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REVIEW article

Front. Med.

Sec. Pulmonary Medicine

Volume 12 - 2025 | doi: 10.3389/fmed.2025.1693114

This article is part of the Research TopicComplex Interplay Between Lung Diseases and Multisystem Disorders: Pathogenesis, management, and OutcomeView all 12 articles

Breath Biopsy Biomarkers: Cell-free Nucleic Acids in Exhaled Breath Condensate

Provisionally accepted
  • 1Univerzita Komenskeho v Bratislave Vedecky park, Bratislava, Slovakia
  • 2Geneton sro, Bratislava, Slovakia
  • 3Univerzita Komenskeho v Bratislave Lekarska fakulta, Bratislava, Slovakia
  • 4Debreceni Egyetem Humangenetikai Tanszek, Debrecen, Hungary
  • 5Semmelweis Egyetem I Sz Sebeszeti es Intervencios Gasztroenterologiai Klinika, Budapest, Hungary
  • 6European Molecular Biology Laboratory, Heidelberg, Germany
  • 7Univerzita Komenskeho v Bratislave Prirodovedecka fakulta, Bratislava, Slovakia

The final, formatted version of the article will be published soon.

Exhaled breath condensate (EBC) has emerged as a promising, organ-specific biofluid for non-invasive molecular diagnostics. While breath analysis has traditionally focused on volatile organic compounds (VOCs), recent advances have shifted attention toward non-volatile constituents, particularly cell-free nucleic acids (cfNAs) such as genomic DNA, mitochondrial DNA, mRNA, miRNA, long non-coding RNA, and microbial genetic material. These molecules reflect the respiratory tract biology and can serve as biomarkers for a range of clinical conditions, including lung cancer, obstructive lung diseases, infections, and potentially even systemic disorders. This review summarizes the current knowledge on cfNAs in EBC, highlighting technical challenges in sample collection and nucleic acid extraction. We provide a comparison of EBC collection devices, discuss optimization strategies for nucleic acid recovery, and examine emerging applications such as early cancer detection, treatment monitoring, infection diagnostics, and endotyping of chronic airway diseases. The feasibility of at-home EBC sampling with portable collection devices offers additional advantages, potentially overcoming logistical and psychological barriers that often delay clinical care. Although limitations remain, including low cfNA yield and lack of standardization, ongoing innovation in sampling and molecular techniques is rapidly expanding the translational potential of breath biopsy. With further development, EBC-based cfNA profiling may complement or even rival blood-based liquid biopsies in certain respiratory and systemic disease contexts.

Keywords: breath biopsy, Exhaled breath condensate (EBC), Cell-free nucleic acids, Lung cancer biomarkers, liquid biopsy

Received: 26 Aug 2025; Accepted: 07 Oct 2025.

Copyright: © 2025 Pös, Styk, Kubanova, Bokorova, Buglyo, Soltesz, Lukasz, Benes, Repiska, Nagy and Szemes. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Monika Kubanova, kubanova26@uniba.sk

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