PXD007052 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma |
Description | The inter-patient variability of tumor proteomes has been investigated on a large scale but many tumors display also intra-tumoral heterogeneity (ITH) regarding morphological and genetic features. To what extent the local proteome of tumors intrinsically differs remains largely unknown. Here, we used hepatocellular carcinoma (HCC) as a model system, to quantify both inter- and intra-tumor heterogeneity across human patient specimens with spatial resolution. We first defined proteomic features that robustly distinguish neoplastic from the directly adjacent non-neoplastic tissue by integrating proteomic data from human patient samples and genetically defined mouse models with available gene expression data. We then demonstrated the existence of intra-tumoral variations in protein abundance that re-occur across different patient samples, and affect clinically relevant proteins, even in the absence of obvious morphological differences or genetic alterations. Our work demonstrates the suitability and the benefits of using mass spectrometry based proteomics to analyze diagnostic tumor specimens with spatial resolution |
HostingRepository | PRIDE |
AnnounceDate | 2018-01-24 |
AnnouncementXML | Submission_2018-01-25_01:29:43.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Katarzyna Buczak |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos; Q Exactive HF; LTQ Orbitrap Velos; Orbitrap Fusion |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-07-14 06:40:36 | ID requested | |
⏵ 1 | 2018-01-25 01:29:44 | announced | |
2 | 2018-01-30 06:30:28 | announced | Updated publication reference for PubMed record(s): 29363612. |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Biomedical |
submitter keyword: Hepatocellular carcinoma, liver, intra-tumoral heterogeneity |
Contact List
Martin Beck |
contact affiliation | European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany |
contact email | martin.beck@embl.de |
lab head | |
Katarzyna Buczak |
contact affiliation | European Molecular Biology Laboratory |
contact email | buczak@embl.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD007052
- Label: PRIDE project
- Name: Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma