PXD011681

PXD011681 is an original dataset announced via ProteomeXchange.

Title	Cross-omics analysis of archival human renal cell carcinoma biopsies to identify emerging treatment avenues
Description	Renal cell cancer is among the most common forms of cancer in humans, with around 35,000 deaths attributed to kidney carcinoma in the European Union (EU) in 2012 alone. Clear cell renal cell carcinoma (ccRCC) represents the most common form of kidney cancer and the most lethal of all genitourinary cancers. Here we apply omics technologies to archival core biopsies to investigate the biology underlying ccRCC. Knowledge of these underlying processes should be useful for the discovery and/or confirmation of novel therapeutic approaches and ccRCC biomarker development. From partial or full nephrectomies of 11 patients, paired core biopsies of ccRCC affected tissue and adjacent non-tumorous tissue were both sampled and subjected to proteomics analyses. We combined proteomics results with our published mRNA-seq from the same patients and with published miRNA-seq data from an overlapping patient cohort from our institution. Statistical analysis and pathway analysis were performed with JMP Genomics (SAS) and Ingenuity Pathway Analysis (IPA, Qiagen), respectively. Proteomics analysis confirmed the involvement of metabolism and oxidative stress-related pathways in ccRCC, while the most affected pathways in the mRNA-seq data were related to the immune system. Unlike proteomics or mRNA-seq alone, a combinatorial cross-omics pathway analysis approach captured a broad spectrum of biological processes underlying ccRCC, such as mitochondrial damage, repression of apoptosis, and immune system pathways. Sirtuins, immunoproteasome genes and CD74 are proposed as potential targets for the treatment of ccRCC.
HostingRepository	PRIDE
AnnounceDate	2019-04-25
AnnouncementXML	Submission_2019-04-25_01:28:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kenneth Finne
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-13 05:38:36	ID requested
⏵ 1	2019-04-25 01:28:23	announced

Koch E, Finne K, Eikrem Ø, Landolt L, Beisland C, Leh S, Delaleu N, Granly M, Vikse BE, Osman T, Scherer A, Marti HP, Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enables identification of molecular mechanisms. Am J Physiol Renal Physiol, 316(5):F1053-F1067(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Proteomics, cross-omics, immunoproteasome, CD74, kidney cancer

Hans-Peter Marti
contact affiliation	Renal Research Group Department of Clinical Medicine University of Bergen, Norway
contact email	Hans-Peter.Marti@uib.no
lab head
Kenneth Finne
contact affiliation	University of Bergen
contact email	kenneth.finne@uib.no
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/04/PXD011681

PRIDE project URI

• PRIDE
  1. PXD011681
     1. Label: PRIDE project
     2. Name: Cross-omics analysis of archival human renal cell carcinoma biopsies to identify emerging treatment avenues