PXD060683-1

PXD060683 is an original dataset announced via ProteomeXchange.

Title	A comparative proteomic, transcriptomic and glycomic analysis of extracellular vesicle isolation techniques highlights ExoGAG efficiency for a more complete identification of breast milk molecular signaling pathways
Description	Background: Human milk (HM) is the earliest form of extrauterine communication between mother and infant. We recently showed a functional characterization of HM, unmasking the molecular mechanisms related to EV signaling and its functional role in prematurity. In that study, we identified the need to establish and optimize a standard isolation protocol for human milk extracellular vesicles (mEVs). Results: ExoGAG and UC proved to be the most efficient of the four techniques compared for mEVS isolation. However, ExoGAG compared to UC provided a higher concentration of total and vesicle-related proteins and peptides and a higher glycoprotein count keeping all the glycan subgroups. Despite ExoGAG and UC show similar vesicle profiles in terms of size, concentration, tetraspanin subpopulations and EV markers, ExoGAG was the most efficient technique in terms of accuracy, consistency and reproducibility for omics studies. Furthermore, results allowed us to identify that EVs are involved in the signaling pathways of infant biological development, immune system maturation and protein metabolism. Methods: Four mEVs isolation methods were compared: ultracentrifugation (UC), size exclusion chromatography (SEC), immunoprecipitation with tetraspanin CD9 (IP_CD9) and ExoGAG. Three pools of human milk (each composed of samples from ten donor mothers) were used and isolation of mEVs was performed starting from the same volume for each method. The proteomic, transcriptomic and glycomic composition of the extracellular vesicles obtained after isolation was then analyzed for each method. The sensitivity, specificity and quality of the results were also determined. A comparison of the results obtained common to all methods was carried out in order to establish the possible signaling pathways related to mEVs. Conclusions: This study establishes UC and ExoGAG as reliable methods for mEVs isolation and describes its protocol, being ExoGAG the most efficient. Also, confirms that mEVs play a role in the defense system against external agents (specific role in the immune system pathway) and in the correct establishment of the neural structure (developmental pathway), while providing all the nutritional requirements for the correct growth of the newborn (metabolic pathway).
HostingRepository	PRIDE
AnnounceDate	2025-10-13
AnnouncementXML	Submission_2025-10-12_16:32:01.263.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Susana Bravo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-11 07:37:27	ID requested
⏵ 1	2025-10-12 16:32:02	announced

10.1186/s12964-025-02390-x;

Pereira-Hern, á, ndez M, Pic, á, ns-Leis R, V, á, zquez-Mosquera ME, Lago-Baameiro N, Fortes-Gonz, á, lez P, L, ó, pez-Valverde L, de la Iglesia AB, N, ú, ñ, ez-Gonz, á, lez L, Bravo SB, Pardo M, Couce ML, Garcia-Gonzalez MA, A comparative proteomic, transcriptomic and glycomic analysis of extracellular vesicle isolation techniques highlights ExoGAG efficiency for a more complete identification of breast milk molecular signaling pathways. Cell Commun Signal, 23(1):412(2025) [pubmed]

submitter keyword: glycomics., proteomics,extracellular vesicles, human milk, transcriptomics, isolation method

Susana B
contact affiliation	Instituto de Investigaciones Sanitarias de Santiago de Compostela
contact email	Sbbravo@gmail.com
lab head
Susana Bravo
contact affiliation	FIDIS
contact email	sbbravo@gmail.com
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/2025/10/PXD060683

PRIDE project URI

• PRIDE
  1. PXD060683
     1. Label: PRIDE project
     2. Name: A comparative proteomic, transcriptomic and glycomic analysis of extracellular vesicle isolation techniques highlights ExoGAG efficiency for a more complete identification of breast milk molecular signaling pathways