Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma

ABSTRACT: Human isotopic tracer studies are fast becoming the gold standard model to study cancer metabolism in vivo. Analysed tissues are typically retrieved after surgical resection, which exposes them to a variable extent 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 metabolic profile of tissues sampled intraoperatively, when blood supply is intact, versus post-surgical resection, which exposes the tissue to ischaemia. We show that ischaemia significantly affects the metabolic landscape of ccRCC, masking some critical features, such as suppressed gluconeogenesis. Furthermore, in orthotopic ccRCC-derived xenografts, we identified that prolonged exposure to ischaemia disrupts the tissue metabolome stability. Therefore, minimising tissue ischaemia is

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: Alex von Kriegsheim

LAB HEAD: Christian Frezza

PROVIDER: PXD054588 | Pride | 2025-08-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	10_16kidney-WIT-60-mins_2.raw	Raw
	11_16kidney-WIT-60-mins_3.raw	Raw
	12_17tumour-in-vivo_1.raw	Raw
	13_17tumour-in-vivo_2.raw	Raw
	14_17tumour-in-vivo_3.raw	Raw

Items per page:

1 - 5 of 52

Similar Datasets

Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma

Project description:Human isotopic tracer studies are fast becoming the gold standard model to study cancer metabolism in vivo. Analysed tissues are typically retrieved after surgical resection, which exposes them to a variable extent 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 metabolic profile of tissues sampled intraoperatively, when blood supply is intact, versus post-surgical resection, which exposes the tissue to ischaemia. We show that ischaemia significantly affects the metabolic landscape of ccRCC, masking some critical features, such as suppressed gluconeogenesis. Furthermore, in orthotopic ccRCC-derived xenografts, we identified that prolonged exposure to ischaemia disrupts the tissue metabolome stability. Therefore, minimising tissue ischaemia is pivotal in accurately profiling cancer metabolism in these important and resource-intense patient studies.

2025-08-31 | GSE274774 | GEO

microRNAseq of clear-cell renal cell carcinoma on surgical resection specimens of untreated primary tumors in humans

Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).

2020-07-22 | E-MTAB-9380 | biostudies-arrayexpress

RNA-seq of human hepatocellular carcinoma (HCC) patients

Project description:Tumor samples and matching healthy tissue from 23 human hepatocellular carcinoma (HCC) patients and one hepatocellular adenoma patient were collected after surgical resection. Total RNA was harvested and sequenced with a strand-specific single-end RNA-seq protocol.

2021-12-23 | E-MTAB-8915 | biostudies-arrayexpress

The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors

Project description:Uninvolved tissue taken at the time of primary surgical resection of an adenocarcinoma. Uninvolved status determined by surgical margin and gross appearance, not pathology

2014-05-22 | GSE48067 | GEO

PD-1 blockade mitigates surgery-induced immunosuppression and increases the efficacy of photodynamic therapy for malignant pleural mesothelioma

Project description:Surgical resection can influence tissue behavior and immune interactions, leading to an altered inflammatory state. Our clinical trial delivers intraoperative photodynamic therapy (PDT) to the thoracic cavity after macroscopic complete resection of malignant pleural mesothelioma (MPM) tumors. We have previously published evidence of systemic inflammation via increases in circulating levels of IL-6 after surgical resection. Thus, we expect surgery to alter local signal transduction in the resection field by the time that PDT is delivered. To detect these signaling changes, RNA sequencing analysis was performed on tumor tissue isolated at different time intervals during the surgery (and prior to PDT) from 33 MPM patients. We discovered several pathways associated with tumor behavior and immune function were activated over the course of surgery.

2025-04-29 | GSE272176 | GEO

Spatial multiomics for liver cancer

Project description:We selected 24 formalin-fixed paraffin-embedded tissue blocks from 6 patients with primary liver cancer (PLC) and who underwent surgical resection at Eastern Hepatobiliary Surgery Hospital (EHBH) for proteomics analysis,

2024-07-19 | PXD054095 |

Mitochondrial complex I promotes kidney cancer metastasis

Project description:Most kidney cancers display metabolic dysfunction but how this relates to cancer progression in humans is unknown. We infused 13C-labeled nutrients during surgical tumour resection in over 80 patients with kidney cancer. Labeling from [U-13C]glucose varies across subtypes, indicating that the kidney environment alone cannot account for all metabolic reprogramming in these tumours. Compared to the adjacent kidney, clear cell renal cell carcinomas (ccRCC) display suppressed labelling of tricarboxylic acid (TCA) cycle intermediates in vivo and in organotypic cultures ex vivo, indicating that suppressed labeling is tissue intrinsic. Infusions of [1,2-13C]acetate and [U-13C]glutamine in patients, coupled with measurements of respiration in mitochondria isolated from kidneys and tumours, reveal electron transport chain (ETC) defects in ccRCC. However, ccRCC metastases unexpectedly have enhanced TCA cycle labeling compared to primary ccRCCs, indicating a divergent metabolic program during metastasis in patients. In mice, stimulating respiration or NADH recycling in kidney cancer cells is sufficient to promote metastasis, while inhibiting ETC complex I decreases metastasis. These findings indicate that metabolic properties and liabilities evolve during kidney cancer progression in humans, and that mitochondrial function is limiting for metastasis but not for growth at the original site.

2024-06-17 | GSE251905 | GEO

The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors

Project description:Uninvolved tissue taken at the time of primary surgical resection of an adenocarcinoma. Uninvolved status determined by surgical margin and gross appearance, not pathology 35 biologically distinct samples, no replicates, no controls

2014-05-22 | E-GEOD-48067 | biostudies-arrayexpress

Single-cell ATAC-Seq of pediatric high-grade glioma

Project description:We performed scATAC-seq on glioblastoma tissue samples taken at time of initial surgical resection to map the global chromatin profiles of glioblastoma cells and associated non-neoplastic cells

2021-10-20 | GSE163655 | GEO

Expression data from total knee arthroplasty patients

Project description:Ischaemic preconditioning is a method of protecting tissue against ischaemia-reperfusion injury. It is an innate protective mechanism that increases a tissue's tolerance to prolonged ischaemia when it is first subjected to short burst of ischaemia and reperfusion. It is thought to provide this protection by increasing the tissue's tolerance to ischaemia, therby reducing oxidative stress, inflammation and apoptosis in the preconditioned tissue. We used microarrays to investigate the genomic response induced by ischaemic preconditioning in muscle biopsies taken from the operative leg of total knee arthroplasty patients in order to gain insight into the ischaemic preconditioning mechanism.

2010-04-02 | GSE21164 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data