PXD035261

PXD035261 is an original dataset announced via ProteomeXchange.

Title	Tumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer
Description	Tumor initiation and progression are critically dependent on interaction of cancer cells with their cellular and extracellular microenvironment. Alterations in the composition, integrity, and mechanical properties of the extracellular matrix (ECM) dictate tumor processes including proliferation, migration, and invasion. Also in primary liver cancers, consisting of hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), the dysregulation of the extracellular environment by liver fibrosis and tumor desmoplasia is pertinent. Yet, in-depth characterization of liver cancer ECM and underlying tumor-promoting mechanisms remain largely unknown. Herein, we used an integrative molecular and mechanical approach to extensively characterize the ECM of HCC and CCA tumors by utilizing decellularization techniques. We identified a myriad of ECM-related proteins in both tumor and adjacent liver tissue, highlighting the complexity of the primary liver cancer matrisome. The differences in ECM protein abundance result in divergent mechanical properties on a macro- and micro-scale that is tumor-type specific. Furthermore, we employed the decellularized tumor ECM to create a tumor-specific hydrogel that support patient-derived tumor organoids. This provides a new avenue for personalized medicine by combining patient-derived tumor ECM and cancer cells. Taken together, this study provides better understanding of alterations to key aspects of the ECM that occur during primary liver cancer development.
HostingRepository	PRIDE
AnnounceDate	2023-03-28
AnnouncementXML	Submission_2023-03-28_08:10:33.750.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	JeroenDemmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-11 13:56:06	ID requested
⏵ 1	2023-03-28 08:10:34	announced

van Tienderen GS, Conboy J, Muntz I, Willemse J, Tieleman J, Monfils K, Schurink IJ, Demmers JAA, Doukas M, Koenderink GH, van der Laan LJW, Verstegen MMA, Tumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer. Biomater Adv, 146():213289(2023) [pubmed]

submitter keyword: decellularization

extracellular matrix

primary liver cancer

hepatocellular carcinoma

cholangiocarcinoma

JeroenDemmers
contact affiliation	Erasmus MC
contact email	j.demmers@erasmusmc.nl
lab head
JeroenDemmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
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/2023/03/PXD035261

PRIDE project URI

• PRIDE
  1. PXD035261
     1. Label: PRIDE project
     2. Name: Tumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer