PXD058625-1

PXD058625 is an original dataset announced via ProteomeXchange.

Title	Impact of Culture Platform Transition on Adipose-derived Mesenchymal Stromal Cells Molecular Signatures: A Multi-Omics Analysis of Small-Scale versus Large-Scale Production
Description	Mesenchymal stromal cells (MSCs) are being tested in numerous clinical trials, yet the limited progression of these trials to advanced stages indicates unresolved translational challenges. Expanding MSCs is a critical step in most therapeutic applications and bioreactor-based culture offers large-scale production compared to monolayer cultures. Nevertheless, since MSCs sense their microenvironment, it is crucial to understand how these systems affect their properties. We expanded human adipose-derived mesenchymal stromal cells (AD-MSCs) from the same donors in both small- and large-scale platforms. Bulk-RNA sequencing and mass-spectrometry analysis demonstrate that small-scale culture had a broader range of differentially expressed genes and proteins within immunomodulatory, cell migration and cell adhesion pathways. In contrast, the large-scale culture showed a lower amount of differentially expressed genes - and proteins were proteinsparticularly associated mainly with extracellular matrix synthesis. Our findings demonstrate that expansion platforms significantly impact MSCs’ properties of MSCs, highlighting the need with optimise expansion conditions to obtain high cell yield without compromising MSCs’ their attributes.
HostingRepository	PRIDE
AnnounceDate	2025-06-24
AnnouncementXML	Submission_2025-06-24_10:39:18.249.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonas Elsborg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-05 11:47:31	ID requested
⏵ 1	2025-06-24 10:39:18	announced

10.1016/J.OMTM.2025.101512;

submitter keyword: MSCs,LC-MS, bioreactor, proteome

Beatrice Dyring-Andersen
contact affiliation	Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
contact email	beatriceda@sund.ku.dk
lab head
Jonas Elsborg
contact affiliation	NNF Center for Protein Research
contact email	jonas.elsborg@cpr.ku.dk
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/2025/06/PXD058625

PRIDE project URI

• PRIDE
  1. PXD058625
     1. Label: PRIDE project
     2. Name: Impact of Culture Platform Transition on Adipose-derived Mesenchymal Stromal Cells Molecular Signatures: A Multi-Omics Analysis of Small-Scale versus Large-Scale Production