mins	mouse kidney
SA484681	CY6_35	WIT 5mins	mouse kidney
SA484682	CY6_27	WIT 5mins	mouse kidney
SA484683	EMKC016 T5	WIT 60mins	human ccRCC
SA484684	CY3_37	WIT 60mins	human ccRCC
SA484685	EMKC016 T4	WIT 60mins	human ccRCC
SA484686	EMKC016 T6	WIT 60mins	human ccRCC
SA484687	EMKC016 K5	WIT 60mins	human kidney
SA484688	EMKC016 K6	WIT 60mins	human kidney
SA484689	CY3_38	WIT 60mins	human kidney
SA484690	EMKC016 K4	WIT 60mins	human kidney

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Collection:

Collection ID:	CO004352
Collection Summary:	Tissue samples were homogenized (6000 rpm, 2 x 30 secs, Precellys®24 tissue homogenizer, Bertin Instruments, France) in an extraction buffer (25 µL/mg tissue) containing 50% methanol, 30% acetonitrile, 20% ultrapure water, and 5µM valine-d8 (CK isotopes, UK) as an internal standard. Sample controls were the respective patient kidney tissues and there were 1-3 biological replicates. Samples were incubated on dry ice for 20 mins, mixed (Thermomixer, Eppendorf, Germany, 3000 rpm, 15 mins, 4°C) and then centrifuged (16,000 g, 20 mins, 4°C) with the supernatants stored at -80°C until analysis.
Sample Type:	tissues
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004368
Treatment Summary:	All patients had matched tissue samples acquired in two conditions: in vivo (intraoperatively with tissues perfused) and WIT (warm ischaemia time) conditions. WIT was measured by the time of ligation of renal blood vessels to the earliest opportunity for research tissue sampling after removal of the tumour-bearing kidney. Mice had tissue samples acquired from both tumour (786-0 ccRCC) and adjacent kidney at time 0 (in vivo), 5, 30, and 60 minutes of WIT.

Treatment ID:

TR004368

Treatment Summary:

All patients had matched tissue samples acquired in two conditions: in vivo (intraoperatively with tissues perfused) and WIT (warm ischaemia time) conditions. WIT was measured by the time of ligation of renal blood vessels to the earliest opportunity for research tissue sampling after removal of the tumour-bearing kidney. Mice had tissue samples acquired from both tumour (786-0 ccRCC) and adjacent kidney at time 0 (in vivo), 5, 30, and 60 minutes of WIT.

Sample Preparation:

Sampleprep ID:	SP004365
Sampleprep Summary:	Tissue samples were homogenized (6000 rpm, 2 x 30 secs, Precellys®24 tissue homogenizer, Bertin Instruments, France) in an extraction buffer (25 µl/mg tissue) containing 50% methanol, 30% acetonitrile, 20% ultrapure water, and 5µM valine-d8 (CK isotopes, UK) as an internal standard. Sample controls were the respective patient kidney tissues and there were 1-3 biological replicates. Samples were incubated on dry ice for 20 mins, mixed (Thermomixer, Eppendorf, Germany, 3000 rpm, 15 mins, 4°C) and then centrifuged (16,000 g, 20 mins, 4°C) with the supernatants stored at -80°C until analysis. Samples were analyzed on a Q Exactive Hybrid Quadrupole-Orbitrap Mass spectrometer (Thermo Scientific, USA) coupled to a Dionex Ultimate 3000 UHPLC (Dionex, USA). HILIC chromatographic separation of metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm, Merck, USA) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A contained 20 mM ammonium carbonate, 0.05% ammonium hydroxide; and Solvent B was acetonitrile. The column oven and autosampler tray were held at 40°C and 4°C, respectively. The chromatographic gradient flow rate was run at 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.

Sampleprep ID:

SP004365

Sampleprep Summary:

Tissue samples were homogenized (6000 rpm, 2 x 30 secs, Precellys®24 tissue homogenizer, Bertin Instruments, France) in an extraction buffer (25 µl/mg tissue) containing 50% methanol, 30% acetonitrile, 20% ultrapure water, and 5µM valine-d8 (CK isotopes, UK) as an internal standard. Sample controls were the respective patient kidney tissues and there were 1-3 biological replicates. Samples were incubated on dry ice for 20 mins, mixed (Thermomixer, Eppendorf, Germany, 3000 rpm, 15 mins, 4°C) and then centrifuged (16,000 g, 20 mins, 4°C) with the supernatants stored at -80°C until analysis. Samples were analyzed on a Q Exactive Hybrid Quadrupole-Orbitrap Mass spectrometer (Thermo Scientific, USA) coupled to a Dionex Ultimate 3000 UHPLC (Dionex, USA). HILIC chromatographic separation of metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm, Merck, USA) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A contained 20 mM ammonium carbonate, 0.05% ammonium hydroxide; and Solvent B was acetonitrile. The column oven and autosampler tray were held at 40°C and 4°C, respectively. The chromatographic gradient flow rate was run at 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.

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

Analysis:

Analysis ID:	AN006997
Analysis Type:	MS
Chromatography ID:	CH005313
Num Factors:	18
Num Metabolites:	406
Units:	normalized total ion count