PXD007052

PXD007052 is an original dataset announced via ProteomeXchange.

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_2018-01-30_06:30:27.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

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.

Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M, Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC). Mol Cell Proteomics, 17(4):810-825(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Hepatocellular carcinoma, liver, intra-tumoral heterogeneity

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

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/2018/01/PXD007052

PRIDE project URI

• PRIDE
  1. PXD007052
     1. Label: PRIDE project
     2. Name: Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma