Dataset Information

Quantitative Proteomic Profiling of Bronchoalveolar Lavage-Derived Extracellular Vesicles in Murine Asthma Model

ABSTRACT: Extracellular vesicles (EVs) are increasingly recognized as key mediators of intercellular communication and immune regulation. However, their proteomic composition in allergic asthma remains poorly understood. In this study, we performed tandem mass tag (TMT)-based quantitative proteomic analyses of the whole bronchoalveolar lavage fluid (BALF) supernatant and EVs enriched from BALF in a murine model of house dust mite (HDM)-induced asthma. Using LC-MS/MS analysis in the data-dependent acquisition (DDA) mode, we identified more than 400 proteins across all samples, revealing distinct enrichment of canonical EV markers in EV fractions. HDM challenge induced significant upregulation of Th2-associated proteins, e.g., CLCA1, FCGBP, CHIL3, CHIL4, and RETNLA, consistent with hallmark features of asthma. Notably, proteins such as EPX and CKM were detected exclusively in EVs, not in whole BALF, underscoring the potential of EVs to selectively carry disease-relevant proteins. Our results provided insights into the distinct proteomic profiles of EV-associated versus BALF proteins, highlighting potential EV-mediated mechanisms in asthma pathogenesis.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Bronchoalveolar Lavage

DISEASE(S): Asthma

SUBMITTER: Zachary Hutchins

LAB HEAD: Yinsheng Wang

PROVIDER: PXD073977 | Pride | 2026-04-20

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	MaxQuant_Search_Evidence.txt	Txt
	MaxQuant_Search_ProteinGroups.txt	Txt
	NonUC_Even_TMT_ShamHDM.raw	Raw
	NonUC_Odd_TMT_ShamHDM.raw	Raw
	UC_TMT_Even.raw	Raw

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Project 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.

Dataset Information

Quantitative Proteomic Profiling of Bronchoalveolar Lavage-Derived Extracellular Vesicles in Murine Asthma Model

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