Potential Asthma Biomarkers Identified by Nontargeted Proteomics of Extracellular Vesicles in Exhaled Breath Condensate

Overview

Journal J Allergy Clin Immunol Glob

Specialty Allergy & Immunology

Date 2025 Mar 6

PMID 40046156

Authors

Reina Hara

Yoshito Takeda

Takatoshi Enomoto

Hanako Yoshimura

Makoto Yamamoto

Satoshi Tanizaki

Yuya Shirai

Takahiro Kawasaki

Mana Nakayama

Saori Amiya

Yuichi Adachi

Yoshimi Noda

Takayuki Niitsu

Ryuya Edahiro

Moto Yaga

Yuki Hosono

Maiko Naito

Kentaro Masuhiro

Yujiro Naito

Takayuki Shiroyama

Kotaro Miyake

Kiyoharu Fukushima

Shohei Koyama

Kota Iwahori

Haruhiko Hirata

Izumi Nagatomo

Yusuke Kawashima

Mari Nogami-Itoh

Atsushi Kumanogoh

Affiliations

Soon will be listed here.

Abstract

Background: Bronchial asthma (BA) and chronic obstructive pulmonary disease (COPD) are often misdiagnosed or undiagnosed, highlighting the need for more noninvasive and accessible diagnostic tools. Although exhaled breath condensate (EBC) is recognized as a biomarker resource for respiratory diseases, nontargeted proteomics of extracellular vesicles (EVs) in EBC has not been explored.

Objective: Our aim was to identify protein signatures in EBC-derived EVs (EBC-EVs) and potential biomarkers for BA and COPD.

Methods: EBC-EVs were isolated from 8 patients with BA, 5 patients with COPD, and 9 healthy controls by using the phosphatidylserine affinity method. The isolated EBC-EVs were analyzed by using data-independent acquisition proteomics to identify differentially expressed proteins (DEPs) and their associations with clinical parameters.

Results: Overall, 2524 proteins were identified. In the patients with BA, 20 proteins were upregulated, and 34 were downregulated. In the patients with COPD, 46 proteins were upregulated and 67 were downregulated. Although the enriched pathways and protein networks showed similarities between BA and COPD, they also indicated distinct pathophysiologic differences. In all, 5 BA-DEPs and 2 COPD-DEPs correlated with clinical parameters. For BA, S100 calcium-binding protein P levels were inversely correlated with FEV value, and ribosomal protein S10 levels were inversely correlated with blood eosinophil count. Clathrin heavy chain 2 correlated with serum IgE levels. For COPD, 14-3-3 protein theta and galectin-related protein showed positive and negative correlations with FEV value, respectively.

Conclusions: Proteomics of EBC-EVs has enabled the identification of potential diagnostic biomarkers for BA and COPD. "Breathomics" of EBC-EVs offers a promising noninvasive approach for diagnosis and phenotyping of respiratory diseases.

References

Royle S, Bright N, Lagnado L . Clathrin is required for the function of the mitotic spindle. Nature. 2005; 434(7037):1152-7. PMC: 3492753. DOI: 10.1038/nature03502. View

Horvath I, Barnes P, Loukides S, Sterk P, Hogman M, Olin A . A European Respiratory Society technical standard: exhaled biomarkers in lung disease. Eur Respir J. 2017; 49(4). DOI: 10.1183/13993003.00965-2016. View

Pirmoradi S, Hosseiniyan Khatibi S, Zununi Vahed S, Homaei Rad H, Mahdi Khamaneh A, Akbarpour Z . Unraveling the link between PTBP1 and severe asthma through machine learning and association rule mining method. Sci Rep. 2023; 13(1):15399. PMC: 10505163. DOI: 10.1038/s41598-023-42581-5. View

Zhang Y, Jing Y, Qiao J, Luan B, Wang X, Wang L . Activation of the mTOR signaling pathway is required for asthma onset. Sci Rep. 2017; 7(1):4532. PMC: 5495772. DOI: 10.1038/s41598-017-04826-y. View

