PXD003632

PXD003632 is an original dataset announced via ProteomeXchange.

Title	Proteomic characterization of microdissected epithelium, tumor cells, and stroma from breast tissues
Description	Tissue of the breast is heterogeneous, consisting of a variety of cell types and connective tissue. This heterogeneity is also present in breast tumors and will complicate proteomic analysis, as it is not always clear whether a signal originates from the stromal environment, from normal epithelial or tumor cells. Here we microdissected a variety of cell types and stroma from benign and malignant breast tissues. We compared proteomic differences between these tissues, both from cells of epithelial origin and the stromal environment. Differences in protein abundances corresponded with several hallmarks of cancer, including loss of cell adhesion, transformation to a migratory phenotype, and enhanced energy metabolism. Furthermore, despite enriching for (tumor) epithelial cells, many changes to the extracellular matrix were detected in microdissected cells of epithelial origin. The stromal compartment was heterogeneous and richer in the number of fibroblast and immune cells in malignant sections, compared to benign tissue sections. Although this heterogeneity complicated detection of differentially abundant proteins, several markers were exclusively detected in stroma. However, as heterogeneity in the stroma is more difficult to be reduced through microdissection, comparative analysis was most informative in microdissected cells of epithelial origin, and provided a relatively complete picture of malignant transformations.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:10:04.636.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rene Braakman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-15 01:21:28	ID requested
1	2017-01-11 02:59:19	announced
2	2017-10-24 04:43:30	announced	Updated project metadata.
⏵ 3	2024-10-22 04:10:08	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201600213;

Braakman RB, Stingl C, Tilanus-Linthorst MM, van Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation. Proteomics, 17(5):(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: proteomics, microdissection, mass spectrometry,breast cancer, tumor microenvironment

John W. M. Martens
contact affiliation	Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.martens@erasmusmc.nl
lab head
Rene Braakman
contact affiliation	Erasmus MC, Department of Medical Oncology, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
contact email	r.braakman@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/2017/01/PXD003632

PRIDE project URI

• PRIDE
  1. PXD003632
     1. Label: PRIDE project
     2. Name: Proteomic characterization of microdissected epithelium, tumor cells, and stroma from breast tissues