Project PXD010467

PRIDE Assigned Tags:
Biomedical Dataset
Dataset Belongs to:
Cancer (B/D-HPP)



Integrative analysis of mesenchymal stromal cell conversion by breast cancer secretomes in blank slate 3D microenvironments


The ability of primary tumour cells to invade and metastasise is responsible for over 90% of cancer patient deaths. During tumour growth and progression, cancer cells secrete factors that recruit and reprogram otherwise healthy cells to facilitate the formation of a favourable tumour microenvironment. Here, we have investigated how breast cancer cells convert normal mesenchymal stromal cells (MSCs) into tumour-associated MSCs (TA-MSCs) using unbiased global approaches. We compared the secretomes produced by non-invasive MCF-7 cells with invasive MDA-MB-231 cells, and identified extracellular matrix and exosome components associated with invasion. We then treated MSCs cultured in fully-defined, synthetic 3D hydrogels with invasive/non-invasive cancer secretomes and analysed their responses by kinase activity profiling and RNA sequencing, which led us to identify an invasion-associated signature of MSC conversion. Finally, we investigated whether there is an organ-specific metastasis-associated reprogramming of MSCs, and found that breast cancer cells from different metastatic sites have different secretome profiles that induce reprogramming of MSCs. These data describe at a systems-level how breast cancer cells with different invasion and metastatic abilities secrete molecules that activate MSCs and convert them into TA-MSCs.

Sample Processing Protocol

10kDa MW cutoff filtration of conditioned media. Buffer exchange into 6M GdCl, 10mM TCEP, 40mM CAA, 50mM HEPES pH8.5. Two step digest with lysC and Trypsin, subsequent StageTip C18 purification

Data Processing Protocol

Raw files were analyzed using MaxQuant version and standard settings. Briefly, label-free quantitation (LFQ) was enabled with a requirement of 2 unique peptides per protein, and iBAQ quantitation was also enabled during the search. Variable modifications were set as Oxidation (M) and Acetyl (protein N-term). Fixed modifications were set as Carbamidomethyl (C), false discovery rate was set to 1% and “match between runs” was enabled, with a 2 minute alignment window.


Erwin Schoof, Technical University of Denmark
Janine Erler, Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), DK-2200 Copenhagen, Denmark ( lab head )

Submission Date


Publication Date



Not available


Q Exactive


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Experiment Type

Shotgun proteomics


    Blache U, Horton ER, Xia T, Schoof EM, Blicher LH, Schönenberger A, Snedeker JG, Martin I, Erler JT, Ehrbar M. Mesenchymal stromal cell activation by breast cancer secretomes in bioengineered 3D microenvironments. Life Sci Alliance. 2019 2(3) PubMed: 31160380