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PXD003497-1

PXD003497 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantification of Proteome heterogeneity in benign and malignant prostate tissues
DescriptionIntra-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.
HostingRepositoryPRIDE
AnnounceDate2018-08-13
AnnouncementXMLSubmission_2018-08-13_12:22:05.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTiannan Guo
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-01-21 01:45:58ID requested
12018-08-13 12:22:06announced
22024-10-22 04:27:53announced2024-10-22: Updated project metadata.
Publication List
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]
Keyword List
curator keyword: Biomedical
submitter keyword: intra-tumor heterogeneity
prostate cancer
PCT-SWATH
Contact List
Ruedi Aebersold
contact affiliationETH Zurich, Switzerland
contact emailaebersold@imsb.biol.ethz.ch
lab head
Tiannan Guo
contact affiliationETH Zurich
contact emailtiannan.guo@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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