PXD054702

PXD054702 is an original dataset announced via ProteomeXchange.

Title	Characterization of equine bronchoalveolar lavage fluid extracellular vesicle proteomes across four isolation methods
Description	Growing evidence supports the importance of extracellular vesicle (EV) as mediators of communication in pathological processes, including those underlying respiratory disease. However, establishing methods for isolating and characterizing EVs remains challenging, particularly for respiratory samples. This study set out to address this challenge by comparing different EV isolation methods and evaluating their impacts on EV yield, markers of purity, and proteomic signatures, utilizing equine/horse bronchoalveolar lavage samples. Horses are an excellent translational animal model for respiratory studies due to similarities with human immune responses, shared environmental exposures, and naturally occurring respiratory diseases including asthma. Further, horses are long-lived large animals that allow for longitudinal sample collection, and provide large sample volume and cell yield, which are particularly useful since EV research is commonly limited by low sample yields. Here, EVs were isolated from horse bronchoalveolar lavage fluid (BALF) using four different methods (ultracentrifugation, microcentrifugation, and two sizes of size exclusion chromatography columns) and characterized by measuring particle counts, EV purity, total protein yield, and proteomic cargo, with a specific focus on vesicle surface marker expression potentially informing cell type of origin. We found that size exclusion chromatography yielded the highest particle counts, greatest EV purity markers and elevated vesicle surface marker expression. Overall proteomic profiles differed across isolation methods, with size exclusion chromatography clustering separately from centrifugation. Taken together, our results demonstrate that different isolation methods impact characteristics of EVs, notably that size exclusion chromatography, compared to centrifugation methods, resulted in higher EV purity and better characterized proteomic diversity, including information on EV cell of origin. This is the first study to characterize proteomic profiles of EVs following different isolation methods using equine BALF. The results of this study will pave the way for future studies using equine samples as a model to characterize human respiratory tract EVs.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_23:37:02.501.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Angie Mordant
SpeciesList	scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-08 04:12:26	ID requested
⏵ 1	2025-05-06 23:37:03	announced

10.1371/journal.pone.0315743;

Hickman E, Carberry V, Carberry C, Cooper B, Mordant AL, Mills A, Sokolsky M, Herring LE, Alexis NE, Rebuli ME, Jaspers I, Sheats K, Rager JE, Respiratory extracellular vesicle isolation optimization through proteomic profiling of equine samples and identification of candidates for cell-of-origin studies. PLoS One, 20(1):e0315743(2025) [pubmed]

submitter keyword: methods optimization, respiratory, bronchoalveolar lavage,extracellular vesicles, equine, proteome, cell surface markers, LC-MS/MS

Julia Rager
contact affiliation	UNC-CH Department of Environmental Sciences and Engineering
contact email	jrager@unc.edu
lab head
Angie Mordant
contact affiliation	UNC Proteomics Core, Department of Pharmacology, University of North Carolina at Chapel Hill
contact email	angie_mordant@med.unc.edu
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/2025/05/PXD054702

PRIDE project URI

• PRIDE
  1. PXD054702
     1. Label: PRIDE project
     2. Name: Characterization of equine bronchoalveolar lavage fluid extracellular vesicle proteomes across four isolation methods