PXD028408

PXD028408 is an original dataset announced via ProteomeXchange.

Title	Patient-derived model combining organoids and matrix reveals cholangiocarcinoma promoting properties of the microenvironment
Description	Cholangiocarcinoma (CCA) is a rare but aggressive type of primary liver cancer, with an overall 5-year survival rate of <10%. The extracellular matrix (ECM) plays a particularly important role in CCA tumor biology, manifested in the desmoplastic tumor environment. This study aim is to design an in vitro CCA model combining patient-derived cells and patient-derived ECM mimicking the native microenvironment. decellularized Patient CCA tissue (CCA-matrix; CCA-M) and tumor-free liver tissue (TFL-M) was decellularized and repopulated with CCA organoids (CCAOs). Culture was performed with amino acids labeled with stable heavy isotopes to enable separation of pre-existing ECM from proteins produced by the cells in the mass spectrometry (MS) analysis. CCAOs on decellularized matrix form complex morphological structures, with environment-dependent proliferation and migration dynamics, driven by the occurrence of EMT. CCAOs in TFL-M or CCA-M can be used to study the initiation or progression of desmoplasia in CCA, respectively. Furthermore, in-depth transcriptomic and proteomic analysis reveals that CCA-M induces a transcriptome more resembling in vivo CCA tumor tissue, with an accompanying protective effect of the desmoplastic environment on tumor survival.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:27:36.222.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD028408
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Oskar Rosmark
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	4-hydroxy-L-proline; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 09:01:01	ID requested
1	2023-03-04 11:11:44	announced
⏵ 2	2023-11-14 08:27:36	announced	2023-11-14: Updated project metadata.

10.6019/PXD028408;

van Tienderen GS, Rosmark O, Lieshout R, Willemse J, de Weijer F, Elowsson Rendin L, Westergren-Thorsson G, Doukas M, Groot Koerkamp B, van Royen ME, van der Laan LJ, Verstegen MM, Extracellular matrix drives tumor organoids toward desmoplastic matrix deposition and mesenchymal transition. Acta Biomater, 158():115-131(2023) [pubmed]

submitter keyword: Human, organoids, tissue culture, liver, cholangiocarcionoma, extracellular matrix

Prof. Luc van der Laan
contact affiliation	Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
contact email	l.vanderlaan@erasmusmc.nl
lab head
Oskar Rosmark
contact affiliation	Lung Biology, Department Experimental Medical Science, Lund University, Lund, Sweden.
contact email	oskar.rosmark@med.lu.se
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/PXD028408

PRIDE project URI

• PRIDE
  1. PXD028408
     1. Label: PRIDE project
     2. Name: Patient-derived model combining organoids and matrix reveals cholangiocarcinoma promoting properties of the microenvironment