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. 2025 May 12;20(5):e0321626.
doi: 10.1371/journal.pone.0321626. eCollection 2025.

The application of cell-free DNA methylation patterns in critical illnesses: A protocol paper

Shih-Han Kao  1   2 , K Greer Stumpf  1   2 , Hunter A Gaudio  1   2 , John C Greenwood  3 , Samuel S Shin  1   3 , Frances S Shofer  3 , David H Jang  3
Affiliations

The application of cell-free DNA methylation patterns in critical illnesses: A protocol paper

Shih-Han Kao et al. PLoS One. .

Abstract

Biomarkers in clinical medicine are typically employed to gauge severity of disease, prognosis and to monitor response to treatment. While various biomarkers have been employed in clinical medicine with variable performance characteristics, the use of cell-free DNA (cfDNA) have gained increased traction as a novel biomarker in a wide range of disease states such as cancer and trauma. While the quantification of cfDNA have been correlated with disease severity, the use of methylation pattens of cfDNA can be used to localize the site of injury that may have implications regarding prognosis and therapeutics. We propose a procedure using samples in a swine model of cardiac arrest where carbon monoxide is being used as a therapeutic to demonstrate our method and feasibility to obtain plasma cfDNA methylation patterns to help identify tissue origin with potential application in critical care medicine.

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Conflict of interest statement

The authors have declared that no competing interests exist

Figures

Fig 1
Fig 1. Profiling of differentially methylation regions (DMRs) in sham and CO groups.
(A) Heatmap and dendrogram showing clustering of DMRs with similar methylation levels in samples: Sham-2h, CO-2h, Sham-end, CO-end. Sham-2h or CO-2h: hours of administering sham or CO treatment; sham-end or CO-end: termination of ROSC in sham or CO. *P < 0.05.
Fig 2
Fig 2. Profiling of differentially methylation regions (DMRs) in sham and CO groups.
(B) Volcano plot for both brain hypermethylated (red) and hypomethylated (blue) DMRs in brain, compared with blood. *P < 0.05.
Fig 3
Fig 3. Profiling of differentially methylation regions (DMRs) in sham and CO groups.
(C) Levels of unmethylated BD, a potential brain-specific biomarker, designated as BD, in the Sham and CO group. *P < 0.05.
See this image and copyright information in PMC

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