PXD003497-1

PXD003497 is an original dataset announced via ProteomeXchange.

Title	Quantification of Proteome heterogeneity in benign and malignant prostate tissues
Description	Intra-tumor heterogeneity (ITH) has been studied at the morphologic, genomic, and transcriptomic level, but not proteomic level. Recent advances in mass spectrometric (MS) proteome quantification techniques, exemplified by SWATH-MS, a massively parallel targeting method, now also support precise quantitative proteomic comparisons across multiple samples, thus identifying molecular and implied functional differences. Here we used SWATH-MS to analyze the proteome profiles of a set of fresh-frozen prostate tissue samples derived from radical prostatectomy specimens. A high confidence set of 1,906 proteins were consistently quantified across 60 biopsy-level tissue samples from three prostatectomy patients, each consisting of 1.0 mm punch biopsies from histologically malignant (acinar and ductal adenocarcinoma) and matching benign prostatic hyperplasia tissues. The quantitative protein profiles allowed independent quantification of the degree of intra-tumor heterogeneity for each protein in benign and malignant tissues. We found that while majority of the proteins showed comparably low intra-tumor variability, 122 proteins were highly variable in malignant and/or matching benign tissues. We observed that proteins that varied between patients or tissue types also tended to be highly variable within prostate tissues, suggesting that these variability patterns will be a critical selection criterion in future protein biomarker studies. The data also permitted investigation of the heterogeneity of multiple biochemical pathways. The high variability of several of the pathways, including Glypican-1 network, alpha-linolenic acid metabolism and celecoxib pathway, explained contradictory results regarding them in the literature. In conclusion, we demonstrated a methodology for investigating proteomic intra-tumor heterogeneity from biopsy-level tissue samples, and quantified the degree of intra-tumor heterogeneity of 1,906 proteins in prostate tumors. The method and data presented here have advanced our understanding of tumor biology and offered critical insights for future biomarker development.
HostingRepository	PRIDE
AnnounceDate	2018-08-13
AnnouncementXML	Submission_2018-08-13_12:22:05.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tiannan Guo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-01-21 01:45:58	ID requested
⏵ 1	2018-08-13 12:22:06	announced
2	2024-10-22 04:27:53	announced	2024-10-22: Updated project metadata.

Guo T, Li L, Zhong Q, Rupp NJ, Charmpi K, Wong CE, Wagner U, Rueschoff JH, Jochum W, Fankhauser CD, Saba K, Poyet C, Wild PJ, Aebersold R, Beyer A, Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers. Life Sci Alliance, 1(2):(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: intra-tumor heterogeneity

prostate cancer

PCT-SWATH

Ruedi Aebersold
contact affiliation	ETH Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Tiannan Guo
contact affiliation	ETH Zurich
contact email	tiannan.guo@gmail.com
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/2018/08/PXD003497

PRIDE project URI

• PRIDE
  1. PXD003497
     1. Label: PRIDE project
     2. Name: Quantification of Proteome heterogeneity in benign and malignant prostate tissues