Koba T, Takeda Y, Narumi R, Shiromizu T, Nojima Y, Ito M . Proteomics of serum extracellular vesicles identifies a novel COPD biomarker, fibulin-3 from elastic fibres. ERJ Open Res. 2021; 7(1). PMC: 7983195. DOI: 10.1183/23120541.00658-2020. View

Welsh J, Goberdhan D, ODriscoll L, Buzas E, Blenkiron C, Bussolati B . Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles. 2024; 13(2):e12404. PMC: 10850029. DOI: 10.1002/jev2.12404. View

Yoo E, Kim J, Stransky S, Spivack S, Sidoli S . Advances in proteomics methods for the analysis of exhaled breath condensate. Mass Spectrom Rev. 2023; 43(4):713-722. DOI: 10.1002/mas.21871. View

Aitken A . 14-3-3 proteins: a historic overview. Semin Cancer Biol. 2006; 16(3):162-72. DOI: 10.1016/j.semcancer.2006.03.005. View

Yanez-Mo M, Siljander P, Andreu Z, Bedina Zavec A, Borras F, Buzas E . Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles. 2015; 4:27066. PMC: 4433489. DOI: 10.3402/jev.v4.27066. View

10.

Dompeling E, Jobsis Q . Proteomics of exhaled breath condensate: a realistic approach in children with asthma?. Clin Exp Allergy. 2011; 41(3):299-301. DOI: 10.1111/j.1365-2222.2010.03686.x. View

11.

Ma L, Muscat J, Sinha R, Sun D, Xiu G . Proteomics of exhaled breath condensate in lung cancer and controls using data-independent acquisition (DIA): a pilot study. J Breath Res. 2020; 15(2). DOI: 10.1088/1752-7163/abd07e. View

12.

Denton E, Price D, Tran T, Canonica G, Menzies-Gow A, FitzGerald J . Cluster Analysis of Inflammatory Biomarker Expression in the International Severe Asthma Registry. J Allergy Clin Immunol Pract. 2021; 9(7):2680-2688.e7. DOI: 10.1016/j.jaip.2021.02.059. View

13.

Kawasaki T, Takeda Y, Kumanogoh A . Proteomics of blood extracellular vesicles in inflammatory respiratory diseases for biomarker discovery and new insights into pathophysiology. Inflamm Regen. 2024; 44(1):38. PMC: 11409490. DOI: 10.1186/s41232-024-00351-4. View

14.

The UniProt Consortium . UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2018; 46(5):2699. PMC: 5861450. DOI: 10.1093/nar/gky092. View

15.

Kierbiedz-Guzik N, Sozanska B . The Potential Role of Serum and Exhaled Breath Condensate miRNAs in Diagnosis and Predicting Exacerbations in Pediatric Asthma. Biomedicines. 2023; 11(3). PMC: 10045893. DOI: 10.3390/biomedicines11030763. View

16.

Loewenthal L, Menzies-Gow A . FeNO in Asthma. Semin Respir Crit Care Med. 2022; 43(5):635-645. DOI: 10.1055/s-0042-1743290. View

17.

Purghe B, Manfredi M, Ragnoli B, Baldanzi G, Malerba M . Exosomes in chronic respiratory diseases. Biomed Pharmacother. 2021; 144:112270. DOI: 10.1016/j.biopha.2021.112270. View

18.

Sinha A, Yadav A, Chakraborty S, Kabra S, Lodha R, Kumar M . Exosome-enclosed microRNAs in exhaled breath hold potential for biomarker discovery in patients with pulmonary diseases. J Allergy Clin Immunol. 2013; 132(1):219-22. DOI: 10.1016/j.jaci.2013.03.035. View

19.

Kuruvilla M, Lee F, Lee G . Understanding Asthma Phenotypes, Endotypes, and Mechanisms of Disease. Clin Rev Allergy Immunol. 2018; 56(2):219-233. PMC: 6411459. DOI: 10.1007/s12016-018-8712-1. View

20.

Pinkerton M, Chinchilli V, Banta E, Craig T, August A, Bascom R . Differential expression of microRNAs in exhaled breath condensates of patients with asthma, patients with chronic obstructive pulmonary disease, and healthy adults. J Allergy Clin Immunol. 2013; 132(1):217-9. DOI: 10.1016/j.jaci.2013.03.006. View